INFO(129104159627072)2025-04-22 09:47:43,822:************************* INFO(129104159627072)2025-04-22 09:47:43,822:deblurring started WARNING(129104159627072)2025-04-22 09:47:43,822:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data WARNING(129104159627072)2025-04-22 09:47:43,822:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': (), 'neg_ref_fp': (), 'neg_ref_db_fp': (), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 4, 'is_worker_thread': False, 'logger': } INFO(129104159627072)2025-04-22 09:47:43,823:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129104159627072)2025-04-22 09:47:43,823:deblur main program started INFO(129104159627072)2025-04-22 09:47:43,823:processing directory /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data INFO(129104159627072)2025-04-22 09:47:43,824:building negative db sortmerna index files INFO(129104159627072)2025-04-22 09:47:43,824:build_index_sortmerna files ['/home/sam/programs/miniforge3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/deblur/support_files/artifacts.fa'] to dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(129104159627072)2025-04-22 09:47:43,864:building positive db sortmerna index files INFO(129104159627072)2025-04-22 09:47:43,864:build_index_sortmerna files ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',) to dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(129104159627072)2025-04-22 11:00:42,204:parallel processing per sample fasta files INFO(129104159627072)2025-04-22 11:00:42,205:parallel deblur started for 54 inputs INFO(126529039062848)2025-04-22 11:00:43,146:************************* INFO(126529039062848)2025-04-22 11:00:43,147:deblurring started WARNING(126529039062848)2025-04-22 11:00:43,147:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1m_16_L001_R1_001.fastq.gz WARNING(126529039062848)2025-04-22 11:00:43,147:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1m_16_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(126529039062848)2025-04-22 11:00:43,147:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(126529039062848)2025-04-22 11:00:43,147:deblur worker thread started INFO(126529039062848)2025-04-22 11:00:43,148:processing per sample fasta files INFO(126529039062848)2025-04-22 11:00:43,148:-------------------------------------------------------- INFO(126529039062848)2025-04-22 11:00:43,148:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1m_16_L001_R1_001.fastq.gz INFO(139299484165952)2025-04-22 11:00:43,293:************************* INFO(139299484165952)2025-04-22 11:00:43,293:deblurring started WARNING(139299484165952)2025-04-22 11:00:43,293:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1r_21_L001_R1_001.fastq.gz WARNING(139299484165952)2025-04-22 11:00:43,293:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1r_21_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(139299484165952)2025-04-22 11:00:43,293:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(139299484165952)2025-04-22 11:00:43,293:deblur worker thread started INFO(139299484165952)2025-04-22 11:00:43,294:processing per sample fasta files INFO(139299484165952)2025-04-22 11:00:43,294:-------------------------------------------------------- INFO(139299484165952)2025-04-22 11:00:43,294:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1r_21_L001_R1_001.fastq.gz INFO(136640968521536)2025-04-22 11:00:43,299:************************* INFO(136640968521536)2025-04-22 11:00:43,299:deblurring started WARNING(136640968521536)2025-04-22 11:00:43,300:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5aa_31_L001_R1_001.fastq.gz WARNING(136640968521536)2025-04-22 11:00:43,300:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5aa_31_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(136640968521536)2025-04-22 11:00:43,300:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(136640968521536)2025-04-22 11:00:43,300:deblur worker thread started INFO(136640968521536)2025-04-22 11:00:43,300:processing per sample fasta files INFO(136640968521536)2025-04-22 11:00:43,300:-------------------------------------------------------- INFO(136640968521536)2025-04-22 11:00:43,300:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5aa_31_L001_R1_001.fastq.gz INFO(138021800122176)2025-04-22 11:00:43,321:************************* INFO(138021800122176)2025-04-22 11:00:43,322:deblurring started WARNING(138021800122176)2025-04-22 11:00:43,322:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1e_10_L001_R1_001.fastq.gz WARNING(138021800122176)2025-04-22 11:00:43,322:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1e_10_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138021800122176)2025-04-22 11:00:43,322:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138021800122176)2025-04-22 11:00:43,322:deblur worker thread started INFO(138021800122176)2025-04-22 11:00:43,322:processing per sample fasta files INFO(138021800122176)2025-04-22 11:00:43,322:-------------------------------------------------------- INFO(138021800122176)2025-04-22 11:00:43,322:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1e_10_L001_R1_001.fastq.gz INFO(138021800122176)2025-04-22 11:00:50,542:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim INFO(138021800122176)2025-04-22 11:00:50,559:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim.derep INFO(138021800122176)2025-04-22 11:00:51,118:total sequences 543, passing sequences 543, failing sequences 0 INFO(138021800122176)2025-04-22 11:00:51,118:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(138021800122176)2025-04-22 11:00:52,767:deblurring 543 sequences INFO(138021800122176)2025-04-22 11:00:53,042:360 unique sequences left following deblurring INFO(138021800122176)2025-04-22 11:00:53,044:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(138021800122176)2025-04-22 11:00:53,128:finished processing file INFO(138021800122176)2025-04-22 11:00:53,128:finished processing per sample fasta files INFO(138021800122176)2025-04-22 11:00:53,128:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1e_10_L001_R1_001.fastq.gz finished INFO(124594806019904)2025-04-22 11:00:54,336:************************* INFO(124594806019904)2025-04-22 11:00:54,336:deblurring started WARNING(124594806019904)2025-04-22 11:00:54,337:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1a_3_L001_R1_001.fastq.gz WARNING(124594806019904)2025-04-22 11:00:54,337:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1a_3_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124594806019904)2025-04-22 11:00:54,337:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124594806019904)2025-04-22 11:00:54,337:deblur worker thread started INFO(124594806019904)2025-04-22 11:00:54,337:processing per sample fasta files INFO(124594806019904)2025-04-22 11:00:54,337:-------------------------------------------------------- INFO(124594806019904)2025-04-22 11:00:54,338:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1a_3_L001_R1_001.fastq.gz INFO(126529039062848)2025-04-22 11:01:16,075:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim INFO(126529039062848)2025-04-22 11:01:16,157:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim.derep INFO(126529039062848)2025-04-22 11:01:16,997:total sequences 3401, passing sequences 3401, failing sequences 0 INFO(126529039062848)2025-04-22 11:01:17,002:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(139299484165952)2025-04-22 11:01:17,328:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim INFO(139299484165952)2025-04-22 11:01:17,386:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim.derep INFO(139299484165952)2025-04-22 11:01:18,132:total sequences 2945, passing sequences 2945, failing sequences 0 INFO(139299484165952)2025-04-22 11:01:18,133:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(139299484165952)2025-04-22 11:01:29,153:deblurring 2945 sequences INFO(126529039062848)2025-04-22 11:01:31,169:deblurring 3401 sequences INFO(139299484165952)2025-04-22 11:01:35,083:1352 unique sequences left following deblurring INFO(139299484165952)2025-04-22 11:01:35,092:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(139299484165952)2025-04-22 11:01:35,504:finished processing file INFO(139299484165952)2025-04-22 11:01:35,505:finished processing per sample fasta files INFO(139299484165952)2025-04-22 11:01:35,505:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1r_21_L001_R1_001.fastq.gz finished INFO(137613046069056)2025-04-22 11:01:36,584:************************* INFO(137613046069056)2025-04-22 11:01:36,584:deblurring started WARNING(137613046069056)2025-04-22 11:01:36,584:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1p_19_L001_R1_001.fastq.gz WARNING(137613046069056)2025-04-22 11:01:36,584:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1p_19_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(137613046069056)2025-04-22 11:01:36,585:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(137613046069056)2025-04-22 11:01:36,585:deblur worker thread started INFO(137613046069056)2025-04-22 11:01:36,585:processing per sample fasta files INFO(137613046069056)2025-04-22 11:01:36,585:-------------------------------------------------------- INFO(137613046069056)2025-04-22 11:01:36,585:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1p_19_L001_R1_001.fastq.gz INFO(126529039062848)2025-04-22 11:01:40,101:1726 unique sequences left following deblurring INFO(126529039062848)2025-04-22 11:01:40,113:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(126529039062848)2025-04-22 11:01:40,690:finished processing file INFO(126529039062848)2025-04-22 11:01:40,691:finished processing per sample fasta files INFO(126529039062848)2025-04-22 11:01:40,691:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1m_16_L001_R1_001.fastq.gz finished INFO(124594806019904)2025-04-22 11:01:41,400:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim INFO(124594806019904)2025-04-22 11:01:41,528:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim.derep INFO(124594806019904)2025-04-22 11:01:42,090:total sequences 2178, passing sequences 2178, failing sequences 0 INFO(124594806019904)2025-04-22 11:01:42,090:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(132651509589824)2025-04-22 11:01:42,105:************************* INFO(132651509589824)2025-04-22 11:01:42,105:deblurring started WARNING(132651509589824)2025-04-22 11:01:42,106:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5cc_35_L001_R1_001.fastq.gz WARNING(132651509589824)2025-04-22 11:01:42,106:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5cc_35_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(132651509589824)2025-04-22 11:01:42,106:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(132651509589824)2025-04-22 11:01:42,106:deblur worker thread started INFO(132651509589824)2025-04-22 11:01:42,106:processing per sample fasta files INFO(132651509589824)2025-04-22 11:01:42,106:-------------------------------------------------------- INFO(132651509589824)2025-04-22 11:01:42,107:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5cc_35_L001_R1_001.fastq.gz INFO(136640968521536)2025-04-22 11:01:46,546:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim INFO(136640968521536)2025-04-22 11:01:46,684:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim.derep INFO(136640968521536)2025-04-22 11:01:47,605:total sequences 5700, passing sequences 5700, failing sequences 0 INFO(136640968521536)2025-04-22 11:01:47,606:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124594806019904)2025-04-22 11:01:48,250:deblurring 2178 sequences INFO(124594806019904)2025-04-22 11:01:51,859:1142 unique sequences left following deblurring INFO(124594806019904)2025-04-22 11:01:51,873:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(124594806019904)2025-04-22 11:01:52,266:finished processing file INFO(124594806019904)2025-04-22 11:01:52,267:finished processing per sample fasta files INFO(124594806019904)2025-04-22 11:01:52,267:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1a_3_L001_R1_001.fastq.gz finished INFO(139638504376128)2025-04-22 11:01:53,766:************************* INFO(139638504376128)2025-04-22 11:01:53,766:deblurring started WARNING(139638504376128)2025-04-22 11:01:53,767:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5s_49_L001_R1_001.fastq.gz WARNING(139638504376128)2025-04-22 11:01:53,767:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5s_49_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(139638504376128)2025-04-22 11:01:53,767:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(139638504376128)2025-04-22 11:01:53,767:deblur worker thread started INFO(139638504376128)2025-04-22 11:01:53,768:processing per sample fasta files INFO(139638504376128)2025-04-22 11:01:53,768:-------------------------------------------------------- INFO(139638504376128)2025-04-22 11:01:53,768:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5s_49_L001_R1_001.fastq.gz INFO(139638504376128)2025-04-22 11:02:19,562:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim INFO(139638504376128)2025-04-22 11:02:19,607:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim.derep INFO(136640968521536)2025-04-22 11:02:20,016:deblurring 5700 sequences INFO(139638504376128)2025-04-22 11:02:20,197:total sequences 2652, passing sequences 2652, failing sequences 0 INFO(139638504376128)2025-04-22 11:02:20,197:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(139638504376128)2025-04-22 11:02:28,182:deblurring 2652 sequences INFO(139638504376128)2025-04-22 11:02:33,654:1468 unique sequences left following deblurring INFO(139638504376128)2025-04-22 11:02:33,662:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(139638504376128)2025-04-22 11:02:34,142:finished processing file INFO(139638504376128)2025-04-22 11:02:34,143:finished processing per sample fasta files INFO(139638504376128)2025-04-22 11:02:34,143:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5s_49_L001_R1_001.fastq.gz finished INFO(130663800723264)2025-04-22 11:02:35,460:************************* INFO(130663800723264)2025-04-22 11:02:35,461:deblurring started WARNING(130663800723264)2025-04-22 11:02:35,461:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1w_25_L001_R1_001.fastq.gz WARNING(130663800723264)2025-04-22 11:02:35,461:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1w_25_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(130663800723264)2025-04-22 11:02:35,461:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(130663800723264)2025-04-22 11:02:35,462:deblur worker thread started INFO(130663800723264)2025-04-22 11:02:35,462:processing per sample fasta files INFO(130663800723264)2025-04-22 11:02:35,462:-------------------------------------------------------- INFO(130663800723264)2025-04-22 11:02:35,462:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1w_25_L001_R1_001.fastq.gz INFO(136640968521536)2025-04-22 11:02:39,448:2306 unique sequences left following deblurring INFO(136640968521536)2025-04-22 11:02:39,465:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(136640968521536)2025-04-22 11:02:40,139:finished processing file INFO(136640968521536)2025-04-22 11:02:40,140:finished processing per sample fasta files INFO(136640968521536)2025-04-22 11:02:40,140:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5aa_31_L001_R1_001.fastq.gz finished INFO(138402711934784)2025-04-22 11:02:41,313:************************* INFO(138402711934784)2025-04-22 11:02:41,314:deblurring started WARNING(138402711934784)2025-04-22 11:02:41,314:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1cc_7_L001_R1_001.fastq.gz WARNING(138402711934784)2025-04-22 11:02:41,314:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1cc_7_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138402711934784)2025-04-22 11:02:41,315:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138402711934784)2025-04-22 11:02:41,315:deblur worker thread started INFO(138402711934784)2025-04-22 11:02:41,315:processing per sample fasta files INFO(138402711934784)2025-04-22 11:02:41,315:-------------------------------------------------------- INFO(138402711934784)2025-04-22 11:02:41,315:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1cc_7_L001_R1_001.fastq.gz INFO(132651509589824)2025-04-22 11:03:05,949:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim INFO(132651509589824)2025-04-22 11:03:06,164:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim.derep INFO(132651509589824)2025-04-22 11:03:06,862:total sequences 7549, passing sequences 7549, failing sequences 0 INFO(132651509589824)2025-04-22 11:03:06,862:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(130663800723264)2025-04-22 11:03:13,934:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim INFO(130663800723264)2025-04-22 11:03:14,069:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim.derep INFO(130663800723264)2025-04-22 11:03:14,989:total sequences 2838, passing sequences 2838, failing sequences 0 INFO(130663800723264)2025-04-22 11:03:14,992:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(130663800723264)2025-04-22 11:03:24,441:deblurring 2838 sequences INFO(130663800723264)2025-04-22 11:03:29,703:1157 unique sequences left following deblurring INFO(130663800723264)2025-04-22 11:03:29,720:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(130663800723264)2025-04-22 11:03:30,162:finished processing file INFO(130663800723264)2025-04-22 11:03:30,163:finished processing per sample fasta files INFO(130663800723264)2025-04-22 11:03:30,163:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1w_25_L001_R1_001.fastq.gz finished INFO(137854364636992)2025-04-22 11:03:31,361:************************* INFO(137854364636992)2025-04-22 11:03:31,361:deblurring started WARNING(137854364636992)2025-04-22 11:03:31,362:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1b_4_L001_R1_001.fastq.gz WARNING(137854364636992)2025-04-22 11:03:31,362:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1b_4_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(137854364636992)2025-04-22 11:03:31,362:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(137854364636992)2025-04-22 11:03:31,362:deblur worker thread started INFO(137854364636992)2025-04-22 11:03:31,363:processing per sample fasta files INFO(137854364636992)2025-04-22 11:03:31,363:-------------------------------------------------------- INFO(137854364636992)2025-04-22 11:03:31,363:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1b_4_L001_R1_001.fastq.gz INFO(138402711934784)2025-04-22 11:03:53,554:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim INFO(138402711934784)2025-04-22 11:03:53,650:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim.derep INFO(138402711934784)2025-04-22 11:03:54,294:total sequences 4718, passing sequences 4718, failing sequences 0 INFO(138402711934784)2025-04-22 11:03:54,294:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(137854364636992)2025-04-22 11:04:02,185:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim INFO(137854364636992)2025-04-22 11:04:02,249:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim.derep INFO(132651509589824)2025-04-22 11:04:02,595:deblurring 7549 sequences INFO(137854364636992)2025-04-22 11:04:02,812:total sequences 3405, passing sequences 3405, failing sequences 0 INFO(137854364636992)2025-04-22 11:04:02,812:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(137854364636992)2025-04-22 11:04:16,924:deblurring 3405 sequences INFO(138402711934784)2025-04-22 11:04:19,167:deblurring 4718 sequences INFO(137854364636992)2025-04-22 11:04:27,543:1977 unique sequences left following deblurring INFO(137854364636992)2025-04-22 11:04:27,556:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(137854364636992)2025-04-22 11:04:28,215:finished processing file INFO(137854364636992)2025-04-22 11:04:28,216:finished processing per sample fasta files INFO(137854364636992)2025-04-22 11:04:28,216:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1b_4_L001_R1_001.fastq.gz finished INFO(139840419723072)2025-04-22 11:04:29,542:************************* INFO(139840419723072)2025-04-22 11:04:29,543:deblurring started WARNING(139840419723072)2025-04-22 11:04:29,543:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5v_51_L001_R1_001.fastq.gz WARNING(139840419723072)2025-04-22 11:04:29,543:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5v_51_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(139840419723072)2025-04-22 11:04:29,543:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(139840419723072)2025-04-22 11:04:29,543:deblur worker thread started INFO(139840419723072)2025-04-22 11:04:29,543:processing per sample fasta files INFO(139840419723072)2025-04-22 11:04:29,543:-------------------------------------------------------- INFO(139840419723072)2025-04-22 11:04:29,543:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5v_51_L001_R1_001.fastq.gz INFO(138402711934784)2025-04-22 11:04:33,869:1864 unique sequences left following deblurring INFO(138402711934784)2025-04-22 11:04:33,931:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(138402711934784)2025-04-22 11:04:34,719:finished processing file INFO(138402711934784)2025-04-22 11:04:34,720:finished processing per sample fasta files INFO(138402711934784)2025-04-22 11:04:34,721:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1cc_7_L001_R1_001.fastq.gz finished INFO(129514003236672)2025-04-22 11:04:36,022:************************* INFO(129514003236672)2025-04-22 11:04:36,023:deblurring started WARNING(129514003236672)2025-04-22 11:04:36,027:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5c_34_L001_R1_001.fastq.gz WARNING(129514003236672)2025-04-22 11:04:36,027:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5c_34_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129514003236672)2025-04-22 11:04:36,027:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129514003236672)2025-04-22 11:04:36,027:deblur worker thread started INFO(129514003236672)2025-04-22 11:04:36,027:processing per sample fasta files INFO(129514003236672)2025-04-22 11:04:36,027:-------------------------------------------------------- INFO(129514003236672)2025-04-22 11:04:36,027:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5c_34_L001_R1_001.fastq.gz INFO(139840419723072)2025-04-22 11:04:47,409:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim INFO(139840419723072)2025-04-22 11:04:47,478:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim.derep INFO(139840419723072)2025-04-22 11:04:48,039:total sequences 1168, passing sequences 1168, failing sequences 0 INFO(139840419723072)2025-04-22 11:04:48,039:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(129514003236672)2025-04-22 11:04:48,318:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim INFO(129514003236672)2025-04-22 11:04:48,345:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim.derep INFO(132651509589824)2025-04-22 11:04:48,842:2965 unique sequences left following deblurring INFO(132651509589824)2025-04-22 11:04:48,866:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(129514003236672)2025-04-22 11:04:48,919:total sequences 1165, passing sequences 1165, failing sequences 0 INFO(129514003236672)2025-04-22 11:04:48,922:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(132651509589824)2025-04-22 11:04:49,869:finished processing file INFO(132651509589824)2025-04-22 11:04:49,871:finished processing per sample fasta files INFO(132651509589824)2025-04-22 11:04:49,872:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5cc_35_L001_R1_001.fastq.gz finished INFO(139840419723072)2025-04-22 11:04:50,365:deblurring 1168 sequences INFO(134257422792512)2025-04-22 11:04:51,194:************************* INFO(134257422792512)2025-04-22 11:04:51,194:deblurring started WARNING(134257422792512)2025-04-22 11:04:51,195:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5w_52_L001_R1_001.fastq.gz WARNING(134257422792512)2025-04-22 11:04:51,195:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5w_52_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134257422792512)2025-04-22 11:04:51,195:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134257422792512)2025-04-22 11:04:51,195:deblur worker thread started INFO(134257422792512)2025-04-22 11:04:51,195:processing per sample fasta files INFO(134257422792512)2025-04-22 11:04:51,195:-------------------------------------------------------- INFO(134257422792512)2025-04-22 11:04:51,195:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5w_52_L001_R1_001.fastq.gz INFO(134257422792512)2025-04-22 11:04:51,201:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5w_52_L001_R1_001.fastq.gz.trim INFO(134257422792512)2025-04-22 11:04:51,206:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5w_52_L001_R1_001.fastq.gz.trim.derep WARNING(134257422792512)2025-04-22 11:04:51,206:file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5w_52_L001_R1_001.fastq.gz.trim.derep has size 0, continuing WARNING(134257422792512)2025-04-22 11:04:51,209:remove artifacts failed, aborting WARNING(134257422792512)2025-04-22 11:04:51,209:deblurring failed for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5w_52_L001_R1_001.fastq.gz INFO(134257422792512)2025-04-22 11:04:51,209:finished processing per sample fasta files INFO(134257422792512)2025-04-22 11:04:51,209:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5w_52_L001_R1_001.fastq.gz finished INFO(139840419723072)2025-04-22 11:04:51,270:482 unique sequences left following deblurring INFO(139840419723072)2025-04-22 11:04:51,273:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(129514003236672)2025-04-22 11:04:51,284:deblurring 1165 sequences INFO(139840419723072)2025-04-22 11:04:51,392:finished processing file INFO(139840419723072)2025-04-22 11:04:51,392:finished processing per sample fasta files INFO(139840419723072)2025-04-22 11:04:51,393:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5v_51_L001_R1_001.fastq.gz finished INFO(126121370892096)2025-04-22 11:04:52,652:************************* INFO(126121370892096)2025-04-22 11:04:52,652:deblurring started WARNING(126121370892096)2025-04-22 11:04:52,652:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1d_8_L001_R1_001.fastq.gz WARNING(126121370892096)2025-04-22 11:04:52,652:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1d_8_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(126121370892096)2025-04-22 11:04:52,653:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(126121370892096)2025-04-22 11:04:52,653:deblur worker thread started INFO(126121370892096)2025-04-22 11:04:52,653:processing per sample fasta files INFO(126121370892096)2025-04-22 11:04:52,653:-------------------------------------------------------- INFO(126121370892096)2025-04-22 11:04:52,653:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1d_8_L001_R1_001.fastq.gz INFO(129259911878464)2025-04-22 11:04:52,682:************************* INFO(129259911878464)2025-04-22 11:04:52,682:deblurring started WARNING(129259911878464)2025-04-22 11:04:52,683:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5o_45_L001_R1_001.fastq.gz WARNING(129259911878464)2025-04-22 11:04:52,683:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5o_45_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129259911878464)2025-04-22 11:04:52,683:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129259911878464)2025-04-22 11:04:52,683:deblur worker thread started INFO(129259911878464)2025-04-22 11:04:52,683:processing per sample fasta files INFO(129259911878464)2025-04-22 11:04:52,683:-------------------------------------------------------- INFO(129259911878464)2025-04-22 11:04:52,683:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5o_45_L001_R1_001.fastq.gz INFO(129514003236672)2025-04-22 11:04:52,774:741 unique sequences left following deblurring INFO(129514003236672)2025-04-22 11:04:52,778:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(129514003236672)2025-04-22 11:04:53,045:finished processing file INFO(129514003236672)2025-04-22 11:04:53,045:finished processing per sample fasta files INFO(129514003236672)2025-04-22 11:04:53,045:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5c_34_L001_R1_001.fastq.gz finished INFO(138273889290048)2025-04-22 11:04:54,226:************************* INFO(138273889290048)2025-04-22 11:04:54,227:deblurring started WARNING(138273889290048)2025-04-22 11:04:54,227:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1z_27_L001_R1_001.fastq.gz WARNING(138273889290048)2025-04-22 11:04:54,227:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1z_27_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138273889290048)2025-04-22 11:04:54,227:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138273889290048)2025-04-22 11:04:54,228:deblur worker thread started INFO(138273889290048)2025-04-22 11:04:54,228:processing per sample fasta files INFO(138273889290048)2025-04-22 11:04:54,228:-------------------------------------------------------- INFO(138273889290048)2025-04-22 11:04:54,228:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1z_27_L001_R1_001.fastq.gz INFO(129259911878464)2025-04-22 11:05:17,868:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim INFO(129259911878464)2025-04-22 11:05:18,041:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim.derep INFO(129259911878464)2025-04-22 11:05:18,741:total sequences 2487, passing sequences 2487, failing sequences 0 INFO(129259911878464)2025-04-22 11:05:18,741:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(137613046069056)2025-04-22 11:05:21,205:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim INFO(137613046069056)2025-04-22 11:05:21,707:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim.derep INFO(137613046069056)2025-04-22 11:05:23,143:total sequences 13856, passing sequences 13856, failing sequences 0 INFO(137613046069056)2025-04-22 11:05:23,144:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(138273889290048)2025-04-22 11:05:28,162:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim INFO(138273889290048)2025-04-22 11:05:28,235:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim.derep INFO(129259911878464)2025-04-22 11:05:28,299:deblurring 2487 sequences INFO(138273889290048)2025-04-22 11:05:29,122:total sequences 2092, passing sequences 2092, failing sequences 0 INFO(138273889290048)2025-04-22 11:05:29,126:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(129259911878464)2025-04-22 11:05:32,348:939 unique sequences left following deblurring INFO(129259911878464)2025-04-22 11:05:32,354:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(129259911878464)2025-04-22 11:05:32,778:finished processing file INFO(129259911878464)2025-04-22 11:05:32,779:finished processing per sample fasta files INFO(129259911878464)2025-04-22 11:05:32,779:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5o_45_L001_R1_001.fastq.gz finished INFO(124802339858240)2025-04-22 11:05:34,648:************************* INFO(124802339858240)2025-04-22 11:05:34,648:deblurring started WARNING(124802339858240)2025-04-22 11:05:34,648:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1o_18_L001_R1_001.fastq.gz WARNING(124802339858240)2025-04-22 11:05:34,649:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1o_18_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124802339858240)2025-04-22 11:05:34,649:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124802339858240)2025-04-22 11:05:34,649:deblur worker thread started INFO(124802339858240)2025-04-22 11:05:34,649:processing per sample fasta files INFO(124802339858240)2025-04-22 11:05:34,649:-------------------------------------------------------- INFO(124802339858240)2025-04-22 11:05:34,649:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1o_18_L001_R1_001.fastq.gz INFO(126121370892096)2025-04-22 11:05:35,434:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim INFO(126121370892096)2025-04-22 11:05:35,553:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim.derep INFO(138273889290048)2025-04-22 11:05:35,750:deblurring 2092 sequences INFO(126121370892096)2025-04-22 11:05:36,346:total sequences 3526, passing sequences 3526, failing sequences 0 INFO(126121370892096)2025-04-22 11:05:36,346:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(138273889290048)2025-04-22 11:05:39,222:881 unique sequences left following deblurring INFO(138273889290048)2025-04-22 11:05:39,228:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(138273889290048)2025-04-22 11:05:39,533:finished processing file INFO(138273889290048)2025-04-22 11:05:39,534:finished processing per sample fasta files INFO(138273889290048)2025-04-22 11:05:39,534:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1z_27_L001_R1_001.fastq.gz finished INFO(128321609496384)2025-04-22 11:05:40,742:************************* INFO(128321609496384)2025-04-22 11:05:40,742:deblurring started WARNING(128321609496384)2025-04-22 11:05:40,743:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1s_22_L001_R1_001.fastq.gz WARNING(128321609496384)2025-04-22 11:05:40,743:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1s_22_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(128321609496384)2025-04-22 11:05:40,743:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(128321609496384)2025-04-22 11:05:40,743:deblur worker thread started INFO(128321609496384)2025-04-22 11:05:40,743:processing per sample fasta files INFO(128321609496384)2025-04-22 11:05:40,743:-------------------------------------------------------- INFO(128321609496384)2025-04-22 11:05:40,743:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1s_22_L001_R1_001.fastq.gz INFO(126121370892096)2025-04-22 11:05:51,167:deblurring 3526 sequences INFO(126121370892096)2025-04-22 11:06:01,221:1814 unique sequences left following deblurring INFO(126121370892096)2025-04-22 11:06:01,235:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(126121370892096)2025-04-22 11:06:01,829:finished processing file INFO(126121370892096)2025-04-22 11:06:01,830:finished processing per sample fasta files INFO(126121370892096)2025-04-22 11:06:01,830:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1d_8_L001_R1_001.fastq.gz finished INFO(128987628824384)2025-04-22 11:06:03,099:************************* INFO(128987628824384)2025-04-22 11:06:03,099:deblurring started WARNING(128987628824384)2025-04-22 11:06:03,099:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5m_43_L001_R1_001.fastq.gz WARNING(128987628824384)2025-04-22 11:06:03,099:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5m_43_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(128987628824384)2025-04-22 11:06:03,100:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(128987628824384)2025-04-22 11:06:03,100:deblur worker thread started INFO(128987628824384)2025-04-22 11:06:03,100:processing per sample fasta files INFO(128987628824384)2025-04-22 11:06:03,100:-------------------------------------------------------- INFO(128987628824384)2025-04-22 11:06:03,100:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5m_43_L001_R1_001.fastq.gz INFO(124802339858240)2025-04-22 11:06:17,611:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim INFO(124802339858240)2025-04-22 11:06:17,698:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim.derep INFO(124802339858240)2025-04-22 11:06:18,357:total sequences 4492, passing sequences 4492, failing sequences 0 INFO(124802339858240)2025-04-22 11:06:18,357:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(128321609496384)2025-04-22 11:06:22,729:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim INFO(128321609496384)2025-04-22 11:06:22,814:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim.derep INFO(128321609496384)2025-04-22 11:06:23,523:total sequences 4269, passing sequences 4269, failing sequences 0 INFO(128321609496384)2025-04-22 11:06:23,524:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(128987628824384)2025-04-22 11:06:27,398:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim INFO(128987628824384)2025-04-22 11:06:27,468:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim.derep INFO(128987628824384)2025-04-22 11:06:28,127:total sequences 2330, passing sequences 2330, failing sequences 0 INFO(128987628824384)2025-04-22 11:06:28,127:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(128987628824384)2025-04-22 11:06:34,572:deblurring 2330 sequences INFO(128987628824384)2025-04-22 11:06:40,113:1445 unique sequences left following deblurring INFO(128987628824384)2025-04-22 11:06:40,124:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(124802339858240)2025-04-22 11:06:40,374:deblurring 4492 sequences INFO(128987628824384)2025-04-22 11:06:40,649:finished processing file INFO(128987628824384)2025-04-22 11:06:40,650:finished processing per sample fasta files INFO(128987628824384)2025-04-22 11:06:40,650:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5m_43_L001_R1_001.fastq.gz finished INFO(138557305857856)2025-04-22 11:06:42,136:************************* INFO(138557305857856)2025-04-22 11:06:42,136:deblurring started WARNING(138557305857856)2025-04-22 11:06:42,136:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5ff_39_L001_R1_001.fastq.gz WARNING(138557305857856)2025-04-22 11:06:42,136:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5ff_39_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138557305857856)2025-04-22 11:06:42,136:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138557305857856)2025-04-22 11:06:42,137:deblur worker thread started INFO(138557305857856)2025-04-22 11:06:42,137:processing per sample fasta files INFO(138557305857856)2025-04-22 11:06:42,137:-------------------------------------------------------- INFO(138557305857856)2025-04-22 11:06:42,137:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5ff_39_L001_R1_001.fastq.gz INFO(128321609496384)2025-04-22 11:06:43,104:deblurring 4269 sequences INFO(128321609496384)2025-04-22 11:06:57,376:1982 unique sequences left following deblurring INFO(128321609496384)2025-04-22 11:06:57,389:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(128321609496384)2025-04-22 11:06:58,039:finished processing file INFO(128321609496384)2025-04-22 11:06:58,040:finished processing per sample fasta files INFO(128321609496384)2025-04-22 11:06:58,040:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1s_22_L001_R1_001.fastq.gz finished INFO(137743797536576)2025-04-22 11:06:59,226:************************* INFO(137743797536576)2025-04-22 11:06:59,226:deblurring started WARNING(137743797536576)2025-04-22 11:06:59,226:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5f_38_L001_R1_001.fastq.gz WARNING(137743797536576)2025-04-22 11:06:59,227:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5f_38_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(137743797536576)2025-04-22 11:06:59,227:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(137743797536576)2025-04-22 11:06:59,227:deblur worker thread started INFO(137743797536576)2025-04-22 11:06:59,227:processing per sample fasta files INFO(137743797536576)2025-04-22 11:06:59,227:-------------------------------------------------------- INFO(137743797536576)2025-04-22 11:06:59,227:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5f_38_L001_R1_001.fastq.gz INFO(124802339858240)2025-04-22 11:06:59,804:2458 unique sequences left following deblurring INFO(124802339858240)2025-04-22 11:06:59,823:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(124802339858240)2025-04-22 11:07:00,658:finished processing file INFO(124802339858240)2025-04-22 11:07:00,660:finished processing per sample fasta files INFO(124802339858240)2025-04-22 11:07:00,660:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1o_18_L001_R1_001.fastq.gz finished INFO(137743797536576)2025-04-22 11:07:01,093:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim INFO(137743797536576)2025-04-22 11:07:01,103:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim.derep INFO(137743797536576)2025-04-22 11:07:01,694:total sequences 292, passing sequences 292, failing sequences 0 INFO(137743797536576)2025-04-22 11:07:01,694:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(132523483445056)2025-04-22 11:07:01,808:************************* INFO(132523483445056)2025-04-22 11:07:01,808:deblurring started WARNING(132523483445056)2025-04-22 11:07:01,808:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5u_50_L001_R1_001.fastq.gz WARNING(132523483445056)2025-04-22 11:07:01,809:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5u_50_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(132523483445056)2025-04-22 11:07:01,809:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(132523483445056)2025-04-22 11:07:01,809:deblur worker thread started INFO(132523483445056)2025-04-22 11:07:01,809:processing per sample fasta files INFO(132523483445056)2025-04-22 11:07:01,809:-------------------------------------------------------- INFO(132523483445056)2025-04-22 11:07:01,809:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5u_50_L001_R1_001.fastq.gz INFO(137743797536576)2025-04-22 11:07:05,293:deblurring 292 sequences INFO(137743797536576)2025-04-22 11:07:05,352:152 unique sequences left following deblurring INFO(137743797536576)2025-04-22 11:07:05,353:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(137743797536576)2025-04-22 11:07:05,385:finished processing file INFO(137743797536576)2025-04-22 11:07:05,385:finished processing per sample fasta files INFO(137743797536576)2025-04-22 11:07:05,385:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5f_38_L001_R1_001.fastq.gz finished INFO(127626354902848)2025-04-22 11:07:06,535:************************* INFO(127626354902848)2025-04-22 11:07:06,536:deblurring started WARNING(127626354902848)2025-04-22 11:07:06,536:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1J_0_L001_R1_001.fastq.gz WARNING(127626354902848)2025-04-22 11:07:06,536:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1J_0_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127626354902848)2025-04-22 11:07:06,536:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127626354902848)2025-04-22 11:07:06,537:deblur worker thread started INFO(127626354902848)2025-04-22 11:07:06,537:processing per sample fasta files INFO(127626354902848)2025-04-22 11:07:06,537:-------------------------------------------------------- INFO(127626354902848)2025-04-22 11:07:06,537:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1J_0_L001_R1_001.fastq.gz INFO(127626354902848)2025-04-22 11:07:08,327:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim INFO(127626354902848)2025-04-22 11:07:08,340:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim.derep INFO(127626354902848)2025-04-22 11:07:08,844:total sequences 364, passing sequences 364, failing sequences 0 INFO(127626354902848)2025-04-22 11:07:08,844:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127626354902848)2025-04-22 11:07:13,720:deblurring 364 sequences INFO(127626354902848)2025-04-22 11:07:13,871:293 unique sequences left following deblurring INFO(127626354902848)2025-04-22 11:07:13,875:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(127626354902848)2025-04-22 11:07:13,951:finished processing file INFO(127626354902848)2025-04-22 11:07:13,952:finished processing per sample fasta files INFO(127626354902848)2025-04-22 11:07:13,952:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1J_0_L001_R1_001.fastq.gz finished INFO(123495169140544)2025-04-22 11:07:15,181:************************* INFO(123495169140544)2025-04-22 11:07:15,181:deblurring started WARNING(123495169140544)2025-04-22 11:07:15,182:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1h_14_L001_R1_001.fastq.gz WARNING(123495169140544)2025-04-22 11:07:15,182:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1h_14_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123495169140544)2025-04-22 11:07:15,182:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123495169140544)2025-04-22 11:07:15,182:deblur worker thread started INFO(123495169140544)2025-04-22 11:07:15,182:processing per sample fasta files INFO(123495169140544)2025-04-22 11:07:15,182:-------------------------------------------------------- INFO(123495169140544)2025-04-22 11:07:15,182:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1h_14_L001_R1_001.fastq.gz INFO(132523483445056)2025-04-22 11:07:19,146:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim INFO(132523483445056)2025-04-22 11:07:19,183:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim.derep INFO(132523483445056)2025-04-22 11:07:19,760:total sequences 1726, passing sequences 1726, failing sequences 0 INFO(132523483445056)2025-04-22 11:07:19,760:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(132523483445056)2025-04-22 11:07:23,698:deblurring 1726 sequences INFO(132523483445056)2025-04-22 11:07:25,835:904 unique sequences left following deblurring INFO(132523483445056)2025-04-22 11:07:25,840:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(132523483445056)2025-04-22 11:07:26,058:finished processing file INFO(132523483445056)2025-04-22 11:07:26,058:finished processing per sample fasta files INFO(132523483445056)2025-04-22 11:07:26,058:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5u_50_L001_R1_001.fastq.gz finished INFO(129928884008768)2025-04-22 11:07:27,180:************************* INFO(129928884008768)2025-04-22 11:07:27,180:deblurring started WARNING(129928884008768)2025-04-22 11:07:27,181:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5q_47_L001_R1_001.fastq.gz WARNING(129928884008768)2025-04-22 11:07:27,181:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5q_47_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129928884008768)2025-04-22 11:07:27,181:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129928884008768)2025-04-22 11:07:27,181:deblur worker thread started INFO(129928884008768)2025-04-22 11:07:27,181:processing per sample fasta files INFO(129928884008768)2025-04-22 11:07:27,181:-------------------------------------------------------- INFO(129928884008768)2025-04-22 11:07:27,181:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5q_47_L001_R1_001.fastq.gz INFO(123495169140544)2025-04-22 11:07:30,085:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim INFO(123495169140544)2025-04-22 11:07:30,108:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim.derep INFO(123495169140544)2025-04-22 11:07:30,635:total sequences 1031, passing sequences 1031, failing sequences 0 INFO(123495169140544)2025-04-22 11:07:30,635:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123495169140544)2025-04-22 11:07:32,941:deblurring 1031 sequences INFO(123495169140544)2025-04-22 11:07:33,763:532 unique sequences left following deblurring INFO(123495169140544)2025-04-22 11:07:33,766:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(123495169140544)2025-04-22 11:07:33,945:finished processing file INFO(123495169140544)2025-04-22 11:07:33,945:finished processing per sample fasta files INFO(123495169140544)2025-04-22 11:07:33,946:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1h_14_L001_R1_001.fastq.gz finished INFO(123713636493120)2025-04-22 11:07:35,162:************************* INFO(123713636493120)2025-04-22 11:07:35,162:deblurring started WARNING(123713636493120)2025-04-22 11:07:35,162:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1L_1_L001_R1_001.fastq.gz WARNING(123713636493120)2025-04-22 11:07:35,162:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1L_1_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123713636493120)2025-04-22 11:07:35,163:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123713636493120)2025-04-22 11:07:35,163:deblur worker thread started INFO(123713636493120)2025-04-22 11:07:35,163:processing per sample fasta files INFO(123713636493120)2025-04-22 11:07:35,163:-------------------------------------------------------- INFO(123713636493120)2025-04-22 11:07:35,163:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1L_1_L001_R1_001.fastq.gz INFO(123713636493120)2025-04-22 11:07:45,633:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim INFO(123713636493120)2025-04-22 11:07:45,682:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim.derep INFO(123713636493120)2025-04-22 11:07:46,267:total sequences 1053, passing sequences 1053, failing sequences 0 INFO(123713636493120)2025-04-22 11:07:46,267:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123713636493120)2025-04-22 11:07:48,462:deblurring 1053 sequences INFO(123713636493120)2025-04-22 11:07:49,433:598 unique sequences left following deblurring INFO(123713636493120)2025-04-22 11:07:49,440:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(123713636493120)2025-04-22 11:07:49,654:finished processing file INFO(123713636493120)2025-04-22 11:07:49,655:finished processing per sample fasta files INFO(123713636493120)2025-04-22 11:07:49,655:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1L_1_L001_R1_001.fastq.gz finished INFO(140152645932864)2025-04-22 11:07:50,861:************************* INFO(140152645932864)2025-04-22 11:07:50,861:deblurring started WARNING(140152645932864)2025-04-22 11:07:50,862:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5k_42_L001_R1_001.fastq.gz WARNING(140152645932864)2025-04-22 11:07:50,862:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5k_42_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(140152645932864)2025-04-22 11:07:50,862:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(140152645932864)2025-04-22 11:07:50,862:deblur worker thread started INFO(140152645932864)2025-04-22 11:07:50,862:processing per sample fasta files INFO(140152645932864)2025-04-22 11:07:50,862:-------------------------------------------------------- INFO(140152645932864)2025-04-22 11:07:50,862:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5k_42_L001_R1_001.fastq.gz INFO(129928884008768)2025-04-22 11:07:58,406:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim INFO(129928884008768)2025-04-22 11:07:58,621:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim.derep INFO(129928884008768)2025-04-22 11:07:59,358:total sequences 6897, passing sequences 6897, failing sequences 0 INFO(129928884008768)2025-04-22 11:07:59,359:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(140152645932864)2025-04-22 11:08:03,050:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim INFO(140152645932864)2025-04-22 11:08:03,079:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim.derep INFO(140152645932864)2025-04-22 11:08:03,682:total sequences 1255, passing sequences 1255, failing sequences 0 INFO(140152645932864)2025-04-22 11:08:03,682:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(140152645932864)2025-04-22 11:08:06,438:deblurring 1255 sequences INFO(138557305857856)2025-04-22 11:08:06,515:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim INFO(138557305857856)2025-04-22 11:08:06,742:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim.derep INFO(138557305857856)2025-04-22 11:08:07,706:total sequences 8154, passing sequences 8154, failing sequences 0 INFO(138557305857856)2025-04-22 11:08:07,706:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(140152645932864)2025-04-22 11:08:07,849:783 unique sequences left following deblurring INFO(140152645932864)2025-04-22 11:08:07,852:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(140152645932864)2025-04-22 11:08:08,100:finished processing file INFO(140152645932864)2025-04-22 11:08:08,100:finished processing per sample fasta files INFO(140152645932864)2025-04-22 11:08:08,101:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5k_42_L001_R1_001.fastq.gz finished INFO(129086691424064)2025-04-22 11:08:09,457:************************* INFO(129086691424064)2025-04-22 11:08:09,457:deblurring started WARNING(129086691424064)2025-04-22 11:08:09,457:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1dd_9_L001_R1_001.fastq.gz WARNING(129086691424064)2025-04-22 11:08:09,457:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1dd_9_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129086691424064)2025-04-22 11:08:09,457:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129086691424064)2025-04-22 11:08:09,457:deblur worker thread started INFO(129086691424064)2025-04-22 11:08:09,457:processing per sample fasta files INFO(129086691424064)2025-04-22 11:08:09,457:-------------------------------------------------------- INFO(129086691424064)2025-04-22 11:08:09,457:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1dd_9_L001_R1_001.fastq.gz INFO(137613046069056)2025-04-22 11:08:43,204:deblurring 13856 sequences INFO(129928884008768)2025-04-22 11:08:45,281:deblurring 6897 sequences INFO(138557305857856)2025-04-22 11:09:11,961:deblurring 8154 sequences INFO(129086691424064)2025-04-22 11:09:14,049:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim INFO(129086691424064)2025-04-22 11:09:14,178:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim.derep INFO(129086691424064)2025-04-22 11:09:15,408:total sequences 5382, passing sequences 5382, failing sequences 0 INFO(129086691424064)2025-04-22 11:09:15,408:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(129928884008768)2025-04-22 11:09:39,934:4786 unique sequences left following deblurring INFO(129928884008768)2025-04-22 11:09:40,001:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(129928884008768)2025-04-22 11:09:42,456:finished processing file INFO(129928884008768)2025-04-22 11:09:42,459:finished processing per sample fasta files INFO(129928884008768)2025-04-22 11:09:42,460:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5q_47_L001_R1_001.fastq.gz finished INFO(129014518564672)2025-04-22 11:09:44,189:************************* INFO(129014518564672)2025-04-22 11:09:44,189:deblurring started WARNING(129014518564672)2025-04-22 11:09:44,190:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5h_41_L001_R1_001.fastq.gz WARNING(129014518564672)2025-04-22 11:09:44,190:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5h_41_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129014518564672)2025-04-22 11:09:44,190:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129014518564672)2025-04-22 11:09:44,190:deblur worker thread started INFO(129014518564672)2025-04-22 11:09:44,190:processing per sample fasta files INFO(129014518564672)2025-04-22 11:09:44,190:-------------------------------------------------------- INFO(129014518564672)2025-04-22 11:09:44,190:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5h_41_L001_R1_001.fastq.gz INFO(129086691424064)2025-04-22 11:09:51,765:deblurring 5382 sequences INFO(138557305857856)2025-04-22 11:09:58,686:3328 unique sequences left following deblurring INFO(138557305857856)2025-04-22 11:09:58,716:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(138557305857856)2025-04-22 11:10:00,617:finished processing file INFO(138557305857856)2025-04-22 11:10:00,620:finished processing per sample fasta files INFO(138557305857856)2025-04-22 11:10:00,620:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5ff_39_L001_R1_001.fastq.gz finished INFO(126524982818624)2025-04-22 11:10:02,502:************************* INFO(126524982818624)2025-04-22 11:10:02,503:deblurring started WARNING(126524982818624)2025-04-22 11:10:02,504:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1q_20_L001_R1_001.fastq.gz WARNING(126524982818624)2025-04-22 11:10:02,504:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1q_20_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(126524982818624)2025-04-22 11:10:02,504:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(126524982818624)2025-04-22 11:10:02,504:deblur worker thread started INFO(126524982818624)2025-04-22 11:10:02,505:processing per sample fasta files INFO(126524982818624)2025-04-22 11:10:02,505:-------------------------------------------------------- INFO(126524982818624)2025-04-22 11:10:02,505:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1q_20_L001_R1_001.fastq.gz INFO(129086691424064)2025-04-22 11:10:16,812:2050 unique sequences left following deblurring INFO(129086691424064)2025-04-22 11:10:16,828:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(129086691424064)2025-04-22 11:10:17,575:finished processing file INFO(129086691424064)2025-04-22 11:10:17,577:finished processing per sample fasta files INFO(129086691424064)2025-04-22 11:10:17,577:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1dd_9_L001_R1_001.fastq.gz finished INFO(123890670200640)2025-04-22 11:10:18,952:************************* INFO(123890670200640)2025-04-22 11:10:18,952:deblurring started WARNING(123890670200640)2025-04-22 11:10:18,953:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1y_26_L001_R1_001.fastq.gz WARNING(123890670200640)2025-04-22 11:10:18,953:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1y_26_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123890670200640)2025-04-22 11:10:18,953:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123890670200640)2025-04-22 11:10:18,953:deblur worker thread started INFO(123890670200640)2025-04-22 11:10:18,953:processing per sample fasta files INFO(123890670200640)2025-04-22 11:10:18,954:-------------------------------------------------------- INFO(123890670200640)2025-04-22 11:10:18,954:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1y_26_L001_R1_001.fastq.gz INFO(137613046069056)2025-04-22 11:10:33,805:3387 unique sequences left following deblurring INFO(137613046069056)2025-04-22 11:10:33,850:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(137613046069056)2025-04-22 11:10:35,173:finished processing file INFO(137613046069056)2025-04-22 11:10:35,177:finished processing per sample fasta files INFO(137613046069056)2025-04-22 11:10:35,177:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1p_19_L001_R1_001.fastq.gz finished INFO(137282987763520)2025-04-22 11:10:36,395:************************* INFO(137282987763520)2025-04-22 11:10:36,395:deblurring started WARNING(137282987763520)2025-04-22 11:10:36,395:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5J_28_L001_R1_001.fastq.gz WARNING(137282987763520)2025-04-22 11:10:36,395:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5J_28_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(137282987763520)2025-04-22 11:10:36,395:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(137282987763520)2025-04-22 11:10:36,395:deblur worker thread started INFO(137282987763520)2025-04-22 11:10:36,396:processing per sample fasta files INFO(137282987763520)2025-04-22 11:10:36,396:-------------------------------------------------------- INFO(137282987763520)2025-04-22 11:10:36,396:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5J_28_L001_R1_001.fastq.gz INFO(137282987763520)2025-04-22 11:10:36,423:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5J_28_L001_R1_001.fastq.gz.trim INFO(137282987763520)2025-04-22 11:10:36,435:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5J_28_L001_R1_001.fastq.gz.trim.derep WARNING(137282987763520)2025-04-22 11:10:36,435:file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5J_28_L001_R1_001.fastq.gz.trim.derep has size 0, continuing WARNING(137282987763520)2025-04-22 11:10:36,436:remove artifacts failed, aborting WARNING(137282987763520)2025-04-22 11:10:36,436:deblurring failed for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5J_28_L001_R1_001.fastq.gz INFO(137282987763520)2025-04-22 11:10:36,436:finished processing per sample fasta files INFO(137282987763520)2025-04-22 11:10:36,436:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5J_28_L001_R1_001.fastq.gz finished INFO(135744001869632)2025-04-22 11:10:37,668:************************* INFO(135744001869632)2025-04-22 11:10:37,668:deblurring started WARNING(135744001869632)2025-04-22 11:10:37,668:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5L_29_L001_R1_001.fastq.gz WARNING(135744001869632)2025-04-22 11:10:37,669:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5L_29_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(135744001869632)2025-04-22 11:10:37,669:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(135744001869632)2025-04-22 11:10:37,669:deblur worker thread started INFO(135744001869632)2025-04-22 11:10:37,669:processing per sample fasta files INFO(135744001869632)2025-04-22 11:10:37,669:-------------------------------------------------------- INFO(135744001869632)2025-04-22 11:10:37,669:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5L_29_L001_R1_001.fastq.gz INFO(126524982818624)2025-04-22 11:10:40,333:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim INFO(126524982818624)2025-04-22 11:10:40,358:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim.derep INFO(126524982818624)2025-04-22 11:10:40,850:total sequences 965, passing sequences 965, failing sequences 0 INFO(126524982818624)2025-04-22 11:10:40,850:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(126524982818624)2025-04-22 11:10:43,150:deblurring 965 sequences INFO(126524982818624)2025-04-22 11:10:43,819:536 unique sequences left following deblurring INFO(126524982818624)2025-04-22 11:10:43,823:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(126524982818624)2025-04-22 11:10:43,981:finished processing file INFO(126524982818624)2025-04-22 11:10:43,981:finished processing per sample fasta files INFO(126524982818624)2025-04-22 11:10:43,982:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1q_20_L001_R1_001.fastq.gz finished INFO(123779389265728)2025-04-22 11:10:45,177:************************* INFO(123779389265728)2025-04-22 11:10:45,177:deblurring started WARNING(123779389265728)2025-04-22 11:10:45,177:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5b_32_L001_R1_001.fastq.gz WARNING(123779389265728)2025-04-22 11:10:45,177:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5b_32_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123779389265728)2025-04-22 11:10:45,177:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123779389265728)2025-04-22 11:10:45,178:deblur worker thread started INFO(123779389265728)2025-04-22 11:10:45,178:processing per sample fasta files INFO(123779389265728)2025-04-22 11:10:45,178:-------------------------------------------------------- INFO(123779389265728)2025-04-22 11:10:45,178:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5b_32_L001_R1_001.fastq.gz INFO(123890670200640)2025-04-22 11:10:51,644:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim INFO(123890670200640)2025-04-22 11:10:51,718:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim.derep INFO(123890670200640)2025-04-22 11:10:52,358:total sequences 3287, passing sequences 3287, failing sequences 0 INFO(123890670200640)2025-04-22 11:10:52,358:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123890670200640)2025-04-22 11:11:03,877:deblurring 3287 sequences INFO(129014518564672)2025-04-22 11:11:07,733:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim INFO(129014518564672)2025-04-22 11:11:07,789:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim.derep INFO(129014518564672)2025-04-22 11:11:08,385:total sequences 1546, passing sequences 1546, failing sequences 0 INFO(129014518564672)2025-04-22 11:11:08,386:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123890670200640)2025-04-22 11:11:10,692:1392 unique sequences left following deblurring INFO(123890670200640)2025-04-22 11:11:10,701:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(123890670200640)2025-04-22 11:11:11,127:finished processing file INFO(123890670200640)2025-04-22 11:11:11,128:finished processing per sample fasta files INFO(123890670200640)2025-04-22 11:11:11,129:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1y_26_L001_R1_001.fastq.gz finished INFO(129014518564672)2025-04-22 11:11:12,246:deblurring 1546 sequences INFO(133097300862784)2025-04-22 11:11:12,288:************************* INFO(133097300862784)2025-04-22 11:11:12,289:deblurring started WARNING(133097300862784)2025-04-22 11:11:12,289:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5e_36_L001_R1_001.fastq.gz WARNING(133097300862784)2025-04-22 11:11:12,289:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5e_36_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133097300862784)2025-04-22 11:11:12,289:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133097300862784)2025-04-22 11:11:12,289:deblur worker thread started INFO(133097300862784)2025-04-22 11:11:12,289:processing per sample fasta files INFO(133097300862784)2025-04-22 11:11:12,289:-------------------------------------------------------- INFO(133097300862784)2025-04-22 11:11:12,289:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5e_36_L001_R1_001.fastq.gz INFO(129014518564672)2025-04-22 11:11:13,693:511 unique sequences left following deblurring INFO(129014518564672)2025-04-22 11:11:13,696:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(129014518564672)2025-04-22 11:11:13,851:finished processing file INFO(129014518564672)2025-04-22 11:11:13,852:finished processing per sample fasta files INFO(129014518564672)2025-04-22 11:11:13,852:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5h_41_L001_R1_001.fastq.gz finished INFO(135744001869632)2025-04-22 11:11:14,715:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim INFO(135744001869632)2025-04-22 11:11:14,788:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim.derep INFO(132388584916800)2025-04-22 11:11:15,174:************************* INFO(132388584916800)2025-04-22 11:11:15,175:deblurring started WARNING(132388584916800)2025-04-22 11:11:15,175:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1g_13_L001_R1_001.fastq.gz WARNING(132388584916800)2025-04-22 11:11:15,175:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1g_13_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(132388584916800)2025-04-22 11:11:15,176:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(132388584916800)2025-04-22 11:11:15,176:deblur worker thread started INFO(132388584916800)2025-04-22 11:11:15,176:processing per sample fasta files INFO(132388584916800)2025-04-22 11:11:15,176:-------------------------------------------------------- INFO(132388584916800)2025-04-22 11:11:15,176:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1g_13_L001_R1_001.fastq.gz INFO(135744001869632)2025-04-22 11:11:15,379:total sequences 3817, passing sequences 3817, failing sequences 0 INFO(135744001869632)2025-04-22 11:11:15,379:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123779389265728)2025-04-22 11:11:26,601:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim INFO(123779389265728)2025-04-22 11:11:26,651:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim.derep INFO(123779389265728)2025-04-22 11:11:27,205:total sequences 2458, passing sequences 2458, failing sequences 0 INFO(123779389265728)2025-04-22 11:11:27,206:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(135744001869632)2025-04-22 11:11:29,806:deblurring 3817 sequences INFO(123779389265728)2025-04-22 11:11:34,490:deblurring 2458 sequences INFO(123779389265728)2025-04-22 11:11:38,158:1022 unique sequences left following deblurring INFO(123779389265728)2025-04-22 11:11:38,166:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(123779389265728)2025-04-22 11:11:38,456:finished processing file INFO(123779389265728)2025-04-22 11:11:38,459:finished processing per sample fasta files INFO(123779389265728)2025-04-22 11:11:38,459:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5b_32_L001_R1_001.fastq.gz finished INFO(132381535749952)2025-04-22 11:11:39,698:************************* INFO(132381535749952)2025-04-22 11:11:39,698:deblurring started WARNING(132381535749952)2025-04-22 11:11:39,699:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1U_2_L001_R1_001.fastq.gz WARNING(132381535749952)2025-04-22 11:11:39,699:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1U_2_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(132381535749952)2025-04-22 11:11:39,699:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(132381535749952)2025-04-22 11:11:39,699:deblur worker thread started INFO(132381535749952)2025-04-22 11:11:39,699:processing per sample fasta files INFO(132381535749952)2025-04-22 11:11:39,700:-------------------------------------------------------- INFO(132381535749952)2025-04-22 11:11:39,700:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1U_2_L001_R1_001.fastq.gz INFO(135744001869632)2025-04-22 11:11:42,855:2318 unique sequences left following deblurring INFO(135744001869632)2025-04-22 11:11:42,874:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(135744001869632)2025-04-22 11:11:43,597:finished processing file INFO(135744001869632)2025-04-22 11:11:43,599:finished processing per sample fasta files INFO(135744001869632)2025-04-22 11:11:43,599:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5L_29_L001_R1_001.fastq.gz finished INFO(133471079130944)2025-04-22 11:11:44,670:************************* INFO(133471079130944)2025-04-22 11:11:44,670:deblurring started WARNING(133471079130944)2025-04-22 11:11:44,670:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5bb_33_L001_R1_001.fastq.gz WARNING(133471079130944)2025-04-22 11:11:44,677:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5bb_33_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133471079130944)2025-04-22 11:11:44,677:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133471079130944)2025-04-22 11:11:44,677:deblur worker thread started INFO(133471079130944)2025-04-22 11:11:44,677:processing per sample fasta files INFO(133471079130944)2025-04-22 11:11:44,677:-------------------------------------------------------- INFO(133471079130944)2025-04-22 11:11:44,677:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5bb_33_L001_R1_001.fastq.gz INFO(132381535749952)2025-04-22 11:11:48,196:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim INFO(132381535749952)2025-04-22 11:11:48,230:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim.derep INFO(132381535749952)2025-04-22 11:11:48,823:total sequences 1527, passing sequences 1527, failing sequences 0 INFO(132381535749952)2025-04-22 11:11:48,823:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(132381535749952)2025-04-22 11:11:52,519:deblurring 1527 sequences INFO(132381535749952)2025-04-22 11:11:54,978:1111 unique sequences left following deblurring INFO(132381535749952)2025-04-22 11:11:54,994:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(132381535749952)2025-04-22 11:11:55,272:finished processing file INFO(132381535749952)2025-04-22 11:11:55,273:finished processing per sample fasta files INFO(132381535749952)2025-04-22 11:11:55,273:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1U_2_L001_R1_001.fastq.gz finished INFO(130351275382592)2025-04-22 11:11:56,336:************************* INFO(130351275382592)2025-04-22 11:11:56,336:deblurring started WARNING(130351275382592)2025-04-22 11:11:56,337:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1n_17_L001_R1_001.fastq.gz WARNING(130351275382592)2025-04-22 11:11:56,337:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1n_17_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(130351275382592)2025-04-22 11:11:56,337:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(130351275382592)2025-04-22 11:11:56,337:deblur worker thread started INFO(130351275382592)2025-04-22 11:11:56,338:processing per sample fasta files INFO(130351275382592)2025-04-22 11:11:56,338:-------------------------------------------------------- INFO(130351275382592)2025-04-22 11:11:56,338:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1n_17_L001_R1_001.fastq.gz INFO(132388584916800)2025-04-22 11:11:57,451:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim INFO(132388584916800)2025-04-22 11:11:57,555:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim.derep INFO(132388584916800)2025-04-22 11:11:58,116:total sequences 3187, passing sequences 3187, failing sequences 0 INFO(132388584916800)2025-04-22 11:11:58,116:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(132388584916800)2025-04-22 11:12:09,077:deblurring 3187 sequences INFO(132388584916800)2025-04-22 11:12:15,325:1183 unique sequences left following deblurring INFO(132388584916800)2025-04-22 11:12:15,334:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(132388584916800)2025-04-22 11:12:15,735:finished processing file INFO(132388584916800)2025-04-22 11:12:15,736:finished processing per sample fasta files INFO(132388584916800)2025-04-22 11:12:15,736:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1g_13_L001_R1_001.fastq.gz finished INFO(140289332537152)2025-04-22 11:12:17,157:************************* INFO(140289332537152)2025-04-22 11:12:17,157:deblurring started WARNING(140289332537152)2025-04-22 11:12:17,158:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1k_15_L001_R1_001.fastq.gz WARNING(140289332537152)2025-04-22 11:12:17,158:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1k_15_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(140289332537152)2025-04-22 11:12:17,158:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(140289332537152)2025-04-22 11:12:17,158:deblur worker thread started INFO(140289332537152)2025-04-22 11:12:17,158:processing per sample fasta files INFO(140289332537152)2025-04-22 11:12:17,158:-------------------------------------------------------- INFO(140289332537152)2025-04-22 11:12:17,158:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1k_15_L001_R1_001.fastq.gz INFO(133097300862784)2025-04-22 11:12:22,050:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim INFO(133097300862784)2025-04-22 11:12:22,186:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim.derep INFO(133097300862784)2025-04-22 11:12:22,736:total sequences 3017, passing sequences 3017, failing sequences 0 INFO(133097300862784)2025-04-22 11:12:22,736:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(133097300862784)2025-04-22 11:12:33,806:deblurring 3017 sequences INFO(133097300862784)2025-04-22 11:12:37,992:999 unique sequences left following deblurring INFO(133097300862784)2025-04-22 11:12:38,001:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(133097300862784)2025-04-22 11:12:38,271:finished processing file INFO(133097300862784)2025-04-22 11:12:38,271:finished processing per sample fasta files INFO(133097300862784)2025-04-22 11:12:38,272:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5e_36_L001_R1_001.fastq.gz finished INFO(136773887969088)2025-04-22 11:12:39,509:************************* INFO(136773887969088)2025-04-22 11:12:39,509:deblurring started WARNING(136773887969088)2025-04-22 11:12:39,509:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5a_30_L001_R1_001.fastq.gz WARNING(136773887969088)2025-04-22 11:12:39,510:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5a_30_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(136773887969088)2025-04-22 11:12:39,510:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(136773887969088)2025-04-22 11:12:39,510:deblur worker thread started INFO(136773887969088)2025-04-22 11:12:39,510:processing per sample fasta files INFO(136773887969088)2025-04-22 11:12:39,510:-------------------------------------------------------- INFO(136773887969088)2025-04-22 11:12:39,510:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5a_30_L001_R1_001.fastq.gz INFO(140289332537152)2025-04-22 11:12:41,649:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim INFO(140289332537152)2025-04-22 11:12:41,699:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim.derep INFO(140289332537152)2025-04-22 11:12:42,259:total sequences 2521, passing sequences 2521, failing sequences 0 INFO(140289332537152)2025-04-22 11:12:42,259:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(130351275382592)2025-04-22 11:12:45,628:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim INFO(130351275382592)2025-04-22 11:12:45,718:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim.derep INFO(130351275382592)2025-04-22 11:12:46,448:total sequences 4681, passing sequences 4681, failing sequences 0 INFO(130351275382592)2025-04-22 11:12:46,448:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(140289332537152)2025-04-22 11:12:50,095:deblurring 2521 sequences INFO(140289332537152)2025-04-22 11:12:54,159:1140 unique sequences left following deblurring INFO(140289332537152)2025-04-22 11:12:54,166:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(140289332537152)2025-04-22 11:12:54,535:finished processing file INFO(140289332537152)2025-04-22 11:12:54,536:finished processing per sample fasta files INFO(140289332537152)2025-04-22 11:12:54,536:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1k_15_L001_R1_001.fastq.gz finished INFO(130869134657344)2025-04-22 11:12:55,751:************************* INFO(130869134657344)2025-04-22 11:12:55,751:deblurring started WARNING(130869134657344)2025-04-22 11:12:55,752:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5z_53_L001_R1_001.fastq.gz WARNING(130869134657344)2025-04-22 11:12:55,752:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5z_53_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(130869134657344)2025-04-22 11:12:55,752:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(130869134657344)2025-04-22 11:12:55,752:deblur worker thread started INFO(130869134657344)2025-04-22 11:12:55,752:processing per sample fasta files INFO(130869134657344)2025-04-22 11:12:55,752:-------------------------------------------------------- INFO(130869134657344)2025-04-22 11:12:55,752:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5z_53_L001_R1_001.fastq.gz INFO(133471079130944)2025-04-22 11:13:02,903:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim INFO(133471079130944)2025-04-22 11:13:03,175:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim.derep INFO(133471079130944)2025-04-22 11:13:04,005:total sequences 7234, passing sequences 7234, failing sequences 0 INFO(133471079130944)2025-04-22 11:13:04,005:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(130351275382592)2025-04-22 11:13:08,794:deblurring 4681 sequences INFO(136773887969088)2025-04-22 11:13:11,407:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim INFO(136773887969088)2025-04-22 11:13:11,429:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim.derep INFO(136773887969088)2025-04-22 11:13:11,965:total sequences 902, passing sequences 902, failing sequences 0 INFO(136773887969088)2025-04-22 11:13:11,965:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(136773887969088)2025-04-22 11:13:14,127:deblurring 902 sequences INFO(136773887969088)2025-04-22 11:13:14,811:495 unique sequences left following deblurring INFO(136773887969088)2025-04-22 11:13:14,815:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(136773887969088)2025-04-22 11:13:14,933:finished processing file INFO(136773887969088)2025-04-22 11:13:14,934:finished processing per sample fasta files INFO(136773887969088)2025-04-22 11:13:14,934:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5a_30_L001_R1_001.fastq.gz finished INFO(127165205686080)2025-04-22 11:13:16,154:************************* INFO(127165205686080)2025-04-22 11:13:16,154:deblurring started WARNING(127165205686080)2025-04-22 11:13:16,155:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1t_23_L001_R1_001.fastq.gz WARNING(127165205686080)2025-04-22 11:13:16,155:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1t_23_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127165205686080)2025-04-22 11:13:16,155:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127165205686080)2025-04-22 11:13:16,155:deblur worker thread started INFO(127165205686080)2025-04-22 11:13:16,155:processing per sample fasta files INFO(127165205686080)2025-04-22 11:13:16,156:-------------------------------------------------------- INFO(127165205686080)2025-04-22 11:13:16,156:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1t_23_L001_R1_001.fastq.gz INFO(130351275382592)2025-04-22 11:13:26,096:2322 unique sequences left following deblurring INFO(130351275382592)2025-04-22 11:13:26,113:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(130351275382592)2025-04-22 11:13:26,844:finished processing file INFO(130351275382592)2025-04-22 11:13:26,845:finished processing per sample fasta files INFO(130351275382592)2025-04-22 11:13:26,846:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1n_17_L001_R1_001.fastq.gz finished INFO(136871280871232)2025-04-22 11:13:28,153:************************* INFO(136871280871232)2025-04-22 11:13:28,153:deblurring started WARNING(136871280871232)2025-04-22 11:13:28,154:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1ee_11_L001_R1_001.fastq.gz WARNING(136871280871232)2025-04-22 11:13:28,154:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1ee_11_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(136871280871232)2025-04-22 11:13:28,154:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(136871280871232)2025-04-22 11:13:28,154:deblur worker thread started INFO(136871280871232)2025-04-22 11:13:28,154:processing per sample fasta files INFO(136871280871232)2025-04-22 11:13:28,154:-------------------------------------------------------- INFO(136871280871232)2025-04-22 11:13:28,154:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1ee_11_L001_R1_001.fastq.gz INFO(133471079130944)2025-04-22 11:13:59,012:deblurring 7234 sequences INFO(127165205686080)2025-04-22 11:13:59,635:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim INFO(127165205686080)2025-04-22 11:13:59,722:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim.derep INFO(127165205686080)2025-04-22 11:14:00,526:total sequences 4668, passing sequences 4668, failing sequences 0 INFO(127165205686080)2025-04-22 11:14:00,526:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(136871280871232)2025-04-22 11:14:17,763:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim INFO(136871280871232)2025-04-22 11:14:17,835:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim.derep INFO(136871280871232)2025-04-22 11:14:18,561:total sequences 3407, passing sequences 3407, failing sequences 0 INFO(136871280871232)2025-04-22 11:14:18,562:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127165205686080)2025-04-22 11:14:23,711:deblurring 4668 sequences INFO(136871280871232)2025-04-22 11:14:32,404:deblurring 3407 sequences INFO(133471079130944)2025-04-22 11:14:36,463:2772 unique sequences left following deblurring INFO(133471079130944)2025-04-22 11:14:36,519:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(133471079130944)2025-04-22 11:14:37,619:finished processing file INFO(133471079130944)2025-04-22 11:14:37,621:finished processing per sample fasta files INFO(133471079130944)2025-04-22 11:14:37,625:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5bb_33_L001_R1_001.fastq.gz finished INFO(125353813657408)2025-04-22 11:14:38,926:************************* INFO(125353813657408)2025-04-22 11:14:38,926:deblurring started WARNING(125353813657408)2025-04-22 11:14:38,926:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5g_40_L001_R1_001.fastq.gz WARNING(125353813657408)2025-04-22 11:14:38,927:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5g_40_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(125353813657408)2025-04-22 11:14:38,927:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(125353813657408)2025-04-22 11:14:38,927:deblur worker thread started INFO(125353813657408)2025-04-22 11:14:38,927:processing per sample fasta files INFO(125353813657408)2025-04-22 11:14:38,927:-------------------------------------------------------- INFO(125353813657408)2025-04-22 11:14:38,927:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5g_40_L001_R1_001.fastq.gz INFO(136871280871232)2025-04-22 11:14:41,708:1904 unique sequences left following deblurring INFO(136871280871232)2025-04-22 11:14:41,719:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(136871280871232)2025-04-22 11:14:42,490:finished processing file INFO(136871280871232)2025-04-22 11:14:42,491:finished processing per sample fasta files INFO(136871280871232)2025-04-22 11:14:42,491:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1ee_11_L001_R1_001.fastq.gz finished INFO(127165205686080)2025-04-22 11:14:42,563:2324 unique sequences left following deblurring INFO(127165205686080)2025-04-22 11:14:42,612:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(130869134657344)2025-04-22 11:14:43,171:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim INFO(130869134657344)2025-04-22 11:14:43,656:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim.derep INFO(127165205686080)2025-04-22 11:14:43,712:finished processing file INFO(127165205686080)2025-04-22 11:14:43,714:finished processing per sample fasta files INFO(127165205686080)2025-04-22 11:14:43,714:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1t_23_L001_R1_001.fastq.gz finished INFO(138370608375616)2025-04-22 11:14:44,088:************************* INFO(138370608375616)2025-04-22 11:14:44,089:deblurring started WARNING(138370608375616)2025-04-22 11:14:44,089:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5n_44_L001_R1_001.fastq.gz WARNING(138370608375616)2025-04-22 11:14:44,089:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5n_44_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138370608375616)2025-04-22 11:14:44,089:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138370608375616)2025-04-22 11:14:44,089:deblur worker thread started INFO(138370608375616)2025-04-22 11:14:44,089:processing per sample fasta files INFO(138370608375616)2025-04-22 11:14:44,090:-------------------------------------------------------- INFO(138370608375616)2025-04-22 11:14:44,090:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5n_44_L001_R1_001.fastq.gz INFO(130869134657344)2025-04-22 11:14:44,627:total sequences 12415, passing sequences 12415, failing sequences 0 INFO(130869134657344)2025-04-22 11:14:44,627:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(133091971372864)2025-04-22 11:14:45,121:************************* INFO(133091971372864)2025-04-22 11:14:45,121:deblurring started WARNING(133091971372864)2025-04-22 11:14:45,122:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1c_6_L001_R1_001.fastq.gz WARNING(133091971372864)2025-04-22 11:14:45,122:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1c_6_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133091971372864)2025-04-22 11:14:45,122:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133091971372864)2025-04-22 11:14:45,122:deblur worker thread started INFO(133091971372864)2025-04-22 11:14:45,122:processing per sample fasta files INFO(133091971372864)2025-04-22 11:14:45,122:-------------------------------------------------------- INFO(133091971372864)2025-04-22 11:14:45,122:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1c_6_L001_R1_001.fastq.gz INFO(125353813657408)2025-04-22 11:15:03,194:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim INFO(125353813657408)2025-04-22 11:15:03,318:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim.derep INFO(125353813657408)2025-04-22 11:15:04,211:total sequences 5221, passing sequences 5221, failing sequences 0 INFO(125353813657408)2025-04-22 11:15:04,212:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(138370608375616)2025-04-22 11:15:09,871:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim INFO(138370608375616)2025-04-22 11:15:10,014:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim.derep INFO(138370608375616)2025-04-22 11:15:11,117:total sequences 2366, passing sequences 2366, failing sequences 0 INFO(138370608375616)2025-04-22 11:15:11,118:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(133091971372864)2025-04-22 11:15:15,859:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim INFO(133091971372864)2025-04-22 11:15:15,910:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim.derep INFO(133091971372864)2025-04-22 11:15:16,818:total sequences 2341, passing sequences 2341, failing sequences 0 INFO(133091971372864)2025-04-22 11:15:16,824:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(138370608375616)2025-04-22 11:15:20,351:deblurring 2366 sequences INFO(133091971372864)2025-04-22 11:15:25,559:deblurring 2341 sequences INFO(138370608375616)2025-04-22 11:15:26,403:1270 unique sequences left following deblurring INFO(138370608375616)2025-04-22 11:15:26,433:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(138370608375616)2025-04-22 11:15:26,781:finished processing file INFO(138370608375616)2025-04-22 11:15:26,782:finished processing per sample fasta files INFO(138370608375616)2025-04-22 11:15:26,782:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5n_44_L001_R1_001.fastq.gz finished INFO(140612330895168)2025-04-22 11:15:28,235:************************* INFO(140612330895168)2025-04-22 11:15:28,239:deblurring started WARNING(140612330895168)2025-04-22 11:15:28,243:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1f_12_L001_R1_001.fastq.gz WARNING(140612330895168)2025-04-22 11:15:28,243:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1f_12_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(140612330895168)2025-04-22 11:15:28,243:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(140612330895168)2025-04-22 11:15:28,246:deblur worker thread started INFO(140612330895168)2025-04-22 11:15:28,247:processing per sample fasta files INFO(140612330895168)2025-04-22 11:15:28,247:-------------------------------------------------------- INFO(140612330895168)2025-04-22 11:15:28,247:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1f_12_L001_R1_001.fastq.gz INFO(133091971372864)2025-04-22 11:15:31,097:1258 unique sequences left following deblurring INFO(133091971372864)2025-04-22 11:15:31,108:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(133091971372864)2025-04-22 11:15:31,651:finished processing file INFO(133091971372864)2025-04-22 11:15:31,652:finished processing per sample fasta files INFO(133091971372864)2025-04-22 11:15:31,652:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1c_6_L001_R1_001.fastq.gz finished INFO(127919527528256)2025-04-22 11:15:33,558:************************* INFO(127919527528256)2025-04-22 11:15:33,558:deblurring started WARNING(127919527528256)2025-04-22 11:15:33,558:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5ee_37_L001_R1_001.fastq.gz WARNING(127919527528256)2025-04-22 11:15:33,559:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5ee_37_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127919527528256)2025-04-22 11:15:33,559:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127919527528256)2025-04-22 11:15:33,559:deblur worker thread started INFO(127919527528256)2025-04-22 11:15:33,559:processing per sample fasta files INFO(127919527528256)2025-04-22 11:15:33,559:-------------------------------------------------------- INFO(127919527528256)2025-04-22 11:15:33,559:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5ee_37_L001_R1_001.fastq.gz INFO(125353813657408)2025-04-22 11:15:38,976:deblurring 5221 sequences INFO(125353813657408)2025-04-22 11:16:00,170:2509 unique sequences left following deblurring INFO(125353813657408)2025-04-22 11:16:00,186:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(125353813657408)2025-04-22 11:16:01,133:finished processing file INFO(125353813657408)2025-04-22 11:16:01,134:finished processing per sample fasta files INFO(125353813657408)2025-04-22 11:16:01,135:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5g_40_L001_R1_001.fastq.gz finished INFO(126713465497408)2025-04-22 11:16:02,470:************************* INFO(126713465497408)2025-04-22 11:16:02,470:deblurring started WARNING(126713465497408)2025-04-22 11:16:02,470:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5r_48_L001_R1_001.fastq.gz WARNING(126713465497408)2025-04-22 11:16:02,471:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5r_48_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(126713465497408)2025-04-22 11:16:02,471:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(126713465497408)2025-04-22 11:16:02,471:deblur worker thread started INFO(126713465497408)2025-04-22 11:16:02,471:processing per sample fasta files INFO(126713465497408)2025-04-22 11:16:02,471:-------------------------------------------------------- INFO(126713465497408)2025-04-22 11:16:02,471:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5r_48_L001_R1_001.fastq.gz INFO(140612330895168)2025-04-22 11:16:34,795:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim INFO(140612330895168)2025-04-22 11:16:34,852:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim.derep INFO(140612330895168)2025-04-22 11:16:35,498:total sequences 1867, passing sequences 1867, failing sequences 0 INFO(140612330895168)2025-04-22 11:16:35,499:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127919527528256)2025-04-22 11:16:41,108:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim INFO(140612330895168)2025-04-22 11:16:41,179:deblurring 1867 sequences INFO(127919527528256)2025-04-22 11:16:41,259:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim.derep INFO(127919527528256)2025-04-22 11:16:42,116:total sequences 3216, passing sequences 3216, failing sequences 0 INFO(127919527528256)2025-04-22 11:16:42,116:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(140612330895168)2025-04-22 11:16:42,821:526 unique sequences left following deblurring INFO(140612330895168)2025-04-22 11:16:42,826:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(140612330895168)2025-04-22 11:16:43,143:finished processing file INFO(140612330895168)2025-04-22 11:16:43,144:finished processing per sample fasta files INFO(140612330895168)2025-04-22 11:16:43,144:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1f_12_L001_R1_001.fastq.gz finished INFO(126713465497408)2025-04-22 11:16:44,389:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim INFO(126713465497408)2025-04-22 11:16:44,449:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim.derep INFO(126713465497408)2025-04-22 11:16:45,056:total sequences 2928, passing sequences 2928, failing sequences 0 INFO(126713465497408)2025-04-22 11:16:45,056:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127919527528256)2025-04-22 11:16:53,306:deblurring 3216 sequences INFO(126713465497408)2025-04-22 11:16:54,544:deblurring 2928 sequences INFO(127919527528256)2025-04-22 11:16:59,937:1427 unique sequences left following deblurring INFO(127919527528256)2025-04-22 11:16:59,947:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(127919527528256)2025-04-22 11:17:00,429:finished processing file INFO(127919527528256)2025-04-22 11:17:00,431:finished processing per sample fasta files INFO(127919527528256)2025-04-22 11:17:00,431:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5ee_37_L001_R1_001.fastq.gz finished INFO(126713465497408)2025-04-22 11:17:01,528:1667 unique sequences left following deblurring INFO(126713465497408)2025-04-22 11:17:01,539:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(140669593421632)2025-04-22 11:17:01,619:************************* INFO(140669593421632)2025-04-22 11:17:01,619:deblurring started WARNING(140669593421632)2025-04-22 11:17:01,619:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5p_46_L001_R1_001.fastq.gz WARNING(140669593421632)2025-04-22 11:17:01,619:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5p_46_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(140669593421632)2025-04-22 11:17:01,619:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(140669593421632)2025-04-22 11:17:01,619:deblur worker thread started INFO(140669593421632)2025-04-22 11:17:01,619:processing per sample fasta files INFO(140669593421632)2025-04-22 11:17:01,619:-------------------------------------------------------- INFO(140669593421632)2025-04-22 11:17:01,620:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5p_46_L001_R1_001.fastq.gz INFO(126713465497408)2025-04-22 11:17:02,049:finished processing file INFO(126713465497408)2025-04-22 11:17:02,051:finished processing per sample fasta files INFO(126713465497408)2025-04-22 11:17:02,051:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5r_48_L001_R1_001.fastq.gz finished INFO(127306299836224)2025-04-22 11:17:03,318:************************* INFO(127306299836224)2025-04-22 11:17:03,318:deblurring started WARNING(127306299836224)2025-04-22 11:17:03,319:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1v_24_L001_R1_001.fastq.gz WARNING(127306299836224)2025-04-22 11:17:03,319:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1v_24_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127306299836224)2025-04-22 11:17:03,319:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127306299836224)2025-04-22 11:17:03,319:deblur worker thread started INFO(127306299836224)2025-04-22 11:17:03,319:processing per sample fasta files INFO(127306299836224)2025-04-22 11:17:03,319:-------------------------------------------------------- INFO(127306299836224)2025-04-22 11:17:03,319:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1v_24_L001_R1_001.fastq.gz INFO(130869134657344)2025-04-22 11:17:22,641:deblurring 12415 sequences INFO(140669593421632)2025-04-22 11:17:28,784:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim INFO(140669593421632)2025-04-22 11:17:28,837:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim.derep INFO(140669593421632)2025-04-22 11:17:29,508:total sequences 3193, passing sequences 3193, failing sequences 0 INFO(140669593421632)2025-04-22 11:17:29,508:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127306299836224)2025-04-22 11:17:37,345:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim INFO(127306299836224)2025-04-22 11:17:37,402:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim.derep INFO(127306299836224)2025-04-22 11:17:37,982:total sequences 2467, passing sequences 2467, failing sequences 0 INFO(127306299836224)2025-04-22 11:17:37,982:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(140669593421632)2025-04-22 11:17:39,834:deblurring 3193 sequences INFO(127306299836224)2025-04-22 11:17:44,834:deblurring 2467 sequences INFO(127306299836224)2025-04-22 11:17:48,788:1239 unique sequences left following deblurring INFO(127306299836224)2025-04-22 11:17:48,795:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(127306299836224)2025-04-22 11:17:49,186:finished processing file INFO(127306299836224)2025-04-22 11:17:49,187:finished processing per sample fasta files INFO(127306299836224)2025-04-22 11:17:49,187:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1v_24_L001_R1_001.fastq.gz finished INFO(140669593421632)2025-04-22 11:17:49,319:2027 unique sequences left following deblurring INFO(140669593421632)2025-04-22 11:17:49,336:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(140669593421632)2025-04-22 11:17:49,882:finished processing file INFO(140669593421632)2025-04-22 11:17:49,883:finished processing per sample fasta files INFO(140669593421632)2025-04-22 11:17:49,883:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5p_46_L001_R1_001.fastq.gz finished INFO(130869134657344)2025-04-22 11:19:29,611:7155 unique sequences left following deblurring INFO(130869134657344)2025-04-22 11:19:29,670:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(130869134657344)2025-04-22 11:19:31,647:finished processing file INFO(130869134657344)2025-04-22 11:19:31,652:finished processing per sample fasta files INFO(130869134657344)2025-04-22 11:19:31,652:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site5z_53_L001_R1_001.fastq.gz finished INFO(136886951683904)2025-04-22 11:19:32,589:************************* INFO(136886951683904)2025-04-22 11:19:32,589:deblurring started WARNING(136886951683904)2025-04-22 11:19:32,589:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1bb_5_L001_R1_001.fastq.gz WARNING(136886951683904)2025-04-22 11:19:32,589:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1bb_5_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpfe_v3e9g', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpfe_v3e9g/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(136886951683904)2025-04-22 11:19:32,589:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(136886951683904)2025-04-22 11:19:32,589:deblur worker thread started INFO(136886951683904)2025-04-22 11:19:32,589:processing per sample fasta files INFO(136886951683904)2025-04-22 11:19:32,589:-------------------------------------------------------- INFO(136886951683904)2025-04-22 11:19:32,589:launch_workflow for file /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1bb_5_L001_R1_001.fastq.gz INFO(136886951683904)2025-04-22 11:19:57,423:dereplicate seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim INFO(136886951683904)2025-04-22 11:19:57,450:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim.derep INFO(136886951683904)2025-04-22 11:19:57,860:total sequences 1030, passing sequences 1030, failing sequences 0 INFO(136886951683904)2025-04-22 11:19:57,860:multiple_sequence_alignment seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(136886951683904)2025-04-22 11:19:59,467:deblurring 1030 sequences INFO(136886951683904)2025-04-22 11:19:59,984:506 unique sequences left following deblurring INFO(136886951683904)2025-04-22 11:19:59,987:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpfe_v3e9g/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpfe_v3e9g/deblur_working_dir INFO(136886951683904)2025-04-22 11:20:00,098:finished processing file INFO(136886951683904)2025-04-22 11:20:00,099:finished processing per sample fasta files INFO(136886951683904)2025-04-22 11:20:00,099:worker thread for /tmp/qiime2/sam/data/f4e40f9d-e79b-4e81-b5f0-5a6cc989e9fc/data/Site1bb_5_L001_R1_001.fastq.gz finished INFO(129104159627072)2025-04-22 11:20:00,235:create_otu_table for 52 samples, into output table /tmp/tmpfe_v3e9g/all.biom INFO(129104159627072)2025-04-22 11:20:02,839:for output biom table loaded 52 samples, 20785 unique sequences INFO(129104159627072)2025-04-22 11:20:02,866:keeping 5670 (out of 20785 sequences) with >=10 reads INFO(129104159627072)2025-04-22 11:20:03,097:saved to biom file /tmp/tmpfe_v3e9g/all.biom INFO(129104159627072)2025-04-22 11:20:03,101:saved sequence fasta file to /tmp/tmpfe_v3e9g/all.seqs.fa INFO(129104159627072)2025-04-22 11:20:03,106:getting 16s sequences from the biom table INFO(129104159627072)2025-04-22 11:20:03,106:remove_artifacts_seqs file /tmp/tmpfe_v3e9g/all.seqs.fa INFO(129104159627072)2025-04-22 11:20:41,071:total sequences 5670, passing sequences 706, failing sequences 4964 INFO(129104159627072)2025-04-22 11:20:41,138:wrote artifact only filtered biom table to /tmp/tmpfe_v3e9g/reference-non-hit.biom INFO(129104159627072)2025-04-22 11:20:41,144:saved biom table sequences to fasta file /tmp/tmpfe_v3e9g/reference-non-hit.seqs.fa WARNING(129104159627072)2025-04-22 11:20:41,148:removed 2 samples with reads per sample<1 INFO(129104159627072)2025-04-22 11:20:41,157:wrote 16s filtered biom table to /tmp/tmpfe_v3e9g/reference-hit.biom INFO(129104159627072)2025-04-22 11:20:41,158:saved biom table sequences to fasta file /tmp/tmpfe_v3e9g/reference-hit.seqs.fa INFO(129104159627072)2025-04-22 11:20:41,159:Keeping temp files INFO(129104159627072)2025-04-22 11:20:41,159:deblur workflow finished INFO(129104159627072)2025-04-22 11:20:41,159:output saved to /tmp/tmpfe_v3e9g/all.biom INFO(129104159627072)2025-04-22 11:20:41,159:------------------ INFO(140138003871552)2025-04-23 11:29:21,693:************************* INFO(140138003871552)2025-04-23 11:29:21,694:deblurring started WARNING(140138003871552)2025-04-23 11:29:21,694:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data WARNING(140138003871552)2025-04-23 11:29:21,694:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': (), 'neg_ref_fp': (), 'neg_ref_db_fp': (), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 4, 'is_worker_thread': False, 'logger': } INFO(140138003871552)2025-04-23 11:29:21,694:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(140138003871552)2025-04-23 11:29:21,694:deblur main program started INFO(140138003871552)2025-04-23 11:29:21,695:processing directory /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data INFO(140138003871552)2025-04-23 11:29:21,696:building negative db sortmerna index files INFO(140138003871552)2025-04-23 11:29:21,696:build_index_sortmerna files ['/home/sam/programs/miniforge3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/deblur/support_files/artifacts.fa'] to dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(140138003871552)2025-04-23 11:29:21,733:building positive db sortmerna index files INFO(140138003871552)2025-04-23 11:29:21,733:build_index_sortmerna files ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',) to dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(140138003871552)2025-04-23 12:42:23,579:parallel processing per sample fasta files INFO(140138003871552)2025-04-23 12:42:23,579:parallel deblur started for 54 inputs INFO(124714412758848)2025-04-23 12:42:24,661:************************* INFO(124714412758848)2025-04-23 12:42:24,661:deblurring started WARNING(124714412758848)2025-04-23 12:42:24,661:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5aa_31_L001_R1_001.fastq.gz WARNING(124714412758848)2025-04-23 12:42:24,662:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5aa_31_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124714412758848)2025-04-23 12:42:24,662:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124714412758848)2025-04-23 12:42:24,662:deblur worker thread started INFO(124714412758848)2025-04-23 12:42:24,662:processing per sample fasta files INFO(124714412758848)2025-04-23 12:42:24,662:-------------------------------------------------------- INFO(124714412758848)2025-04-23 12:42:24,662:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5aa_31_L001_R1_001.fastq.gz INFO(140515819116352)2025-04-23 12:42:24,698:************************* INFO(140515819116352)2025-04-23 12:42:24,698:deblurring started WARNING(140515819116352)2025-04-23 12:42:24,698:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1m_16_L001_R1_001.fastq.gz WARNING(140515819116352)2025-04-23 12:42:24,699:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1m_16_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(140515819116352)2025-04-23 12:42:24,699:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(140515819116352)2025-04-23 12:42:24,699:deblur worker thread started INFO(140515819116352)2025-04-23 12:42:24,699:processing per sample fasta files INFO(140515819116352)2025-04-23 12:42:24,699:-------------------------------------------------------- INFO(140515819116352)2025-04-23 12:42:24,699:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1m_16_L001_R1_001.fastq.gz INFO(132624422876992)2025-04-23 12:42:24,803:************************* INFO(132624422876992)2025-04-23 12:42:24,804:deblurring started WARNING(132624422876992)2025-04-23 12:42:24,804:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1e_10_L001_R1_001.fastq.gz WARNING(132624422876992)2025-04-23 12:42:24,804:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1e_10_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(132624422876992)2025-04-23 12:42:24,804:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(132624422876992)2025-04-23 12:42:24,804:deblur worker thread started INFO(132624422876992)2025-04-23 12:42:24,804:processing per sample fasta files INFO(132624422876992)2025-04-23 12:42:24,804:-------------------------------------------------------- INFO(132624422876992)2025-04-23 12:42:24,804:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1e_10_L001_R1_001.fastq.gz INFO(124698184767296)2025-04-23 12:42:24,828:************************* INFO(124698184767296)2025-04-23 12:42:24,829:deblurring started WARNING(124698184767296)2025-04-23 12:42:24,829:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1r_21_L001_R1_001.fastq.gz WARNING(124698184767296)2025-04-23 12:42:24,829:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1r_21_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124698184767296)2025-04-23 12:42:24,830:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124698184767296)2025-04-23 12:42:24,830:deblur worker thread started INFO(124698184767296)2025-04-23 12:42:24,830:processing per sample fasta files INFO(124698184767296)2025-04-23 12:42:24,830:-------------------------------------------------------- INFO(124698184767296)2025-04-23 12:42:24,830:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1r_21_L001_R1_001.fastq.gz INFO(132624422876992)2025-04-23 12:42:29,827:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim INFO(132624422876992)2025-04-23 12:42:29,842:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim.derep INFO(132624422876992)2025-04-23 12:42:30,277:total sequences 346, passing sequences 346, failing sequences 0 INFO(132624422876992)2025-04-23 12:42:30,278:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(132624422876992)2025-04-23 12:42:34,762:deblurring 346 sequences INFO(132624422876992)2025-04-23 12:42:34,937:244 unique sequences left following deblurring INFO(132624422876992)2025-04-23 12:42:34,938:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(132624422876992)2025-04-23 12:42:35,062:finished processing file INFO(132624422876992)2025-04-23 12:42:35,063:finished processing per sample fasta files INFO(132624422876992)2025-04-23 12:42:35,063:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1e_10_L001_R1_001.fastq.gz finished INFO(139731538536256)2025-04-23 12:42:36,097:************************* INFO(139731538536256)2025-04-23 12:42:36,097:deblurring started WARNING(139731538536256)2025-04-23 12:42:36,097:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1a_3_L001_R1_001.fastq.gz WARNING(139731538536256)2025-04-23 12:42:36,097:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1a_3_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(139731538536256)2025-04-23 12:42:36,097:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(139731538536256)2025-04-23 12:42:36,098:deblur worker thread started INFO(139731538536256)2025-04-23 12:42:36,098:processing per sample fasta files INFO(139731538536256)2025-04-23 12:42:36,098:-------------------------------------------------------- INFO(139731538536256)2025-04-23 12:42:36,098:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1a_3_L001_R1_001.fastq.gz INFO(140515819116352)2025-04-23 12:42:51,507:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim INFO(140515819116352)2025-04-23 12:42:51,605:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim.derep INFO(124698184767296)2025-04-23 12:42:51,883:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim INFO(124698184767296)2025-04-23 12:42:51,953:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim.derep INFO(140515819116352)2025-04-23 12:42:52,219:total sequences 2999, passing sequences 2999, failing sequences 0 INFO(140515819116352)2025-04-23 12:42:52,219:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124698184767296)2025-04-23 12:42:52,520:total sequences 2788, passing sequences 2788, failing sequences 0 INFO(124698184767296)2025-04-23 12:42:52,520:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124698184767296)2025-04-23 12:43:02,692:deblurring 2788 sequences INFO(140515819116352)2025-04-23 12:43:04,035:deblurring 2999 sequences INFO(124698184767296)2025-04-23 12:43:06,343:1032 unique sequences left following deblurring INFO(124698184767296)2025-04-23 12:43:06,349:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(124698184767296)2025-04-23 12:43:06,942:finished processing file INFO(124698184767296)2025-04-23 12:43:06,942:finished processing per sample fasta files INFO(124698184767296)2025-04-23 12:43:06,943:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1r_21_L001_R1_001.fastq.gz finished INFO(130959938553664)2025-04-23 12:43:07,996:************************* INFO(130959938553664)2025-04-23 12:43:07,997:deblurring started WARNING(130959938553664)2025-04-23 12:43:07,997:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1p_19_L001_R1_001.fastq.gz WARNING(130959938553664)2025-04-23 12:43:07,997:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1p_19_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(130959938553664)2025-04-23 12:43:07,997:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(130959938553664)2025-04-23 12:43:07,997:deblur worker thread started INFO(130959938553664)2025-04-23 12:43:07,997:processing per sample fasta files INFO(130959938553664)2025-04-23 12:43:07,997:-------------------------------------------------------- INFO(130959938553664)2025-04-23 12:43:07,997:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1p_19_L001_R1_001.fastq.gz INFO(140515819116352)2025-04-23 12:43:08,497:1220 unique sequences left following deblurring INFO(140515819116352)2025-04-23 12:43:08,504:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(140515819116352)2025-04-23 12:43:09,267:finished processing file INFO(140515819116352)2025-04-23 12:43:09,268:finished processing per sample fasta files INFO(140515819116352)2025-04-23 12:43:09,268:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1m_16_L001_R1_001.fastq.gz finished INFO(133494825604928)2025-04-23 12:43:10,247:************************* INFO(133494825604928)2025-04-23 12:43:10,247:deblurring started WARNING(133494825604928)2025-04-23 12:43:10,247:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5cc_35_L001_R1_001.fastq.gz WARNING(133494825604928)2025-04-23 12:43:10,247:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5cc_35_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133494825604928)2025-04-23 12:43:10,248:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133494825604928)2025-04-23 12:43:10,248:deblur worker thread started INFO(133494825604928)2025-04-23 12:43:10,248:processing per sample fasta files INFO(133494825604928)2025-04-23 12:43:10,248:-------------------------------------------------------- INFO(133494825604928)2025-04-23 12:43:10,248:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5cc_35_L001_R1_001.fastq.gz INFO(139731538536256)2025-04-23 12:43:11,558:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim INFO(139731538536256)2025-04-23 12:43:11,586:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim.derep INFO(139731538536256)2025-04-23 12:43:12,029:total sequences 1091, passing sequences 1091, failing sequences 0 INFO(139731538536256)2025-04-23 12:43:12,029:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(139731538536256)2025-04-23 12:43:14,489:deblurring 1091 sequences INFO(124714412758848)2025-04-23 12:43:14,660:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim INFO(124714412758848)2025-04-23 12:43:14,772:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim.derep INFO(139731538536256)2025-04-23 12:43:15,417:676 unique sequences left following deblurring INFO(139731538536256)2025-04-23 12:43:15,421:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(124714412758848)2025-04-23 12:43:15,426:total sequences 4868, passing sequences 4868, failing sequences 0 INFO(124714412758848)2025-04-23 12:43:15,427:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(139731538536256)2025-04-23 12:43:15,832:finished processing file INFO(139731538536256)2025-04-23 12:43:15,832:finished processing per sample fasta files INFO(139731538536256)2025-04-23 12:43:15,832:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1a_3_L001_R1_001.fastq.gz finished INFO(132211547719488)2025-04-23 12:43:16,880:************************* INFO(132211547719488)2025-04-23 12:43:16,881:deblurring started WARNING(132211547719488)2025-04-23 12:43:16,881:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5s_49_L001_R1_001.fastq.gz WARNING(132211547719488)2025-04-23 12:43:16,881:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5s_49_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(132211547719488)2025-04-23 12:43:16,881:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(132211547719488)2025-04-23 12:43:16,881:deblur worker thread started INFO(132211547719488)2025-04-23 12:43:16,882:processing per sample fasta files INFO(132211547719488)2025-04-23 12:43:16,882:-------------------------------------------------------- INFO(132211547719488)2025-04-23 12:43:16,882:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5s_49_L001_R1_001.fastq.gz INFO(132211547719488)2025-04-23 12:43:39,719:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim INFO(132211547719488)2025-04-23 12:43:39,771:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim.derep INFO(132211547719488)2025-04-23 12:43:40,284:total sequences 2514, passing sequences 2514, failing sequences 0 INFO(132211547719488)2025-04-23 12:43:40,284:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124714412758848)2025-04-23 12:43:41,731:deblurring 4868 sequences INFO(132211547719488)2025-04-23 12:43:49,008:deblurring 2514 sequences INFO(124714412758848)2025-04-23 12:43:51,370:1548 unique sequences left following deblurring INFO(124714412758848)2025-04-23 12:43:51,379:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(124714412758848)2025-04-23 12:43:52,382:finished processing file INFO(124714412758848)2025-04-23 12:43:52,384:finished processing per sample fasta files INFO(124714412758848)2025-04-23 12:43:52,384:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5aa_31_L001_R1_001.fastq.gz finished INFO(132211547719488)2025-04-23 12:43:52,963:1144 unique sequences left following deblurring INFO(132211547719488)2025-04-23 12:43:52,969:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(125571737184064)2025-04-23 12:43:53,414:************************* INFO(125571737184064)2025-04-23 12:43:53,414:deblurring started WARNING(125571737184064)2025-04-23 12:43:53,414:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1cc_7_L001_R1_001.fastq.gz WARNING(125571737184064)2025-04-23 12:43:53,415:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1cc_7_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(125571737184064)2025-04-23 12:43:53,415:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(125571737184064)2025-04-23 12:43:53,415:deblur worker thread started INFO(125571737184064)2025-04-23 12:43:53,415:processing per sample fasta files INFO(125571737184064)2025-04-23 12:43:53,415:-------------------------------------------------------- INFO(125571737184064)2025-04-23 12:43:53,415:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1cc_7_L001_R1_001.fastq.gz INFO(132211547719488)2025-04-23 12:43:53,737:finished processing file INFO(132211547719488)2025-04-23 12:43:53,738:finished processing per sample fasta files INFO(132211547719488)2025-04-23 12:43:53,738:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5s_49_L001_R1_001.fastq.gz finished INFO(127943460681536)2025-04-23 12:43:54,660:************************* INFO(127943460681536)2025-04-23 12:43:54,660:deblurring started WARNING(127943460681536)2025-04-23 12:43:54,661:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1w_25_L001_R1_001.fastq.gz WARNING(127943460681536)2025-04-23 12:43:54,661:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1w_25_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127943460681536)2025-04-23 12:43:54,661:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127943460681536)2025-04-23 12:43:54,661:deblur worker thread started INFO(127943460681536)2025-04-23 12:43:54,661:processing per sample fasta files INFO(127943460681536)2025-04-23 12:43:54,661:-------------------------------------------------------- INFO(127943460681536)2025-04-23 12:43:54,661:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1w_25_L001_R1_001.fastq.gz INFO(133494825604928)2025-04-23 12:44:19,953:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim INFO(133494825604928)2025-04-23 12:44:20,112:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim.derep INFO(133494825604928)2025-04-23 12:44:20,740:total sequences 6572, passing sequences 6572, failing sequences 0 INFO(133494825604928)2025-04-23 12:44:20,741:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127943460681536)2025-04-23 12:44:27,276:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim INFO(127943460681536)2025-04-23 12:44:27,344:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim.derep INFO(127943460681536)2025-04-23 12:44:27,913:total sequences 2251, passing sequences 2251, failing sequences 0 INFO(127943460681536)2025-04-23 12:44:27,913:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127943460681536)2025-04-23 12:44:34,931:deblurring 2251 sequences INFO(127943460681536)2025-04-23 12:44:37,142:739 unique sequences left following deblurring INFO(127943460681536)2025-04-23 12:44:37,146:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(127943460681536)2025-04-23 12:44:37,546:finished processing file INFO(127943460681536)2025-04-23 12:44:37,547:finished processing per sample fasta files INFO(127943460681536)2025-04-23 12:44:37,547:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1w_25_L001_R1_001.fastq.gz finished INFO(136271490959168)2025-04-23 12:44:38,633:************************* INFO(136271490959168)2025-04-23 12:44:38,634:deblurring started WARNING(136271490959168)2025-04-23 12:44:38,634:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1b_4_L001_R1_001.fastq.gz WARNING(136271490959168)2025-04-23 12:44:38,634:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1b_4_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(136271490959168)2025-04-23 12:44:38,635:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(136271490959168)2025-04-23 12:44:38,635:deblur worker thread started INFO(136271490959168)2025-04-23 12:44:38,635:processing per sample fasta files INFO(136271490959168)2025-04-23 12:44:38,635:-------------------------------------------------------- INFO(136271490959168)2025-04-23 12:44:38,635:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1b_4_L001_R1_001.fastq.gz INFO(125571737184064)2025-04-23 12:44:52,865:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim INFO(125571737184064)2025-04-23 12:44:52,964:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim.derep INFO(125571737184064)2025-04-23 12:44:53,559:total sequences 3895, passing sequences 3895, failing sequences 0 INFO(125571737184064)2025-04-23 12:44:53,559:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(136271490959168)2025-04-23 12:45:05,240:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim INFO(136271490959168)2025-04-23 12:45:05,312:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim.derep INFO(136271490959168)2025-04-23 12:45:05,897:total sequences 2754, passing sequences 2754, failing sequences 0 INFO(136271490959168)2025-04-23 12:45:05,898:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(133494825604928)2025-04-23 12:45:07,287:deblurring 6572 sequences INFO(125571737184064)2025-04-23 12:45:11,679:deblurring 3895 sequences INFO(136271490959168)2025-04-23 12:45:15,909:deblurring 2754 sequences INFO(125571737184064)2025-04-23 12:45:18,866:1275 unique sequences left following deblurring INFO(125571737184064)2025-04-23 12:45:18,874:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(125571737184064)2025-04-23 12:45:19,765:finished processing file INFO(125571737184064)2025-04-23 12:45:19,767:finished processing per sample fasta files INFO(125571737184064)2025-04-23 12:45:19,767:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1cc_7_L001_R1_001.fastq.gz finished INFO(136271490959168)2025-04-23 12:45:20,664:1390 unique sequences left following deblurring INFO(136271490959168)2025-04-23 12:45:20,672:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(135437350307648)2025-04-23 12:45:20,794:************************* INFO(135437350307648)2025-04-23 12:45:20,795:deblurring started WARNING(135437350307648)2025-04-23 12:45:20,795:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5c_34_L001_R1_001.fastq.gz WARNING(135437350307648)2025-04-23 12:45:20,795:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5c_34_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(135437350307648)2025-04-23 12:45:20,795:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(135437350307648)2025-04-23 12:45:20,795:deblur worker thread started INFO(135437350307648)2025-04-23 12:45:20,795:processing per sample fasta files INFO(135437350307648)2025-04-23 12:45:20,795:-------------------------------------------------------- INFO(135437350307648)2025-04-23 12:45:20,795:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5c_34_L001_R1_001.fastq.gz INFO(136271490959168)2025-04-23 12:45:21,595:finished processing file INFO(136271490959168)2025-04-23 12:45:21,596:finished processing per sample fasta files INFO(136271490959168)2025-04-23 12:45:21,597:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1b_4_L001_R1_001.fastq.gz finished INFO(138844627203904)2025-04-23 12:45:22,574:************************* INFO(138844627203904)2025-04-23 12:45:22,574:deblurring started WARNING(138844627203904)2025-04-23 12:45:22,575:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5v_51_L001_R1_001.fastq.gz WARNING(138844627203904)2025-04-23 12:45:22,575:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5v_51_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138844627203904)2025-04-23 12:45:22,575:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138844627203904)2025-04-23 12:45:22,575:deblur worker thread started INFO(138844627203904)2025-04-23 12:45:22,575:processing per sample fasta files INFO(138844627203904)2025-04-23 12:45:22,575:-------------------------------------------------------- INFO(138844627203904)2025-04-23 12:45:22,575:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5v_51_L001_R1_001.fastq.gz INFO(133494825604928)2025-04-23 12:45:26,980:2169 unique sequences left following deblurring INFO(133494825604928)2025-04-23 12:45:26,995:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(133494825604928)2025-04-23 12:45:28,392:finished processing file INFO(133494825604928)2025-04-23 12:45:28,394:finished processing per sample fasta files INFO(133494825604928)2025-04-23 12:45:28,394:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5cc_35_L001_R1_001.fastq.gz finished INFO(138193249613632)2025-04-23 12:45:29,391:************************* INFO(138193249613632)2025-04-23 12:45:29,391:deblurring started WARNING(138193249613632)2025-04-23 12:45:29,392:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5w_52_L001_R1_001.fastq.gz WARNING(138193249613632)2025-04-23 12:45:29,392:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5w_52_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138193249613632)2025-04-23 12:45:29,392:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138193249613632)2025-04-23 12:45:29,392:deblur worker thread started INFO(138193249613632)2025-04-23 12:45:29,392:processing per sample fasta files INFO(138193249613632)2025-04-23 12:45:29,392:-------------------------------------------------------- INFO(138193249613632)2025-04-23 12:45:29,392:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5w_52_L001_R1_001.fastq.gz INFO(138193249613632)2025-04-23 12:45:29,398:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5w_52_L001_R1_001.fastq.gz.trim INFO(138193249613632)2025-04-23 12:45:29,402:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5w_52_L001_R1_001.fastq.gz.trim.derep WARNING(138193249613632)2025-04-23 12:45:29,402:file /tmp/tmpn2y_95_r/deblur_working_dir/Site5w_52_L001_R1_001.fastq.gz.trim.derep has size 0, continuing WARNING(138193249613632)2025-04-23 12:45:29,404:remove artifacts failed, aborting WARNING(138193249613632)2025-04-23 12:45:29,405:deblurring failed for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5w_52_L001_R1_001.fastq.gz INFO(138193249613632)2025-04-23 12:45:29,405:finished processing per sample fasta files INFO(138193249613632)2025-04-23 12:45:29,405:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5w_52_L001_R1_001.fastq.gz finished INFO(140703658182464)2025-04-23 12:45:30,446:************************* INFO(140703658182464)2025-04-23 12:45:30,446:deblurring started WARNING(140703658182464)2025-04-23 12:45:30,446:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5o_45_L001_R1_001.fastq.gz WARNING(140703658182464)2025-04-23 12:45:30,446:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5o_45_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(140703658182464)2025-04-23 12:45:30,447:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(140703658182464)2025-04-23 12:45:30,447:deblur worker thread started INFO(140703658182464)2025-04-23 12:45:30,447:processing per sample fasta files INFO(140703658182464)2025-04-23 12:45:30,447:-------------------------------------------------------- INFO(140703658182464)2025-04-23 12:45:30,447:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5o_45_L001_R1_001.fastq.gz INFO(135437350307648)2025-04-23 12:45:31,056:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim INFO(135437350307648)2025-04-23 12:45:31,086:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim.derep INFO(135437350307648)2025-04-23 12:45:31,539:total sequences 1003, passing sequences 1003, failing sequences 0 INFO(135437350307648)2025-04-23 12:45:31,540:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(135437350307648)2025-04-23 12:45:33,816:deblurring 1003 sequences INFO(135437350307648)2025-04-23 12:45:34,493:539 unique sequences left following deblurring INFO(135437350307648)2025-04-23 12:45:34,496:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(135437350307648)2025-04-23 12:45:34,753:finished processing file INFO(135437350307648)2025-04-23 12:45:34,754:finished processing per sample fasta files INFO(135437350307648)2025-04-23 12:45:34,754:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5c_34_L001_R1_001.fastq.gz finished INFO(131962863867712)2025-04-23 12:45:35,983:************************* INFO(131962863867712)2025-04-23 12:45:35,983:deblurring started WARNING(131962863867712)2025-04-23 12:45:35,984:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1z_27_L001_R1_001.fastq.gz WARNING(131962863867712)2025-04-23 12:45:35,984:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1z_27_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(131962863867712)2025-04-23 12:45:35,984:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(131962863867712)2025-04-23 12:45:35,984:deblur worker thread started INFO(131962863867712)2025-04-23 12:45:35,984:processing per sample fasta files INFO(131962863867712)2025-04-23 12:45:35,984:-------------------------------------------------------- INFO(131962863867712)2025-04-23 12:45:35,984:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1z_27_L001_R1_001.fastq.gz INFO(138844627203904)2025-04-23 12:45:36,370:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim INFO(138844627203904)2025-04-23 12:45:36,396:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim.derep INFO(138844627203904)2025-04-23 12:45:36,893:total sequences 795, passing sequences 795, failing sequences 0 INFO(138844627203904)2025-04-23 12:45:36,894:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(138844627203904)2025-04-23 12:45:38,603:deblurring 795 sequences INFO(138844627203904)2025-04-23 12:45:38,941:279 unique sequences left following deblurring INFO(138844627203904)2025-04-23 12:45:38,943:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(138844627203904)2025-04-23 12:45:39,069:finished processing file INFO(138844627203904)2025-04-23 12:45:39,069:finished processing per sample fasta files INFO(138844627203904)2025-04-23 12:45:39,069:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5v_51_L001_R1_001.fastq.gz finished INFO(125307874223936)2025-04-23 12:45:40,020:************************* INFO(125307874223936)2025-04-23 12:45:40,020:deblurring started WARNING(125307874223936)2025-04-23 12:45:40,021:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1d_8_L001_R1_001.fastq.gz WARNING(125307874223936)2025-04-23 12:45:40,021:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1d_8_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(125307874223936)2025-04-23 12:45:40,021:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(125307874223936)2025-04-23 12:45:40,021:deblur worker thread started INFO(125307874223936)2025-04-23 12:45:40,021:processing per sample fasta files INFO(125307874223936)2025-04-23 12:45:40,021:-------------------------------------------------------- INFO(125307874223936)2025-04-23 12:45:40,021:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1d_8_L001_R1_001.fastq.gz INFO(140703658182464)2025-04-23 12:45:48,433:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim INFO(140703658182464)2025-04-23 12:45:48,477:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim.derep INFO(140703658182464)2025-04-23 12:45:48,996:total sequences 1879, passing sequences 1879, failing sequences 0 INFO(140703658182464)2025-04-23 12:45:48,996:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(140703658182464)2025-04-23 12:45:54,057:deblurring 1879 sequences INFO(140703658182464)2025-04-23 12:45:55,527:587 unique sequences left following deblurring INFO(140703658182464)2025-04-23 12:45:55,530:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(140703658182464)2025-04-23 12:45:55,838:finished processing file INFO(140703658182464)2025-04-23 12:45:55,839:finished processing per sample fasta files INFO(140703658182464)2025-04-23 12:45:55,839:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5o_45_L001_R1_001.fastq.gz finished INFO(140657551767360)2025-04-23 12:45:56,846:************************* INFO(140657551767360)2025-04-23 12:45:56,846:deblurring started WARNING(140657551767360)2025-04-23 12:45:56,847:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1o_18_L001_R1_001.fastq.gz WARNING(140657551767360)2025-04-23 12:45:56,847:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1o_18_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(140657551767360)2025-04-23 12:45:56,847:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(140657551767360)2025-04-23 12:45:56,847:deblur worker thread started INFO(140657551767360)2025-04-23 12:45:56,847:processing per sample fasta files INFO(140657551767360)2025-04-23 12:45:56,847:-------------------------------------------------------- INFO(140657551767360)2025-04-23 12:45:56,847:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1o_18_L001_R1_001.fastq.gz INFO(131962863867712)2025-04-23 12:46:00,648:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim INFO(131962863867712)2025-04-23 12:46:00,681:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim.derep INFO(131962863867712)2025-04-23 12:46:01,164:total sequences 1188, passing sequences 1188, failing sequences 0 INFO(131962863867712)2025-04-23 12:46:01,164:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131962863867712)2025-04-23 12:46:03,904:deblurring 1188 sequences INFO(131962863867712)2025-04-23 12:46:04,744:510 unique sequences left following deblurring INFO(131962863867712)2025-04-23 12:46:04,747:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(130959938553664)2025-04-23 12:46:04,918:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim INFO(131962863867712)2025-04-23 12:46:05,014:finished processing file INFO(131962863867712)2025-04-23 12:46:05,015:finished processing per sample fasta files INFO(131962863867712)2025-04-23 12:46:05,015:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1z_27_L001_R1_001.fastq.gz finished INFO(130959938553664)2025-04-23 12:46:05,368:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim.derep INFO(134830892164928)2025-04-23 12:46:06,128:************************* INFO(134830892164928)2025-04-23 12:46:06,128:deblurring started WARNING(134830892164928)2025-04-23 12:46:06,128:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1s_22_L001_R1_001.fastq.gz WARNING(134830892164928)2025-04-23 12:46:06,128:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1s_22_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134830892164928)2025-04-23 12:46:06,129:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134830892164928)2025-04-23 12:46:06,129:deblur worker thread started INFO(134830892164928)2025-04-23 12:46:06,129:processing per sample fasta files INFO(134830892164928)2025-04-23 12:46:06,129:-------------------------------------------------------- INFO(134830892164928)2025-04-23 12:46:06,129:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1s_22_L001_R1_001.fastq.gz INFO(130959938553664)2025-04-23 12:46:06,314:total sequences 12605, passing sequences 12605, failing sequences 0 INFO(130959938553664)2025-04-23 12:46:06,314:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(125307874223936)2025-04-23 12:46:09,297:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim INFO(125307874223936)2025-04-23 12:46:09,375:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim.derep INFO(125307874223936)2025-04-23 12:46:10,020:total sequences 3079, passing sequences 3079, failing sequences 0 INFO(125307874223936)2025-04-23 12:46:10,020:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(125307874223936)2025-04-23 12:46:21,910:deblurring 3079 sequences INFO(125307874223936)2025-04-23 12:46:27,100:1355 unique sequences left following deblurring INFO(125307874223936)2025-04-23 12:46:27,107:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(125307874223936)2025-04-23 12:46:27,939:finished processing file INFO(125307874223936)2025-04-23 12:46:27,940:finished processing per sample fasta files INFO(125307874223936)2025-04-23 12:46:27,940:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1d_8_L001_R1_001.fastq.gz finished INFO(130637090600768)2025-04-23 12:46:28,990:************************* INFO(130637090600768)2025-04-23 12:46:28,991:deblurring started WARNING(130637090600768)2025-04-23 12:46:28,991:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5m_43_L001_R1_001.fastq.gz WARNING(130637090600768)2025-04-23 12:46:28,991:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5m_43_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(130637090600768)2025-04-23 12:46:28,991:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(130637090600768)2025-04-23 12:46:28,991:deblur worker thread started INFO(130637090600768)2025-04-23 12:46:28,991:processing per sample fasta files INFO(130637090600768)2025-04-23 12:46:28,992:-------------------------------------------------------- INFO(130637090600768)2025-04-23 12:46:28,992:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5m_43_L001_R1_001.fastq.gz INFO(140657551767360)2025-04-23 12:46:32,235:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim INFO(140657551767360)2025-04-23 12:46:32,323:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim.derep INFO(140657551767360)2025-04-23 12:46:32,874:total sequences 3633, passing sequences 3633, failing sequences 0 INFO(140657551767360)2025-04-23 12:46:32,874:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134830892164928)2025-04-23 12:46:40,562:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim INFO(134830892164928)2025-04-23 12:46:40,716:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim.derep INFO(134830892164928)2025-04-23 12:46:41,291:total sequences 3747, passing sequences 3747, failing sequences 0 INFO(134830892164928)2025-04-23 12:46:41,292:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(140657551767360)2025-04-23 12:46:49,031:deblurring 3633 sequences INFO(130637090600768)2025-04-23 12:46:49,565:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim INFO(130637090600768)2025-04-23 12:46:49,613:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim.derep INFO(130637090600768)2025-04-23 12:46:50,121:total sequences 2040, passing sequences 2040, failing sequences 0 INFO(130637090600768)2025-04-23 12:46:50,122:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(130637090600768)2025-04-23 12:46:56,429:deblurring 2040 sequences INFO(140657551767360)2025-04-23 12:46:58,117:1824 unique sequences left following deblurring INFO(140657551767360)2025-04-23 12:46:58,129:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(134830892164928)2025-04-23 12:46:58,719:deblurring 3747 sequences INFO(130637090600768)2025-04-23 12:46:59,278:1064 unique sequences left following deblurring INFO(130637090600768)2025-04-23 12:46:59,284:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(140657551767360)2025-04-23 12:46:59,287:finished processing file INFO(140657551767360)2025-04-23 12:46:59,288:finished processing per sample fasta files INFO(140657551767360)2025-04-23 12:46:59,288:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1o_18_L001_R1_001.fastq.gz finished INFO(130637090600768)2025-04-23 12:47:00,007:finished processing file INFO(130637090600768)2025-04-23 12:47:00,007:finished processing per sample fasta files INFO(130637090600768)2025-04-23 12:47:00,008:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5m_43_L001_R1_001.fastq.gz finished INFO(132679047595840)2025-04-23 12:47:00,429:************************* INFO(132679047595840)2025-04-23 12:47:00,429:deblurring started WARNING(132679047595840)2025-04-23 12:47:00,429:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5u_50_L001_R1_001.fastq.gz WARNING(132679047595840)2025-04-23 12:47:00,429:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5u_50_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(132679047595840)2025-04-23 12:47:00,429:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(132679047595840)2025-04-23 12:47:00,429:deblur worker thread started INFO(132679047595840)2025-04-23 12:47:00,429:processing per sample fasta files INFO(132679047595840)2025-04-23 12:47:00,430:-------------------------------------------------------- INFO(132679047595840)2025-04-23 12:47:00,430:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5u_50_L001_R1_001.fastq.gz INFO(139641576281920)2025-04-23 12:47:01,018:************************* INFO(139641576281920)2025-04-23 12:47:01,019:deblurring started WARNING(139641576281920)2025-04-23 12:47:01,019:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ff_39_L001_R1_001.fastq.gz WARNING(139641576281920)2025-04-23 12:47:01,019:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ff_39_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(139641576281920)2025-04-23 12:47:01,019:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(139641576281920)2025-04-23 12:47:01,019:deblur worker thread started INFO(139641576281920)2025-04-23 12:47:01,020:processing per sample fasta files INFO(139641576281920)2025-04-23 12:47:01,020:-------------------------------------------------------- INFO(139641576281920)2025-04-23 12:47:01,020:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ff_39_L001_R1_001.fastq.gz INFO(134830892164928)2025-04-23 12:47:06,601:1509 unique sequences left following deblurring INFO(134830892164928)2025-04-23 12:47:06,611:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(134830892164928)2025-04-23 12:47:07,544:finished processing file INFO(134830892164928)2025-04-23 12:47:07,545:finished processing per sample fasta files INFO(134830892164928)2025-04-23 12:47:07,545:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1s_22_L001_R1_001.fastq.gz finished INFO(133041317197632)2025-04-23 12:47:08,597:************************* INFO(133041317197632)2025-04-23 12:47:08,598:deblurring started WARNING(133041317197632)2025-04-23 12:47:08,598:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5f_38_L001_R1_001.fastq.gz WARNING(133041317197632)2025-04-23 12:47:08,598:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5f_38_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133041317197632)2025-04-23 12:47:08,598:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133041317197632)2025-04-23 12:47:08,598:deblur worker thread started INFO(133041317197632)2025-04-23 12:47:08,598:processing per sample fasta files INFO(133041317197632)2025-04-23 12:47:08,599:-------------------------------------------------------- INFO(133041317197632)2025-04-23 12:47:08,599:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5f_38_L001_R1_001.fastq.gz INFO(133041317197632)2025-04-23 12:47:10,155:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim INFO(133041317197632)2025-04-23 12:47:10,176:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim.derep INFO(133041317197632)2025-04-23 12:47:10,625:total sequences 117, passing sequences 117, failing sequences 0 INFO(133041317197632)2025-04-23 12:47:10,625:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(133041317197632)2025-04-23 12:47:15,307:deblurring 117 sequences INFO(133041317197632)2025-04-23 12:47:15,343:96 unique sequences left following deblurring INFO(133041317197632)2025-04-23 12:47:15,344:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(133041317197632)2025-04-23 12:47:15,412:finished processing file INFO(133041317197632)2025-04-23 12:47:15,413:finished processing per sample fasta files INFO(133041317197632)2025-04-23 12:47:15,413:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5f_38_L001_R1_001.fastq.gz finished INFO(132679047595840)2025-04-23 12:47:15,536:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim INFO(132679047595840)2025-04-23 12:47:15,573:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim.derep INFO(132679047595840)2025-04-23 12:47:16,061:total sequences 1508, passing sequences 1508, failing sequences 0 INFO(132679047595840)2025-04-23 12:47:16,061:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(129809946453824)2025-04-23 12:47:16,391:************************* INFO(129809946453824)2025-04-23 12:47:16,391:deblurring started WARNING(129809946453824)2025-04-23 12:47:16,392:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1J_0_L001_R1_001.fastq.gz WARNING(129809946453824)2025-04-23 12:47:16,392:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1J_0_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129809946453824)2025-04-23 12:47:16,392:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129809946453824)2025-04-23 12:47:16,392:deblur worker thread started INFO(129809946453824)2025-04-23 12:47:16,392:processing per sample fasta files INFO(129809946453824)2025-04-23 12:47:16,392:-------------------------------------------------------- INFO(129809946453824)2025-04-23 12:47:16,392:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1J_0_L001_R1_001.fastq.gz INFO(129809946453824)2025-04-23 12:47:17,778:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim INFO(129809946453824)2025-04-23 12:47:17,794:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim.derep INFO(129809946453824)2025-04-23 12:47:18,216:total sequences 260, passing sequences 260, failing sequences 0 INFO(129809946453824)2025-04-23 12:47:18,216:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(132679047595840)2025-04-23 12:47:20,000:deblurring 1508 sequences INFO(129809946453824)2025-04-23 12:47:21,251:deblurring 260 sequences INFO(132679047595840)2025-04-23 12:47:21,280:690 unique sequences left following deblurring INFO(132679047595840)2025-04-23 12:47:21,283:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(129809946453824)2025-04-23 12:47:21,314:183 unique sequences left following deblurring INFO(129809946453824)2025-04-23 12:47:21,315:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(129809946453824)2025-04-23 12:47:21,396:finished processing file INFO(129809946453824)2025-04-23 12:47:21,397:finished processing per sample fasta files INFO(129809946453824)2025-04-23 12:47:21,397:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1J_0_L001_R1_001.fastq.gz finished INFO(132679047595840)2025-04-23 12:47:21,692:finished processing file INFO(132679047595840)2025-04-23 12:47:21,692:finished processing per sample fasta files INFO(132679047595840)2025-04-23 12:47:21,692:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5u_50_L001_R1_001.fastq.gz finished INFO(128623372994368)2025-04-23 12:47:22,488:************************* INFO(128623372994368)2025-04-23 12:47:22,488:deblurring started WARNING(128623372994368)2025-04-23 12:47:22,489:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1h_14_L001_R1_001.fastq.gz WARNING(128623372994368)2025-04-23 12:47:22,489:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1h_14_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(128623372994368)2025-04-23 12:47:22,489:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(128623372994368)2025-04-23 12:47:22,489:deblur worker thread started INFO(128623372994368)2025-04-23 12:47:22,490:processing per sample fasta files INFO(128623372994368)2025-04-23 12:47:22,490:-------------------------------------------------------- INFO(128623372994368)2025-04-23 12:47:22,490:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1h_14_L001_R1_001.fastq.gz INFO(130330300233536)2025-04-23 12:47:22,762:************************* INFO(130330300233536)2025-04-23 12:47:22,762:deblurring started WARNING(130330300233536)2025-04-23 12:47:22,763:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5q_47_L001_R1_001.fastq.gz WARNING(130330300233536)2025-04-23 12:47:22,763:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5q_47_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(130330300233536)2025-04-23 12:47:22,763:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(130330300233536)2025-04-23 12:47:22,763:deblur worker thread started INFO(130330300233536)2025-04-23 12:47:22,763:processing per sample fasta files INFO(130330300233536)2025-04-23 12:47:22,763:-------------------------------------------------------- INFO(130330300233536)2025-04-23 12:47:22,763:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5q_47_L001_R1_001.fastq.gz INFO(128623372994368)2025-04-23 12:47:34,613:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim INFO(128623372994368)2025-04-23 12:47:34,630:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim.derep INFO(128623372994368)2025-04-23 12:47:35,082:total sequences 614, passing sequences 614, failing sequences 0 INFO(128623372994368)2025-04-23 12:47:35,082:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(128623372994368)2025-04-23 12:47:36,435:deblurring 614 sequences INFO(128623372994368)2025-04-23 12:47:36,728:346 unique sequences left following deblurring INFO(128623372994368)2025-04-23 12:47:36,730:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(128623372994368)2025-04-23 12:47:36,888:finished processing file INFO(128623372994368)2025-04-23 12:47:36,888:finished processing per sample fasta files INFO(128623372994368)2025-04-23 12:47:36,889:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1h_14_L001_R1_001.fastq.gz finished INFO(134575025346368)2025-04-23 12:47:37,968:************************* INFO(134575025346368)2025-04-23 12:47:37,968:deblurring started WARNING(134575025346368)2025-04-23 12:47:37,969:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1L_1_L001_R1_001.fastq.gz WARNING(134575025346368)2025-04-23 12:47:37,969:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1L_1_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134575025346368)2025-04-23 12:47:37,969:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134575025346368)2025-04-23 12:47:37,969:deblur worker thread started INFO(134575025346368)2025-04-23 12:47:37,970:processing per sample fasta files INFO(134575025346368)2025-04-23 12:47:37,970:-------------------------------------------------------- INFO(134575025346368)2025-04-23 12:47:37,970:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1L_1_L001_R1_001.fastq.gz INFO(134575025346368)2025-04-23 12:47:46,013:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim INFO(134575025346368)2025-04-23 12:47:46,033:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim.derep INFO(134575025346368)2025-04-23 12:47:46,489:total sequences 672, passing sequences 672, failing sequences 0 INFO(134575025346368)2025-04-23 12:47:46,489:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134575025346368)2025-04-23 12:47:48,010:deblurring 672 sequences INFO(130330300233536)2025-04-23 12:47:48,279:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim INFO(134575025346368)2025-04-23 12:47:48,397:394 unique sequences left following deblurring INFO(134575025346368)2025-04-23 12:47:48,399:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(130330300233536)2025-04-23 12:47:48,500:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim.derep INFO(134575025346368)2025-04-23 12:47:48,594:finished processing file INFO(134575025346368)2025-04-23 12:47:48,595:finished processing per sample fasta files INFO(134575025346368)2025-04-23 12:47:48,595:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1L_1_L001_R1_001.fastq.gz finished INFO(130330300233536)2025-04-23 12:47:49,200:total sequences 6112, passing sequences 6112, failing sequences 0 INFO(130330300233536)2025-04-23 12:47:49,201:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(138569271007040)2025-04-23 12:47:49,632:************************* INFO(138569271007040)2025-04-23 12:47:49,632:deblurring started WARNING(138569271007040)2025-04-23 12:47:49,632:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5k_42_L001_R1_001.fastq.gz WARNING(138569271007040)2025-04-23 12:47:49,632:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5k_42_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138569271007040)2025-04-23 12:47:49,633:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138569271007040)2025-04-23 12:47:49,633:deblur worker thread started INFO(138569271007040)2025-04-23 12:47:49,633:processing per sample fasta files INFO(138569271007040)2025-04-23 12:47:49,633:-------------------------------------------------------- INFO(138569271007040)2025-04-23 12:47:49,633:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5k_42_L001_R1_001.fastq.gz INFO(138569271007040)2025-04-23 12:47:59,736:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim INFO(138569271007040)2025-04-23 12:47:59,766:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim.derep INFO(138569271007040)2025-04-23 12:48:00,294:total sequences 1074, passing sequences 1074, failing sequences 0 INFO(138569271007040)2025-04-23 12:48:00,294:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(138569271007040)2025-04-23 12:48:03,118:deblurring 1074 sequences INFO(138569271007040)2025-04-23 12:48:03,944:587 unique sequences left following deblurring INFO(138569271007040)2025-04-23 12:48:03,948:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(138569271007040)2025-04-23 12:48:04,299:finished processing file INFO(138569271007040)2025-04-23 12:48:04,300:finished processing per sample fasta files INFO(138569271007040)2025-04-23 12:48:04,300:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5k_42_L001_R1_001.fastq.gz finished INFO(129089263048512)2025-04-23 12:48:05,427:************************* INFO(129089263048512)2025-04-23 12:48:05,427:deblurring started WARNING(129089263048512)2025-04-23 12:48:05,427:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1dd_9_L001_R1_001.fastq.gz WARNING(129089263048512)2025-04-23 12:48:05,428:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1dd_9_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129089263048512)2025-04-23 12:48:05,428:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129089263048512)2025-04-23 12:48:05,428:deblur worker thread started INFO(129089263048512)2025-04-23 12:48:05,428:processing per sample fasta files INFO(129089263048512)2025-04-23 12:48:05,428:-------------------------------------------------------- INFO(129089263048512)2025-04-23 12:48:05,428:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1dd_9_L001_R1_001.fastq.gz INFO(139641576281920)2025-04-23 12:48:09,947:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim INFO(139641576281920)2025-04-23 12:48:10,179:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim.derep INFO(139641576281920)2025-04-23 12:48:10,926:total sequences 8107, passing sequences 8107, failing sequences 0 INFO(139641576281920)2025-04-23 12:48:10,926:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(130330300233536)2025-04-23 12:48:32,597:deblurring 6112 sequences INFO(129089263048512)2025-04-23 12:49:00,225:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim INFO(129089263048512)2025-04-23 12:49:00,348:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim.derep INFO(130959938553664)2025-04-23 12:49:00,415:deblurring 12605 sequences INFO(129089263048512)2025-04-23 12:49:01,032:total sequences 4249, passing sequences 4249, failing sequences 0 INFO(129089263048512)2025-04-23 12:49:01,032:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(130330300233536)2025-04-23 12:49:06,128:3595 unique sequences left following deblurring INFO(130330300233536)2025-04-23 12:49:06,160:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(130330300233536)2025-04-23 12:49:08,611:finished processing file INFO(130330300233536)2025-04-23 12:49:08,613:finished processing per sample fasta files INFO(130330300233536)2025-04-23 12:49:08,614:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5q_47_L001_R1_001.fastq.gz finished INFO(130355734329152)2025-04-23 12:49:09,779:************************* INFO(130355734329152)2025-04-23 12:49:09,780:deblurring started WARNING(130355734329152)2025-04-23 12:49:09,780:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5h_41_L001_R1_001.fastq.gz WARNING(130355734329152)2025-04-23 12:49:09,781:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5h_41_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(130355734329152)2025-04-23 12:49:09,781:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(130355734329152)2025-04-23 12:49:09,781:deblur worker thread started INFO(130355734329152)2025-04-23 12:49:09,781:processing per sample fasta files INFO(130355734329152)2025-04-23 12:49:09,781:-------------------------------------------------------- INFO(130355734329152)2025-04-23 12:49:09,781:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5h_41_L001_R1_001.fastq.gz INFO(129089263048512)2025-04-23 12:49:22,766:deblurring 4249 sequences INFO(139641576281920)2025-04-23 12:49:22,871:deblurring 8107 sequences INFO(129089263048512)2025-04-23 12:49:30,296:1455 unique sequences left following deblurring INFO(129089263048512)2025-04-23 12:49:30,305:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(129089263048512)2025-04-23 12:49:31,218:finished processing file INFO(129089263048512)2025-04-23 12:49:31,219:finished processing per sample fasta files INFO(129089263048512)2025-04-23 12:49:31,219:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1dd_9_L001_R1_001.fastq.gz finished INFO(124134543492928)2025-04-23 12:49:32,294:************************* INFO(124134543492928)2025-04-23 12:49:32,295:deblurring started WARNING(124134543492928)2025-04-23 12:49:32,295:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1y_26_L001_R1_001.fastq.gz WARNING(124134543492928)2025-04-23 12:49:32,296:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1y_26_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124134543492928)2025-04-23 12:49:32,296:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124134543492928)2025-04-23 12:49:32,296:deblur worker thread started INFO(124134543492928)2025-04-23 12:49:32,296:processing per sample fasta files INFO(124134543492928)2025-04-23 12:49:32,296:-------------------------------------------------------- INFO(124134543492928)2025-04-23 12:49:32,296:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1y_26_L001_R1_001.fastq.gz INFO(130959938553664)2025-04-23 12:49:51,746:2480 unique sequences left following deblurring INFO(130959938553664)2025-04-23 12:49:51,774:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(139641576281920)2025-04-23 12:49:52,563:2615 unique sequences left following deblurring INFO(139641576281920)2025-04-23 12:49:52,581:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(130959938553664)2025-04-23 12:49:53,442:finished processing file INFO(130959938553664)2025-04-23 12:49:53,445:finished processing per sample fasta files INFO(130959938553664)2025-04-23 12:49:53,445:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1p_19_L001_R1_001.fastq.gz finished INFO(139641576281920)2025-04-23 12:49:54,428:finished processing file INFO(139641576281920)2025-04-23 12:49:54,430:finished processing per sample fasta files INFO(139641576281920)2025-04-23 12:49:54,431:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ff_39_L001_R1_001.fastq.gz finished INFO(133995751946048)2025-04-23 12:49:54,518:************************* INFO(133995751946048)2025-04-23 12:49:54,518:deblurring started WARNING(133995751946048)2025-04-23 12:49:54,518:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5J_28_L001_R1_001.fastq.gz WARNING(133995751946048)2025-04-23 12:49:54,518:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5J_28_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133995751946048)2025-04-23 12:49:54,518:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133995751946048)2025-04-23 12:49:54,519:deblur worker thread started INFO(133995751946048)2025-04-23 12:49:54,519:processing per sample fasta files INFO(133995751946048)2025-04-23 12:49:54,519:-------------------------------------------------------- INFO(133995751946048)2025-04-23 12:49:54,519:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5J_28_L001_R1_001.fastq.gz INFO(133995751946048)2025-04-23 12:49:54,533:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5J_28_L001_R1_001.fastq.gz.trim INFO(133995751946048)2025-04-23 12:49:54,538:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5J_28_L001_R1_001.fastq.gz.trim.derep WARNING(133995751946048)2025-04-23 12:49:54,538:file /tmp/tmpn2y_95_r/deblur_working_dir/Site5J_28_L001_R1_001.fastq.gz.trim.derep has size 0, continuing WARNING(133995751946048)2025-04-23 12:49:54,539:remove artifacts failed, aborting WARNING(133995751946048)2025-04-23 12:49:54,539:deblurring failed for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5J_28_L001_R1_001.fastq.gz INFO(133995751946048)2025-04-23 12:49:54,539:finished processing per sample fasta files INFO(133995751946048)2025-04-23 12:49:54,539:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5J_28_L001_R1_001.fastq.gz finished INFO(133998249580352)2025-04-23 12:49:55,510:************************* INFO(133998249580352)2025-04-23 12:49:55,510:deblurring started WARNING(133998249580352)2025-04-23 12:49:55,511:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1q_20_L001_R1_001.fastq.gz WARNING(133998249580352)2025-04-23 12:49:55,511:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1q_20_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133998249580352)2025-04-23 12:49:55,511:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133998249580352)2025-04-23 12:49:55,511:deblur worker thread started INFO(133998249580352)2025-04-23 12:49:55,511:processing per sample fasta files INFO(133998249580352)2025-04-23 12:49:55,511:-------------------------------------------------------- INFO(133998249580352)2025-04-23 12:49:55,511:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1q_20_L001_R1_001.fastq.gz INFO(138238936897344)2025-04-23 12:49:55,616:************************* INFO(138238936897344)2025-04-23 12:49:55,616:deblurring started WARNING(138238936897344)2025-04-23 12:49:55,617:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5L_29_L001_R1_001.fastq.gz WARNING(138238936897344)2025-04-23 12:49:55,617:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5L_29_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138238936897344)2025-04-23 12:49:55,617:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138238936897344)2025-04-23 12:49:55,617:deblur worker thread started INFO(138238936897344)2025-04-23 12:49:55,617:processing per sample fasta files INFO(138238936897344)2025-04-23 12:49:55,617:-------------------------------------------------------- INFO(138238936897344)2025-04-23 12:49:55,618:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5L_29_L001_R1_001.fastq.gz INFO(124134543492928)2025-04-23 12:49:58,642:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim INFO(124134543492928)2025-04-23 12:49:58,717:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim.derep INFO(124134543492928)2025-04-23 12:49:59,285:total sequences 2910, passing sequences 2910, failing sequences 0 INFO(124134543492928)2025-04-23 12:49:59,285:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124134543492928)2025-04-23 12:50:09,809:deblurring 2910 sequences WARNING(130355734329152)2025-04-23 12:50:12,872:Vast majority of sequences (351130 / 351451) are shorter than the trim length (230). Are you using the correct -t trim length? INFO(130355734329152)2025-04-23 12:50:12,873:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim INFO(130355734329152)2025-04-23 12:50:12,879:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim.derep INFO(124134543492928)2025-04-23 12:50:13,305:974 unique sequences left following deblurring INFO(124134543492928)2025-04-23 12:50:13,311:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(130355734329152)2025-04-23 12:50:13,432:total sequences 22, passing sequences 22, failing sequences 0 INFO(130355734329152)2025-04-23 12:50:13,432:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124134543492928)2025-04-23 12:50:13,875:finished processing file INFO(124134543492928)2025-04-23 12:50:13,875:finished processing per sample fasta files INFO(124134543492928)2025-04-23 12:50:13,875:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1y_26_L001_R1_001.fastq.gz finished INFO(130355734329152)2025-04-23 12:50:13,925:deblurring 22 sequences INFO(130355734329152)2025-04-23 12:50:13,927:22 unique sequences left following deblurring INFO(130355734329152)2025-04-23 12:50:13,927:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(130355734329152)2025-04-23 12:50:13,939:finished processing file INFO(130355734329152)2025-04-23 12:50:13,940:finished processing per sample fasta files INFO(130355734329152)2025-04-23 12:50:13,940:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5h_41_L001_R1_001.fastq.gz finished INFO(132722703824704)2025-04-23 12:50:14,929:************************* INFO(132722703824704)2025-04-23 12:50:14,929:deblurring started WARNING(132722703824704)2025-04-23 12:50:14,930:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5e_36_L001_R1_001.fastq.gz WARNING(132722703824704)2025-04-23 12:50:14,930:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5e_36_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(132722703824704)2025-04-23 12:50:14,930:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(132722703824704)2025-04-23 12:50:14,930:deblur worker thread started INFO(132722703824704)2025-04-23 12:50:14,930:processing per sample fasta files INFO(132722703824704)2025-04-23 12:50:14,930:-------------------------------------------------------- INFO(132722703824704)2025-04-23 12:50:14,930:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5e_36_L001_R1_001.fastq.gz INFO(123616195950400)2025-04-23 12:50:15,102:************************* INFO(123616195950400)2025-04-23 12:50:15,102:deblurring started WARNING(123616195950400)2025-04-23 12:50:15,102:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1g_13_L001_R1_001.fastq.gz WARNING(123616195950400)2025-04-23 12:50:15,102:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1g_13_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123616195950400)2025-04-23 12:50:15,103:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123616195950400)2025-04-23 12:50:15,103:deblur worker thread started INFO(123616195950400)2025-04-23 12:50:15,103:processing per sample fasta files INFO(123616195950400)2025-04-23 12:50:15,103:-------------------------------------------------------- INFO(123616195950400)2025-04-23 12:50:15,103:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1g_13_L001_R1_001.fastq.gz INFO(133998249580352)2025-04-23 12:50:20,562:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim INFO(133998249580352)2025-04-23 12:50:20,572:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim.derep INFO(133998249580352)2025-04-23 12:50:21,002:total sequences 269, passing sequences 269, failing sequences 0 INFO(133998249580352)2025-04-23 12:50:21,002:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(133998249580352)2025-04-23 12:50:24,350:deblurring 269 sequences INFO(133998249580352)2025-04-23 12:50:24,425:213 unique sequences left following deblurring INFO(133998249580352)2025-04-23 12:50:24,429:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(133998249580352)2025-04-23 12:50:24,514:finished processing file INFO(133998249580352)2025-04-23 12:50:24,514:finished processing per sample fasta files INFO(133998249580352)2025-04-23 12:50:24,514:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1q_20_L001_R1_001.fastq.gz finished INFO(129641197569856)2025-04-23 12:50:25,539:************************* INFO(129641197569856)2025-04-23 12:50:25,539:deblurring started WARNING(129641197569856)2025-04-23 12:50:25,539:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5b_32_L001_R1_001.fastq.gz WARNING(129641197569856)2025-04-23 12:50:25,539:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5b_32_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129641197569856)2025-04-23 12:50:25,540:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129641197569856)2025-04-23 12:50:25,540:deblur worker thread started INFO(129641197569856)2025-04-23 12:50:25,540:processing per sample fasta files INFO(129641197569856)2025-04-23 12:50:25,540:-------------------------------------------------------- INFO(129641197569856)2025-04-23 12:50:25,540:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5b_32_L001_R1_001.fastq.gz INFO(138238936897344)2025-04-23 12:50:26,934:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim INFO(138238936897344)2025-04-23 12:50:27,036:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim.derep INFO(138238936897344)2025-04-23 12:50:27,614:total sequences 3552, passing sequences 3552, failing sequences 0 INFO(138238936897344)2025-04-23 12:50:27,614:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(138238936897344)2025-04-23 12:50:42,882:deblurring 3552 sequences INFO(123616195950400)2025-04-23 12:50:49,713:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim INFO(123616195950400)2025-04-23 12:50:49,781:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim.derep INFO(123616195950400)2025-04-23 12:50:50,302:total sequences 2255, passing sequences 2255, failing sequences 0 INFO(123616195950400)2025-04-23 12:50:50,302:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(138238936897344)2025-04-23 12:50:50,653:1817 unique sequences left following deblurring INFO(138238936897344)2025-04-23 12:50:50,663:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(138238936897344)2025-04-23 12:50:51,855:finished processing file INFO(138238936897344)2025-04-23 12:50:51,856:finished processing per sample fasta files INFO(138238936897344)2025-04-23 12:50:51,856:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5L_29_L001_R1_001.fastq.gz finished INFO(129732748388160)2025-04-23 12:50:53,003:************************* INFO(129732748388160)2025-04-23 12:50:53,003:deblurring started WARNING(129732748388160)2025-04-23 12:50:53,004:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5bb_33_L001_R1_001.fastq.gz WARNING(129732748388160)2025-04-23 12:50:53,004:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5bb_33_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129732748388160)2025-04-23 12:50:53,004:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129732748388160)2025-04-23 12:50:53,004:deblur worker thread started INFO(129732748388160)2025-04-23 12:50:53,004:processing per sample fasta files INFO(129732748388160)2025-04-23 12:50:53,004:-------------------------------------------------------- INFO(129732748388160)2025-04-23 12:50:53,004:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5bb_33_L001_R1_001.fastq.gz INFO(123616195950400)2025-04-23 12:50:57,604:deblurring 2255 sequences INFO(129641197569856)2025-04-23 12:50:58,417:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim INFO(129641197569856)2025-04-23 12:50:58,470:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim.derep INFO(129641197569856)2025-04-23 12:50:58,994:total sequences 2297, passing sequences 2297, failing sequences 0 INFO(129641197569856)2025-04-23 12:50:58,995:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123616195950400)2025-04-23 12:51:00,165:775 unique sequences left following deblurring INFO(123616195950400)2025-04-23 12:51:00,170:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(123616195950400)2025-04-23 12:51:00,592:finished processing file INFO(123616195950400)2025-04-23 12:51:00,593:finished processing per sample fasta files INFO(123616195950400)2025-04-23 12:51:00,593:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1g_13_L001_R1_001.fastq.gz finished INFO(137326360614720)2025-04-23 12:51:01,677:************************* INFO(137326360614720)2025-04-23 12:51:01,677:deblurring started WARNING(137326360614720)2025-04-23 12:51:01,678:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1k_15_L001_R1_001.fastq.gz WARNING(137326360614720)2025-04-23 12:51:01,678:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1k_15_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(137326360614720)2025-04-23 12:51:01,678:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(137326360614720)2025-04-23 12:51:01,678:deblur worker thread started INFO(137326360614720)2025-04-23 12:51:01,678:processing per sample fasta files INFO(137326360614720)2025-04-23 12:51:01,678:-------------------------------------------------------- INFO(137326360614720)2025-04-23 12:51:01,678:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1k_15_L001_R1_001.fastq.gz INFO(129641197569856)2025-04-23 12:51:05,988:deblurring 2297 sequences INFO(129641197569856)2025-04-23 12:51:07,844:667 unique sequences left following deblurring INFO(129641197569856)2025-04-23 12:51:07,849:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(129641197569856)2025-04-23 12:51:08,220:finished processing file INFO(129641197569856)2025-04-23 12:51:08,221:finished processing per sample fasta files INFO(129641197569856)2025-04-23 12:51:08,221:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5b_32_L001_R1_001.fastq.gz finished INFO(130528103929664)2025-04-23 12:51:09,187:************************* INFO(130528103929664)2025-04-23 12:51:09,187:deblurring started WARNING(130528103929664)2025-04-23 12:51:09,188:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1U_2_L001_R1_001.fastq.gz WARNING(130528103929664)2025-04-23 12:51:09,188:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1U_2_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(130528103929664)2025-04-23 12:51:09,188:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(130528103929664)2025-04-23 12:51:09,188:deblur worker thread started INFO(130528103929664)2025-04-23 12:51:09,188:processing per sample fasta files INFO(130528103929664)2025-04-23 12:51:09,188:-------------------------------------------------------- INFO(130528103929664)2025-04-23 12:51:09,189:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1U_2_L001_R1_001.fastq.gz INFO(132722703824704)2025-04-23 12:51:12,172:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim INFO(132722703824704)2025-04-23 12:51:12,188:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim.derep INFO(132722703824704)2025-04-23 12:51:12,640:total sequences 518, passing sequences 518, failing sequences 0 INFO(132722703824704)2025-04-23 12:51:12,640:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(132722703824704)2025-04-23 12:51:13,831:deblurring 518 sequences INFO(132722703824704)2025-04-23 12:51:14,078:367 unique sequences left following deblurring INFO(132722703824704)2025-04-23 12:51:14,080:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(132722703824704)2025-04-23 12:51:14,254:finished processing file INFO(132722703824704)2025-04-23 12:51:14,254:finished processing per sample fasta files INFO(132722703824704)2025-04-23 12:51:14,254:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5e_36_L001_R1_001.fastq.gz finished INFO(125160274544448)2025-04-23 12:51:15,278:************************* INFO(125160274544448)2025-04-23 12:51:15,278:deblurring started WARNING(125160274544448)2025-04-23 12:51:15,279:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5a_30_L001_R1_001.fastq.gz WARNING(125160274544448)2025-04-23 12:51:15,279:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5a_30_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(125160274544448)2025-04-23 12:51:15,279:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(125160274544448)2025-04-23 12:51:15,279:deblur worker thread started INFO(125160274544448)2025-04-23 12:51:15,279:processing per sample fasta files INFO(125160274544448)2025-04-23 12:51:15,279:-------------------------------------------------------- INFO(125160274544448)2025-04-23 12:51:15,279:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5a_30_L001_R1_001.fastq.gz INFO(130528103929664)2025-04-23 12:51:16,424:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim INFO(130528103929664)2025-04-23 12:51:16,465:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim.derep INFO(130528103929664)2025-04-23 12:51:16,987:total sequences 1415, passing sequences 1415, failing sequences 0 INFO(130528103929664)2025-04-23 12:51:16,987:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(130528103929664)2025-04-23 12:51:20,812:deblurring 1415 sequences INFO(137326360614720)2025-04-23 12:51:20,915:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim INFO(137326360614720)2025-04-23 12:51:20,981:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim.derep INFO(137326360614720)2025-04-23 12:51:21,482:total sequences 2390, passing sequences 2390, failing sequences 0 INFO(137326360614720)2025-04-23 12:51:21,482:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(130528103929664)2025-04-23 12:51:22,360:882 unique sequences left following deblurring INFO(130528103929664)2025-04-23 12:51:22,375:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(130528103929664)2025-04-23 12:51:22,835:finished processing file INFO(130528103929664)2025-04-23 12:51:22,836:finished processing per sample fasta files INFO(130528103929664)2025-04-23 12:51:22,836:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1U_2_L001_R1_001.fastq.gz finished INFO(128831277635392)2025-04-23 12:51:23,833:************************* INFO(128831277635392)2025-04-23 12:51:23,833:deblurring started WARNING(128831277635392)2025-04-23 12:51:23,834:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1n_17_L001_R1_001.fastq.gz WARNING(128831277635392)2025-04-23 12:51:23,834:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1n_17_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(128831277635392)2025-04-23 12:51:23,834:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(128831277635392)2025-04-23 12:51:23,834:deblur worker thread started INFO(128831277635392)2025-04-23 12:51:23,834:processing per sample fasta files INFO(128831277635392)2025-04-23 12:51:23,835:-------------------------------------------------------- INFO(128831277635392)2025-04-23 12:51:23,835:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1n_17_L001_R1_001.fastq.gz INFO(137326360614720)2025-04-23 12:51:28,960:deblurring 2390 sequences INFO(137326360614720)2025-04-23 12:51:31,411:836 unique sequences left following deblurring INFO(137326360614720)2025-04-23 12:51:31,416:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(137326360614720)2025-04-23 12:51:31,892:finished processing file INFO(137326360614720)2025-04-23 12:51:31,893:finished processing per sample fasta files INFO(137326360614720)2025-04-23 12:51:31,893:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1k_15_L001_R1_001.fastq.gz finished INFO(133411829327680)2025-04-23 12:51:33,018:************************* INFO(133411829327680)2025-04-23 12:51:33,018:deblurring started WARNING(133411829327680)2025-04-23 12:51:33,018:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5z_53_L001_R1_001.fastq.gz WARNING(133411829327680)2025-04-23 12:51:33,019:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5z_53_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133411829327680)2025-04-23 12:51:33,019:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133411829327680)2025-04-23 12:51:33,019:deblur worker thread started INFO(133411829327680)2025-04-23 12:51:33,019:processing per sample fasta files INFO(133411829327680)2025-04-23 12:51:33,019:-------------------------------------------------------- INFO(133411829327680)2025-04-23 12:51:33,019:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5z_53_L001_R1_001.fastq.gz INFO(125160274544448)2025-04-23 12:51:42,071:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim INFO(125160274544448)2025-04-23 12:51:42,090:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim.derep INFO(125160274544448)2025-04-23 12:51:42,534:total sequences 641, passing sequences 641, failing sequences 0 INFO(125160274544448)2025-04-23 12:51:42,534:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(125160274544448)2025-04-23 12:51:43,849:deblurring 641 sequences INFO(125160274544448)2025-04-23 12:51:44,075:266 unique sequences left following deblurring INFO(125160274544448)2025-04-23 12:51:44,077:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(125160274544448)2025-04-23 12:51:44,200:finished processing file INFO(125160274544448)2025-04-23 12:51:44,201:finished processing per sample fasta files INFO(125160274544448)2025-04-23 12:51:44,201:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5a_30_L001_R1_001.fastq.gz finished INFO(123703453673280)2025-04-23 12:51:45,206:************************* INFO(123703453673280)2025-04-23 12:51:45,206:deblurring started WARNING(123703453673280)2025-04-23 12:51:45,206:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1t_23_L001_R1_001.fastq.gz WARNING(123703453673280)2025-04-23 12:51:45,207:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1t_23_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123703453673280)2025-04-23 12:51:45,207:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123703453673280)2025-04-23 12:51:45,207:deblur worker thread started INFO(123703453673280)2025-04-23 12:51:45,207:processing per sample fasta files INFO(123703453673280)2025-04-23 12:51:45,207:-------------------------------------------------------- INFO(123703453673280)2025-04-23 12:51:45,207:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1t_23_L001_R1_001.fastq.gz INFO(129732748388160)2025-04-23 12:51:55,990:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim INFO(129732748388160)2025-04-23 12:51:56,171:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim.derep INFO(129732748388160)2025-04-23 12:51:56,872:total sequences 7281, passing sequences 7281, failing sequences 0 INFO(129732748388160)2025-04-23 12:51:56,872:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(128831277635392)2025-04-23 12:52:03,520:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim INFO(128831277635392)2025-04-23 12:52:03,609:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim.derep INFO(128831277635392)2025-04-23 12:52:04,165:total sequences 3554, passing sequences 3554, failing sequences 0 INFO(128831277635392)2025-04-23 12:52:04,166:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123703453673280)2025-04-23 12:52:17,090:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim INFO(123703453673280)2025-04-23 12:52:17,182:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim.derep INFO(123703453673280)2025-04-23 12:52:17,803:total sequences 3727, passing sequences 3727, failing sequences 0 INFO(123703453673280)2025-04-23 12:52:17,803:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(128831277635392)2025-04-23 12:52:19,875:deblurring 3554 sequences INFO(128831277635392)2025-04-23 12:52:28,017:1679 unique sequences left following deblurring INFO(128831277635392)2025-04-23 12:52:28,027:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(128831277635392)2025-04-23 12:52:29,052:finished processing file INFO(128831277635392)2025-04-23 12:52:29,053:finished processing per sample fasta files INFO(128831277635392)2025-04-23 12:52:29,053:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1n_17_L001_R1_001.fastq.gz finished INFO(132734093526848)2025-04-23 12:52:30,039:************************* INFO(132734093526848)2025-04-23 12:52:30,039:deblurring started WARNING(132734093526848)2025-04-23 12:52:30,040:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1ee_11_L001_R1_001.fastq.gz WARNING(132734093526848)2025-04-23 12:52:30,040:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1ee_11_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(132734093526848)2025-04-23 12:52:30,040:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(132734093526848)2025-04-23 12:52:30,040:deblur worker thread started INFO(132734093526848)2025-04-23 12:52:30,040:processing per sample fasta files INFO(132734093526848)2025-04-23 12:52:30,041:-------------------------------------------------------- INFO(132734093526848)2025-04-23 12:52:30,041:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1ee_11_L001_R1_001.fastq.gz INFO(123703453673280)2025-04-23 12:52:35,240:deblurring 3727 sequences INFO(123703453673280)2025-04-23 12:52:43,202:1655 unique sequences left following deblurring INFO(123703453673280)2025-04-23 12:52:43,222:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(123703453673280)2025-04-23 12:52:44,283:finished processing file INFO(123703453673280)2025-04-23 12:52:44,285:finished processing per sample fasta files INFO(123703453673280)2025-04-23 12:52:44,285:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1t_23_L001_R1_001.fastq.gz finished INFO(129397321705280)2025-04-23 12:52:45,367:************************* INFO(129397321705280)2025-04-23 12:52:45,367:deblurring started WARNING(129397321705280)2025-04-23 12:52:45,368:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1c_6_L001_R1_001.fastq.gz WARNING(129397321705280)2025-04-23 12:52:45,368:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1c_6_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129397321705280)2025-04-23 12:52:45,368:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129397321705280)2025-04-23 12:52:45,368:deblur worker thread started INFO(129397321705280)2025-04-23 12:52:45,368:processing per sample fasta files INFO(129397321705280)2025-04-23 12:52:45,368:-------------------------------------------------------- INFO(129397321705280)2025-04-23 12:52:45,369:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1c_6_L001_R1_001.fastq.gz INFO(129732748388160)2025-04-23 12:52:54,811:deblurring 7281 sequences INFO(133411829327680)2025-04-23 12:53:01,381:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim INFO(133411829327680)2025-04-23 12:53:01,667:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim.derep INFO(133411829327680)2025-04-23 12:53:02,448:total sequences 10448, passing sequences 10448, failing sequences 0 INFO(133411829327680)2025-04-23 12:53:02,448:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(129397321705280)2025-04-23 12:53:07,545:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim INFO(129397321705280)2025-04-23 12:53:07,588:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim.derep INFO(129397321705280)2025-04-23 12:53:08,042:total sequences 1836, passing sequences 1836, failing sequences 0 INFO(129397321705280)2025-04-23 12:53:08,043:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(132734093526848)2025-04-23 12:53:08,239:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim INFO(132734093526848)2025-04-23 12:53:08,359:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim.derep INFO(132734093526848)2025-04-23 12:53:08,920:total sequences 3560, passing sequences 3560, failing sequences 0 INFO(132734093526848)2025-04-23 12:53:08,921:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(129397321705280)2025-04-23 12:53:13,331:deblurring 1836 sequences INFO(129732748388160)2025-04-23 12:53:14,821:1981 unique sequences left following deblurring INFO(129732748388160)2025-04-23 12:53:14,840:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(129397321705280)2025-04-23 12:53:15,356:891 unique sequences left following deblurring INFO(129397321705280)2025-04-23 12:53:15,361:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(129397321705280)2025-04-23 12:53:15,889:finished processing file INFO(129397321705280)2025-04-23 12:53:15,890:finished processing per sample fasta files INFO(129397321705280)2025-04-23 12:53:15,890:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1c_6_L001_R1_001.fastq.gz finished INFO(129732748388160)2025-04-23 12:53:16,184:finished processing file INFO(129732748388160)2025-04-23 12:53:16,186:finished processing per sample fasta files INFO(129732748388160)2025-04-23 12:53:16,186:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5bb_33_L001_R1_001.fastq.gz finished INFO(123138196977472)2025-04-23 12:53:17,043:************************* INFO(123138196977472)2025-04-23 12:53:17,043:deblurring started WARNING(123138196977472)2025-04-23 12:53:17,043:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ee_37_L001_R1_001.fastq.gz WARNING(123138196977472)2025-04-23 12:53:17,044:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ee_37_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123138196977472)2025-04-23 12:53:17,044:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123138196977472)2025-04-23 12:53:17,044:deblur worker thread started INFO(123138196977472)2025-04-23 12:53:17,044:processing per sample fasta files INFO(123138196977472)2025-04-23 12:53:17,044:-------------------------------------------------------- INFO(123138196977472)2025-04-23 12:53:17,044:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ee_37_L001_R1_001.fastq.gz INFO(135865479620416)2025-04-23 12:53:17,231:************************* INFO(135865479620416)2025-04-23 12:53:17,233:deblurring started WARNING(135865479620416)2025-04-23 12:53:17,234:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5g_40_L001_R1_001.fastq.gz WARNING(135865479620416)2025-04-23 12:53:17,234:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5g_40_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(135865479620416)2025-04-23 12:53:17,234:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(135865479620416)2025-04-23 12:53:17,235:deblur worker thread started INFO(135865479620416)2025-04-23 12:53:17,235:processing per sample fasta files INFO(135865479620416)2025-04-23 12:53:17,235:-------------------------------------------------------- INFO(135865479620416)2025-04-23 12:53:17,235:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5g_40_L001_R1_001.fastq.gz INFO(132734093526848)2025-04-23 12:53:24,717:deblurring 3560 sequences INFO(132734093526848)2025-04-23 12:53:32,300:1615 unique sequences left following deblurring INFO(132734093526848)2025-04-23 12:53:32,310:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(132734093526848)2025-04-23 12:53:33,333:finished processing file INFO(132734093526848)2025-04-23 12:53:33,334:finished processing per sample fasta files INFO(132734093526848)2025-04-23 12:53:33,334:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1ee_11_L001_R1_001.fastq.gz finished INFO(133187184305984)2025-04-23 12:53:34,346:************************* INFO(133187184305984)2025-04-23 12:53:34,347:deblurring started WARNING(133187184305984)2025-04-23 12:53:34,347:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5n_44_L001_R1_001.fastq.gz WARNING(133187184305984)2025-04-23 12:53:34,348:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5n_44_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133187184305984)2025-04-23 12:53:34,348:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133187184305984)2025-04-23 12:53:34,348:deblur worker thread started INFO(133187184305984)2025-04-23 12:53:34,348:processing per sample fasta files INFO(133187184305984)2025-04-23 12:53:34,348:-------------------------------------------------------- INFO(133187184305984)2025-04-23 12:53:34,348:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5n_44_L001_R1_001.fastq.gz INFO(135865479620416)2025-04-23 12:53:35,766:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim INFO(135865479620416)2025-04-23 12:53:35,916:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim.derep INFO(135865479620416)2025-04-23 12:53:36,511:total sequences 5722, passing sequences 5722, failing sequences 0 INFO(135865479620416)2025-04-23 12:53:36,511:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(133187184305984)2025-04-23 12:53:52,882:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim INFO(133187184305984)2025-04-23 12:53:52,918:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim.derep INFO(133187184305984)2025-04-23 12:53:53,365:total sequences 1425, passing sequences 1425, failing sequences 0 INFO(133187184305984)2025-04-23 12:53:53,365:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(133187184305984)2025-04-23 12:53:56,995:deblurring 1425 sequences INFO(133187184305984)2025-04-23 12:53:58,634:849 unique sequences left following deblurring INFO(133187184305984)2025-04-23 12:53:58,639:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(133187184305984)2025-04-23 12:53:59,103:finished processing file INFO(133187184305984)2025-04-23 12:53:59,104:finished processing per sample fasta files INFO(133187184305984)2025-04-23 12:53:59,104:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5n_44_L001_R1_001.fastq.gz finished INFO(128948796524352)2025-04-23 12:54:00,129:************************* INFO(128948796524352)2025-04-23 12:54:00,130:deblurring started WARNING(128948796524352)2025-04-23 12:54:00,130:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1f_12_L001_R1_001.fastq.gz WARNING(128948796524352)2025-04-23 12:54:00,130:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1f_12_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(128948796524352)2025-04-23 12:54:00,130:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(128948796524352)2025-04-23 12:54:00,131:deblur worker thread started INFO(128948796524352)2025-04-23 12:54:00,131:processing per sample fasta files INFO(128948796524352)2025-04-23 12:54:00,131:-------------------------------------------------------- INFO(128948796524352)2025-04-23 12:54:00,131:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1f_12_L001_R1_001.fastq.gz INFO(123138196977472)2025-04-23 12:54:11,823:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim INFO(123138196977472)2025-04-23 12:54:11,889:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim.derep INFO(123138196977472)2025-04-23 12:54:12,435:total sequences 2457, passing sequences 2457, failing sequences 0 INFO(123138196977472)2025-04-23 12:54:12,436:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(135865479620416)2025-04-23 12:54:12,920:deblurring 5722 sequences INFO(123138196977472)2025-04-23 12:54:20,557:deblurring 2457 sequences INFO(123138196977472)2025-04-23 12:54:23,742:958 unique sequences left following deblurring INFO(123138196977472)2025-04-23 12:54:23,763:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(123138196977472)2025-04-23 12:54:24,355:finished processing file INFO(123138196977472)2025-04-23 12:54:24,355:finished processing per sample fasta files INFO(123138196977472)2025-04-23 12:54:24,356:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ee_37_L001_R1_001.fastq.gz finished INFO(136620699490112)2025-04-23 12:54:25,383:************************* INFO(136620699490112)2025-04-23 12:54:25,383:deblurring started WARNING(136620699490112)2025-04-23 12:54:25,384:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5p_46_L001_R1_001.fastq.gz WARNING(136620699490112)2025-04-23 12:54:25,384:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5p_46_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(136620699490112)2025-04-23 12:54:25,384:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(136620699490112)2025-04-23 12:54:25,384:deblur worker thread started INFO(136620699490112)2025-04-23 12:54:25,384:processing per sample fasta files INFO(136620699490112)2025-04-23 12:54:25,384:-------------------------------------------------------- INFO(136620699490112)2025-04-23 12:54:25,384:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5p_46_L001_R1_001.fastq.gz INFO(135865479620416)2025-04-23 12:54:29,706:2145 unique sequences left following deblurring INFO(135865479620416)2025-04-23 12:54:29,719:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(135865479620416)2025-04-23 12:54:31,132:finished processing file INFO(135865479620416)2025-04-23 12:54:31,134:finished processing per sample fasta files INFO(135865479620416)2025-04-23 12:54:31,134:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5g_40_L001_R1_001.fastq.gz finished INFO(132971674040128)2025-04-23 12:54:32,112:************************* INFO(132971674040128)2025-04-23 12:54:32,112:deblurring started WARNING(132971674040128)2025-04-23 12:54:32,113:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5r_48_L001_R1_001.fastq.gz WARNING(132971674040128)2025-04-23 12:54:32,113:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5r_48_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(132971674040128)2025-04-23 12:54:32,113:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(132971674040128)2025-04-23 12:54:32,113:deblur worker thread started INFO(132971674040128)2025-04-23 12:54:32,113:processing per sample fasta files INFO(132971674040128)2025-04-23 12:54:32,113:-------------------------------------------------------- INFO(132971674040128)2025-04-23 12:54:32,113:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5r_48_L001_R1_001.fastq.gz WARNING(128948796524352)2025-04-23 12:54:49,592:Vast majority of sequences (274526 / 276317) are shorter than the trim length (230). Are you using the correct -t trim length? INFO(128948796524352)2025-04-23 12:54:49,593:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim INFO(128948796524352)2025-04-23 12:54:49,599:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim.derep INFO(128948796524352)2025-04-23 12:54:50,023:total sequences 98, passing sequences 98, failing sequences 0 INFO(128948796524352)2025-04-23 12:54:50,023:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(136620699490112)2025-04-23 12:54:51,470:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim INFO(136620699490112)2025-04-23 12:54:51,531:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim.derep INFO(136620699490112)2025-04-23 12:54:52,096:total sequences 2567, passing sequences 2567, failing sequences 0 INFO(136620699490112)2025-04-23 12:54:52,096:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(128948796524352)2025-04-23 12:54:53,444:deblurring 98 sequences INFO(128948796524352)2025-04-23 12:54:53,456:75 unique sequences left following deblurring INFO(128948796524352)2025-04-23 12:54:53,457:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(128948796524352)2025-04-23 12:54:53,488:finished processing file INFO(128948796524352)2025-04-23 12:54:53,488:finished processing per sample fasta files INFO(128948796524352)2025-04-23 12:54:53,489:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1f_12_L001_R1_001.fastq.gz finished INFO(136620699490112)2025-04-23 12:55:00,729:deblurring 2567 sequences INFO(133411829327680)2025-04-23 12:55:02,731:deblurring 10448 sequences INFO(132971674040128)2025-04-23 12:55:05,104:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim INFO(132971674040128)2025-04-23 12:55:05,151:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim.derep INFO(136620699490112)2025-04-23 12:55:05,216:1541 unique sequences left following deblurring INFO(136620699490112)2025-04-23 12:55:05,225:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(132971674040128)2025-04-23 12:55:05,639:total sequences 1962, passing sequences 1962, failing sequences 0 INFO(132971674040128)2025-04-23 12:55:05,639:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(136620699490112)2025-04-23 12:55:06,210:finished processing file INFO(136620699490112)2025-04-23 12:55:06,211:finished processing per sample fasta files INFO(136620699490112)2025-04-23 12:55:06,211:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5p_46_L001_R1_001.fastq.gz finished INFO(132971674040128)2025-04-23 12:55:11,007:deblurring 1962 sequences INFO(132971674040128)2025-04-23 12:55:13,856:1166 unique sequences left following deblurring INFO(132971674040128)2025-04-23 12:55:13,862:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(132971674040128)2025-04-23 12:55:14,473:finished processing file INFO(132971674040128)2025-04-23 12:55:14,474:finished processing per sample fasta files INFO(132971674040128)2025-04-23 12:55:14,474:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5r_48_L001_R1_001.fastq.gz finished INFO(137939113228096)2025-04-23 12:55:15,389:************************* INFO(137939113228096)2025-04-23 12:55:15,389:deblurring started WARNING(137939113228096)2025-04-23 12:55:15,390:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1v_24_L001_R1_001.fastq.gz WARNING(137939113228096)2025-04-23 12:55:15,390:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1v_24_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(137939113228096)2025-04-23 12:55:15,390:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(137939113228096)2025-04-23 12:55:15,390:deblur worker thread started INFO(137939113228096)2025-04-23 12:55:15,390:processing per sample fasta files INFO(137939113228096)2025-04-23 12:55:15,390:-------------------------------------------------------- INFO(137939113228096)2025-04-23 12:55:15,390:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1v_24_L001_R1_001.fastq.gz INFO(137939113228096)2025-04-23 12:55:43,123:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim INFO(137939113228096)2025-04-23 12:55:43,168:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim.derep INFO(137939113228096)2025-04-23 12:55:43,620:total sequences 2074, passing sequences 2074, failing sequences 0 INFO(137939113228096)2025-04-23 12:55:43,620:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(137939113228096)2025-04-23 12:55:49,392:deblurring 2074 sequences INFO(137939113228096)2025-04-23 12:55:51,428:885 unique sequences left following deblurring INFO(137939113228096)2025-04-23 12:55:51,432:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(137939113228096)2025-04-23 12:55:51,893:finished processing file INFO(137939113228096)2025-04-23 12:55:51,894:finished processing per sample fasta files INFO(137939113228096)2025-04-23 12:55:51,894:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1v_24_L001_R1_001.fastq.gz finished INFO(133411829327680)2025-04-23 12:56:21,501:5583 unique sequences left following deblurring INFO(133411829327680)2025-04-23 12:56:21,545:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(133411829327680)2025-04-23 12:56:24,510:finished processing file INFO(133411829327680)2025-04-23 12:56:24,513:finished processing per sample fasta files INFO(133411829327680)2025-04-23 12:56:24,514:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5z_53_L001_R1_001.fastq.gz finished INFO(129845327488832)2025-04-23 12:56:25,320:************************* INFO(129845327488832)2025-04-23 12:56:25,320:deblurring started WARNING(129845327488832)2025-04-23 12:56:25,320:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1bb_5_L001_R1_001.fastq.gz WARNING(129845327488832)2025-04-23 12:56:25,320:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1bb_5_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpn2y_95_r', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpn2y_95_r/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 230, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129845327488832)2025-04-23 12:56:25,320:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129845327488832)2025-04-23 12:56:25,320:deblur worker thread started INFO(129845327488832)2025-04-23 12:56:25,320:processing per sample fasta files INFO(129845327488832)2025-04-23 12:56:25,320:-------------------------------------------------------- INFO(129845327488832)2025-04-23 12:56:25,320:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1bb_5_L001_R1_001.fastq.gz INFO(129845327488832)2025-04-23 12:56:47,694:dereplicate seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim INFO(129845327488832)2025-04-23 12:56:47,708:remove_artifacts_seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim.derep INFO(129845327488832)2025-04-23 12:56:48,087:total sequences 387, passing sequences 387, failing sequences 0 INFO(129845327488832)2025-04-23 12:56:48,087:multiple_sequence_alignment seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(129845327488832)2025-04-23 12:56:53,080:deblurring 387 sequences INFO(129845327488832)2025-04-23 12:56:53,184:223 unique sequences left following deblurring INFO(129845327488832)2025-04-23 12:56:53,186:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpn2y_95_r/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpn2y_95_r/deblur_working_dir INFO(129845327488832)2025-04-23 12:56:53,267:finished processing file INFO(129845327488832)2025-04-23 12:56:53,267:finished processing per sample fasta files INFO(129845327488832)2025-04-23 12:56:53,267:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1bb_5_L001_R1_001.fastq.gz finished INFO(140138003871552)2025-04-23 12:56:53,424:create_otu_table for 52 samples, into output table /tmp/tmpn2y_95_r/all.biom INFO(140138003871552)2025-04-23 12:56:55,161:for output biom table loaded 52 samples, 17265 unique sequences INFO(140138003871552)2025-04-23 12:56:55,180:keeping 4171 (out of 17265 sequences) with >=10 reads INFO(140138003871552)2025-04-23 12:56:55,310:saved to biom file /tmp/tmpn2y_95_r/all.biom INFO(140138003871552)2025-04-23 12:56:55,315:saved sequence fasta file to /tmp/tmpn2y_95_r/all.seqs.fa INFO(140138003871552)2025-04-23 12:56:55,318:getting 16s sequences from the biom table INFO(140138003871552)2025-04-23 12:56:55,318:remove_artifacts_seqs file /tmp/tmpn2y_95_r/all.seqs.fa INFO(140138003871552)2025-04-23 12:57:13,795:total sequences 4171, passing sequences 0, failing sequences 4171 WARNING(140138003871552)2025-04-23 12:57:13,796:input file /tmp/tmpn2y_95_r/all.seqs.fa.no_artifacts does not appear to be FASTA or FASTQ INFO(140138003871552)2025-04-23 12:57:13,842:wrote artifact only filtered biom table to /tmp/tmpn2y_95_r/reference-non-hit.biom INFO(140138003871552)2025-04-23 12:57:13,848:saved biom table sequences to fasta file /tmp/tmpn2y_95_r/reference-non-hit.seqs.fa WARNING(140138003871552)2025-04-23 12:57:13,850:removed 52 samples with reads per sample<1 INFO(140138003871552)2025-04-23 12:57:13,853:wrote 16s filtered biom table to /tmp/tmpn2y_95_r/reference-hit.biom INFO(140138003871552)2025-04-23 12:57:13,853:saved biom table sequences to fasta file /tmp/tmpn2y_95_r/reference-hit.seqs.fa INFO(140138003871552)2025-04-23 12:57:13,854:Keeping temp files INFO(140138003871552)2025-04-23 12:57:13,854:deblur workflow finished INFO(140138003871552)2025-04-23 12:57:13,854:output saved to /tmp/tmpn2y_95_r/all.biom INFO(140138003871552)2025-04-23 12:57:13,854:------------------ INFO(127372641085248)2025-04-23 13:20:42,840:************************* INFO(127372641085248)2025-04-23 13:20:42,840:deblurring started WARNING(127372641085248)2025-04-23 13:20:42,840:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data WARNING(127372641085248)2025-04-23 13:20:42,840:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': (), 'neg_ref_fp': (), 'neg_ref_db_fp': (), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 4, 'is_worker_thread': False, 'logger': } INFO(127372641085248)2025-04-23 13:20:42,840:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127372641085248)2025-04-23 13:20:42,840:deblur main program started INFO(127372641085248)2025-04-23 13:20:42,841:processing directory /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data INFO(127372641085248)2025-04-23 13:20:42,842:building negative db sortmerna index files INFO(127372641085248)2025-04-23 13:20:42,842:build_index_sortmerna files ['/home/sam/programs/miniforge3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/deblur/support_files/artifacts.fa'] to dir /tmp/tmp6ycitqez/deblur_working_dir INFO(127372641085248)2025-04-23 13:20:42,879:building positive db sortmerna index files INFO(127372641085248)2025-04-23 13:20:42,880:build_index_sortmerna files ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',) to dir /tmp/tmp6ycitqez/deblur_working_dir INFO(127372641085248)2025-04-23 14:39:48,703:parallel processing per sample fasta files INFO(127372641085248)2025-04-23 14:39:48,704:parallel deblur started for 54 inputs INFO(135645431818048)2025-04-23 14:39:49,711:************************* INFO(135645431818048)2025-04-23 14:39:49,712:deblurring started WARNING(135645431818048)2025-04-23 14:39:49,712:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1e_10_L001_R1_001.fastq.gz WARNING(135645431818048)2025-04-23 14:39:49,712:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1e_10_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(135645431818048)2025-04-23 14:39:49,712:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(135645431818048)2025-04-23 14:39:49,713:deblur worker thread started INFO(135645431818048)2025-04-23 14:39:49,713:processing per sample fasta files INFO(135645431818048)2025-04-23 14:39:49,713:-------------------------------------------------------- INFO(135645431818048)2025-04-23 14:39:49,713:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1e_10_L001_R1_001.fastq.gz INFO(123450339088192)2025-04-23 14:39:49,820:************************* INFO(123450339088192)2025-04-23 14:39:49,820:deblurring started WARNING(123450339088192)2025-04-23 14:39:49,820:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5aa_31_L001_R1_001.fastq.gz WARNING(123450339088192)2025-04-23 14:39:49,821:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5aa_31_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123450339088192)2025-04-23 14:39:49,821:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123450339088192)2025-04-23 14:39:49,821:deblur worker thread started INFO(123450339088192)2025-04-23 14:39:49,821:processing per sample fasta files INFO(123450339088192)2025-04-23 14:39:49,821:-------------------------------------------------------- INFO(123450339088192)2025-04-23 14:39:49,821:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5aa_31_L001_R1_001.fastq.gz INFO(133030646904640)2025-04-23 14:39:49,880:************************* INFO(133030646904640)2025-04-23 14:39:49,880:deblurring started WARNING(133030646904640)2025-04-23 14:39:49,881:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1m_16_L001_R1_001.fastq.gz WARNING(133030646904640)2025-04-23 14:39:49,881:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1m_16_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133030646904640)2025-04-23 14:39:49,881:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133030646904640)2025-04-23 14:39:49,881:deblur worker thread started INFO(133030646904640)2025-04-23 14:39:49,881:processing per sample fasta files INFO(133030646904640)2025-04-23 14:39:49,881:-------------------------------------------------------- INFO(133030646904640)2025-04-23 14:39:49,881:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1m_16_L001_R1_001.fastq.gz INFO(130660861687616)2025-04-23 14:39:49,894:************************* INFO(130660861687616)2025-04-23 14:39:49,894:deblurring started WARNING(130660861687616)2025-04-23 14:39:49,894:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1r_21_L001_R1_001.fastq.gz WARNING(130660861687616)2025-04-23 14:39:49,895:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1r_21_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(130660861687616)2025-04-23 14:39:49,895:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(130660861687616)2025-04-23 14:39:49,895:deblur worker thread started INFO(130660861687616)2025-04-23 14:39:49,895:processing per sample fasta files INFO(130660861687616)2025-04-23 14:39:49,895:-------------------------------------------------------- INFO(130660861687616)2025-04-23 14:39:49,895:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1r_21_L001_R1_001.fastq.gz INFO(135645431818048)2025-04-23 14:39:56,429:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim INFO(135645431818048)2025-04-23 14:39:56,442:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim.derep INFO(135645431818048)2025-04-23 14:39:57,004:total sequences 543, passing sequences 543, failing sequences 0 INFO(135645431818048)2025-04-23 14:39:57,004:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(135645431818048)2025-04-23 14:39:57,888:deblurring 543 sequences INFO(135645431818048)2025-04-23 14:39:58,131:360 unique sequences left following deblurring INFO(135645431818048)2025-04-23 14:39:58,133:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(135645431818048)2025-04-23 14:39:58,215:finished processing file INFO(135645431818048)2025-04-23 14:39:58,215:finished processing per sample fasta files INFO(135645431818048)2025-04-23 14:39:58,215:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1e_10_L001_R1_001.fastq.gz finished INFO(123222619547456)2025-04-23 14:39:59,209:************************* INFO(123222619547456)2025-04-23 14:39:59,209:deblurring started WARNING(123222619547456)2025-04-23 14:39:59,210:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1a_3_L001_R1_001.fastq.gz WARNING(123222619547456)2025-04-23 14:39:59,210:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1a_3_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123222619547456)2025-04-23 14:39:59,210:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123222619547456)2025-04-23 14:39:59,210:deblur worker thread started INFO(123222619547456)2025-04-23 14:39:59,210:processing per sample fasta files INFO(123222619547456)2025-04-23 14:39:59,210:-------------------------------------------------------- INFO(123222619547456)2025-04-23 14:39:59,210:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1a_3_L001_R1_001.fastq.gz INFO(130660861687616)2025-04-23 14:40:18,712:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim INFO(130660861687616)2025-04-23 14:40:18,794:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim.derep INFO(133030646904640)2025-04-23 14:40:19,510:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim INFO(133030646904640)2025-04-23 14:40:19,596:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim.derep INFO(130660861687616)2025-04-23 14:40:19,682:total sequences 2945, passing sequences 2945, failing sequences 0 INFO(130660861687616)2025-04-23 14:40:19,683:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(133030646904640)2025-04-23 14:40:20,543:total sequences 3401, passing sequences 3401, failing sequences 0 INFO(133030646904640)2025-04-23 14:40:20,543:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(130660861687616)2025-04-23 14:40:28,350:deblurring 2945 sequences INFO(133030646904640)2025-04-23 14:40:31,550:deblurring 3401 sequences INFO(130660861687616)2025-04-23 14:40:33,473:1352 unique sequences left following deblurring INFO(130660861687616)2025-04-23 14:40:33,481:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(130660861687616)2025-04-23 14:40:33,836:finished processing file INFO(130660861687616)2025-04-23 14:40:33,837:finished processing per sample fasta files INFO(130660861687616)2025-04-23 14:40:33,837:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1r_21_L001_R1_001.fastq.gz finished INFO(134255242377024)2025-04-23 14:40:34,861:************************* INFO(134255242377024)2025-04-23 14:40:34,861:deblurring started WARNING(134255242377024)2025-04-23 14:40:34,861:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1p_19_L001_R1_001.fastq.gz WARNING(134255242377024)2025-04-23 14:40:34,861:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1p_19_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134255242377024)2025-04-23 14:40:34,861:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134255242377024)2025-04-23 14:40:34,861:deblur worker thread started INFO(134255242377024)2025-04-23 14:40:34,861:processing per sample fasta files INFO(134255242377024)2025-04-23 14:40:34,861:-------------------------------------------------------- INFO(134255242377024)2025-04-23 14:40:34,861:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1p_19_L001_R1_001.fastq.gz INFO(123222619547456)2025-04-23 14:40:38,274:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim INFO(123222619547456)2025-04-23 14:40:38,316:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim.derep INFO(123222619547456)2025-04-23 14:40:38,821:total sequences 2178, passing sequences 2178, failing sequences 0 INFO(123222619547456)2025-04-23 14:40:38,821:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(133030646904640)2025-04-23 14:40:39,724:1726 unique sequences left following deblurring INFO(133030646904640)2025-04-23 14:40:39,746:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(133030646904640)2025-04-23 14:40:40,296:finished processing file INFO(133030646904640)2025-04-23 14:40:40,297:finished processing per sample fasta files INFO(133030646904640)2025-04-23 14:40:40,297:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1m_16_L001_R1_001.fastq.gz finished INFO(124787137378112)2025-04-23 14:40:41,280:************************* INFO(124787137378112)2025-04-23 14:40:41,280:deblurring started WARNING(124787137378112)2025-04-23 14:40:41,281:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5cc_35_L001_R1_001.fastq.gz WARNING(124787137378112)2025-04-23 14:40:41,281:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5cc_35_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124787137378112)2025-04-23 14:40:41,281:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124787137378112)2025-04-23 14:40:41,281:deblur worker thread started INFO(124787137378112)2025-04-23 14:40:41,281:processing per sample fasta files INFO(124787137378112)2025-04-23 14:40:41,281:-------------------------------------------------------- INFO(124787137378112)2025-04-23 14:40:41,281:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5cc_35_L001_R1_001.fastq.gz INFO(123222619547456)2025-04-23 14:40:44,341:deblurring 2178 sequences INFO(123450339088192)2025-04-23 14:40:44,553:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim INFO(123450339088192)2025-04-23 14:40:44,684:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim.derep INFO(123450339088192)2025-04-23 14:40:45,366:total sequences 5700, passing sequences 5700, failing sequences 0 INFO(123450339088192)2025-04-23 14:40:45,366:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123222619547456)2025-04-23 14:40:47,546:1142 unique sequences left following deblurring INFO(123222619547456)2025-04-23 14:40:47,558:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(123222619547456)2025-04-23 14:40:47,848:finished processing file INFO(123222619547456)2025-04-23 14:40:47,848:finished processing per sample fasta files INFO(123222619547456)2025-04-23 14:40:47,849:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1a_3_L001_R1_001.fastq.gz finished INFO(138333829678912)2025-04-23 14:40:49,076:************************* INFO(138333829678912)2025-04-23 14:40:49,076:deblurring started WARNING(138333829678912)2025-04-23 14:40:49,076:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5s_49_L001_R1_001.fastq.gz WARNING(138333829678912)2025-04-23 14:40:49,076:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5s_49_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138333829678912)2025-04-23 14:40:49,077:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138333829678912)2025-04-23 14:40:49,077:deblur worker thread started INFO(138333829678912)2025-04-23 14:40:49,077:processing per sample fasta files INFO(138333829678912)2025-04-23 14:40:49,077:-------------------------------------------------------- INFO(138333829678912)2025-04-23 14:40:49,077:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5s_49_L001_R1_001.fastq.gz INFO(138333829678912)2025-04-23 14:41:14,905:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim INFO(138333829678912)2025-04-23 14:41:14,994:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim.derep INFO(138333829678912)2025-04-23 14:41:15,514:total sequences 2652, passing sequences 2652, failing sequences 0 INFO(138333829678912)2025-04-23 14:41:15,515:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123450339088192)2025-04-23 14:41:18,518:deblurring 5700 sequences INFO(138333829678912)2025-04-23 14:41:22,778:deblurring 2652 sequences INFO(138333829678912)2025-04-23 14:41:27,702:1468 unique sequences left following deblurring INFO(138333829678912)2025-04-23 14:41:27,710:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(138333829678912)2025-04-23 14:41:28,128:finished processing file INFO(138333829678912)2025-04-23 14:41:28,129:finished processing per sample fasta files INFO(138333829678912)2025-04-23 14:41:28,129:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5s_49_L001_R1_001.fastq.gz finished INFO(127770984417088)2025-04-23 14:41:29,425:************************* INFO(127770984417088)2025-04-23 14:41:29,425:deblurring started WARNING(127770984417088)2025-04-23 14:41:29,425:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1w_25_L001_R1_001.fastq.gz WARNING(127770984417088)2025-04-23 14:41:29,434:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1w_25_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127770984417088)2025-04-23 14:41:29,435:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127770984417088)2025-04-23 14:41:29,435:deblur worker thread started INFO(127770984417088)2025-04-23 14:41:29,435:processing per sample fasta files INFO(127770984417088)2025-04-23 14:41:29,435:-------------------------------------------------------- INFO(127770984417088)2025-04-23 14:41:29,435:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1w_25_L001_R1_001.fastq.gz INFO(123450339088192)2025-04-23 14:41:38,765:2306 unique sequences left following deblurring INFO(123450339088192)2025-04-23 14:41:38,791:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(123450339088192)2025-04-23 14:41:39,779:finished processing file INFO(123450339088192)2025-04-23 14:41:39,781:finished processing per sample fasta files INFO(123450339088192)2025-04-23 14:41:39,781:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5aa_31_L001_R1_001.fastq.gz finished INFO(137255364949824)2025-04-23 14:41:40,868:************************* INFO(137255364949824)2025-04-23 14:41:40,869:deblurring started WARNING(137255364949824)2025-04-23 14:41:40,869:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1cc_7_L001_R1_001.fastq.gz WARNING(137255364949824)2025-04-23 14:41:40,869:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1cc_7_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(137255364949824)2025-04-23 14:41:40,869:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(137255364949824)2025-04-23 14:41:40,869:deblur worker thread started INFO(137255364949824)2025-04-23 14:41:40,870:processing per sample fasta files INFO(137255364949824)2025-04-23 14:41:40,870:-------------------------------------------------------- INFO(137255364949824)2025-04-23 14:41:40,870:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1cc_7_L001_R1_001.fastq.gz INFO(124787137378112)2025-04-23 14:42:03,659:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim INFO(124787137378112)2025-04-23 14:42:03,863:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim.derep INFO(124787137378112)2025-04-23 14:42:04,586:total sequences 7549, passing sequences 7549, failing sequences 0 INFO(124787137378112)2025-04-23 14:42:04,586:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127770984417088)2025-04-23 14:42:09,111:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim INFO(127770984417088)2025-04-23 14:42:09,225:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim.derep INFO(127770984417088)2025-04-23 14:42:09,960:total sequences 2838, passing sequences 2838, failing sequences 0 INFO(127770984417088)2025-04-23 14:42:09,960:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127770984417088)2025-04-23 14:42:19,454:deblurring 2838 sequences INFO(127770984417088)2025-04-23 14:42:25,326:1157 unique sequences left following deblurring INFO(127770984417088)2025-04-23 14:42:25,334:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(127770984417088)2025-04-23 14:42:25,796:finished processing file INFO(127770984417088)2025-04-23 14:42:25,797:finished processing per sample fasta files INFO(127770984417088)2025-04-23 14:42:25,797:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1w_25_L001_R1_001.fastq.gz finished INFO(134468820010816)2025-04-23 14:42:27,126:************************* INFO(134468820010816)2025-04-23 14:42:27,127:deblurring started WARNING(134468820010816)2025-04-23 14:42:27,127:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1b_4_L001_R1_001.fastq.gz WARNING(134468820010816)2025-04-23 14:42:27,127:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1b_4_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134468820010816)2025-04-23 14:42:27,127:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134468820010816)2025-04-23 14:42:27,127:deblur worker thread started INFO(134468820010816)2025-04-23 14:42:27,127:processing per sample fasta files INFO(134468820010816)2025-04-23 14:42:27,128:-------------------------------------------------------- INFO(134468820010816)2025-04-23 14:42:27,128:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1b_4_L001_R1_001.fastq.gz INFO(137255364949824)2025-04-23 14:42:53,629:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim INFO(137255364949824)2025-04-23 14:42:53,743:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim.derep INFO(137255364949824)2025-04-23 14:42:54,545:total sequences 4718, passing sequences 4718, failing sequences 0 INFO(137255364949824)2025-04-23 14:42:54,546:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134468820010816)2025-04-23 14:42:59,131:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim INFO(134468820010816)2025-04-23 14:42:59,268:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim.derep INFO(134468820010816)2025-04-23 14:42:59,977:total sequences 3405, passing sequences 3405, failing sequences 0 INFO(134468820010816)2025-04-23 14:42:59,978:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124787137378112)2025-04-23 14:43:05,625:deblurring 7549 sequences INFO(134468820010816)2025-04-23 14:43:12,637:deblurring 3405 sequences INFO(137255364949824)2025-04-23 14:43:18,547:deblurring 4718 sequences INFO(134468820010816)2025-04-23 14:43:22,077:1977 unique sequences left following deblurring INFO(134468820010816)2025-04-23 14:43:22,091:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(134468820010816)2025-04-23 14:43:22,698:finished processing file INFO(134468820010816)2025-04-23 14:43:22,699:finished processing per sample fasta files INFO(134468820010816)2025-04-23 14:43:22,699:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1b_4_L001_R1_001.fastq.gz finished INFO(135345701926720)2025-04-23 14:43:24,096:************************* INFO(135345701926720)2025-04-23 14:43:24,096:deblurring started WARNING(135345701926720)2025-04-23 14:43:24,097:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5v_51_L001_R1_001.fastq.gz WARNING(135345701926720)2025-04-23 14:43:24,097:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5v_51_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(135345701926720)2025-04-23 14:43:24,097:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(135345701926720)2025-04-23 14:43:24,097:deblur worker thread started INFO(135345701926720)2025-04-23 14:43:24,097:processing per sample fasta files INFO(135345701926720)2025-04-23 14:43:24,097:-------------------------------------------------------- INFO(135345701926720)2025-04-23 14:43:24,097:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5v_51_L001_R1_001.fastq.gz INFO(137255364949824)2025-04-23 14:43:31,442:1864 unique sequences left following deblurring INFO(137255364949824)2025-04-23 14:43:31,480:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(137255364949824)2025-04-23 14:43:32,378:finished processing file INFO(137255364949824)2025-04-23 14:43:32,380:finished processing per sample fasta files INFO(137255364949824)2025-04-23 14:43:32,380:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1cc_7_L001_R1_001.fastq.gz finished INFO(135035926660928)2025-04-23 14:43:34,123:************************* INFO(135035926660928)2025-04-23 14:43:34,123:deblurring started WARNING(135035926660928)2025-04-23 14:43:34,124:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5c_34_L001_R1_001.fastq.gz WARNING(135035926660928)2025-04-23 14:43:34,124:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5c_34_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(135035926660928)2025-04-23 14:43:34,124:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(135035926660928)2025-04-23 14:43:34,124:deblur worker thread started INFO(135035926660928)2025-04-23 14:43:34,124:processing per sample fasta files INFO(135035926660928)2025-04-23 14:43:34,124:-------------------------------------------------------- INFO(135035926660928)2025-04-23 14:43:34,125:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5c_34_L001_R1_001.fastq.gz INFO(135345701926720)2025-04-23 14:43:40,851:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim INFO(135345701926720)2025-04-23 14:43:40,879:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim.derep INFO(135345701926720)2025-04-23 14:43:41,421:total sequences 1168, passing sequences 1168, failing sequences 0 INFO(135345701926720)2025-04-23 14:43:41,421:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(135345701926720)2025-04-23 14:43:43,556:deblurring 1168 sequences INFO(135345701926720)2025-04-23 14:43:44,282:482 unique sequences left following deblurring INFO(135345701926720)2025-04-23 14:43:44,285:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(124787137378112)2025-04-23 14:43:44,341:2965 unique sequences left following deblurring INFO(124787137378112)2025-04-23 14:43:44,372:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(135345701926720)2025-04-23 14:43:44,398:finished processing file INFO(135345701926720)2025-04-23 14:43:44,398:finished processing per sample fasta files INFO(135345701926720)2025-04-23 14:43:44,398:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5v_51_L001_R1_001.fastq.gz finished INFO(124787137378112)2025-04-23 14:43:45,353:finished processing file INFO(124787137378112)2025-04-23 14:43:45,356:finished processing per sample fasta files INFO(124787137378112)2025-04-23 14:43:45,356:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5cc_35_L001_R1_001.fastq.gz finished INFO(138387420268352)2025-04-23 14:43:45,484:************************* INFO(138387420268352)2025-04-23 14:43:45,484:deblurring started WARNING(138387420268352)2025-04-23 14:43:45,484:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1d_8_L001_R1_001.fastq.gz WARNING(138387420268352)2025-04-23 14:43:45,484:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1d_8_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138387420268352)2025-04-23 14:43:45,485:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138387420268352)2025-04-23 14:43:45,485:deblur worker thread started INFO(138387420268352)2025-04-23 14:43:45,485:processing per sample fasta files INFO(138387420268352)2025-04-23 14:43:45,485:-------------------------------------------------------- INFO(138387420268352)2025-04-23 14:43:45,485:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1d_8_L001_R1_001.fastq.gz INFO(135035926660928)2025-04-23 14:43:45,889:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim INFO(135035926660928)2025-04-23 14:43:45,915:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim.derep INFO(135035926660928)2025-04-23 14:43:46,406:total sequences 1165, passing sequences 1165, failing sequences 0 INFO(135035926660928)2025-04-23 14:43:46,407:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131527608993600)2025-04-23 14:43:46,485:************************* INFO(131527608993600)2025-04-23 14:43:46,485:deblurring started WARNING(131527608993600)2025-04-23 14:43:46,485:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5w_52_L001_R1_001.fastq.gz WARNING(131527608993600)2025-04-23 14:43:46,485:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5w_52_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(131527608993600)2025-04-23 14:43:46,485:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(131527608993600)2025-04-23 14:43:46,486:deblur worker thread started INFO(131527608993600)2025-04-23 14:43:46,486:processing per sample fasta files INFO(131527608993600)2025-04-23 14:43:46,486:-------------------------------------------------------- INFO(131527608993600)2025-04-23 14:43:46,486:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5w_52_L001_R1_001.fastq.gz INFO(131527608993600)2025-04-23 14:43:46,491:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5w_52_L001_R1_001.fastq.gz.trim INFO(131527608993600)2025-04-23 14:43:46,497:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5w_52_L001_R1_001.fastq.gz.trim.derep WARNING(131527608993600)2025-04-23 14:43:46,497:file /tmp/tmp6ycitqez/deblur_working_dir/Site5w_52_L001_R1_001.fastq.gz.trim.derep has size 0, continuing WARNING(131527608993600)2025-04-23 14:43:46,497:remove artifacts failed, aborting WARNING(131527608993600)2025-04-23 14:43:46,497:deblurring failed for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5w_52_L001_R1_001.fastq.gz INFO(131527608993600)2025-04-23 14:43:46,497:finished processing per sample fasta files INFO(131527608993600)2025-04-23 14:43:46,497:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5w_52_L001_R1_001.fastq.gz finished INFO(128486096643904)2025-04-23 14:43:47,508:************************* INFO(128486096643904)2025-04-23 14:43:47,508:deblurring started WARNING(128486096643904)2025-04-23 14:43:47,509:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5o_45_L001_R1_001.fastq.gz WARNING(128486096643904)2025-04-23 14:43:47,509:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5o_45_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(128486096643904)2025-04-23 14:43:47,509:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(128486096643904)2025-04-23 14:43:47,509:deblur worker thread started INFO(128486096643904)2025-04-23 14:43:47,509:processing per sample fasta files INFO(128486096643904)2025-04-23 14:43:47,509:-------------------------------------------------------- INFO(128486096643904)2025-04-23 14:43:47,510:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5o_45_L001_R1_001.fastq.gz INFO(135035926660928)2025-04-23 14:43:48,483:deblurring 1165 sequences INFO(135035926660928)2025-04-23 14:43:49,548:741 unique sequences left following deblurring INFO(135035926660928)2025-04-23 14:43:49,554:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(135035926660928)2025-04-23 14:43:49,715:finished processing file INFO(135035926660928)2025-04-23 14:43:49,716:finished processing per sample fasta files INFO(135035926660928)2025-04-23 14:43:49,716:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5c_34_L001_R1_001.fastq.gz finished INFO(127761665959744)2025-04-23 14:43:50,741:************************* INFO(127761665959744)2025-04-23 14:43:50,741:deblurring started WARNING(127761665959744)2025-04-23 14:43:50,742:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1z_27_L001_R1_001.fastq.gz WARNING(127761665959744)2025-04-23 14:43:50,742:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1z_27_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127761665959744)2025-04-23 14:43:50,742:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127761665959744)2025-04-23 14:43:50,742:deblur worker thread started INFO(127761665959744)2025-04-23 14:43:50,742:processing per sample fasta files INFO(127761665959744)2025-04-23 14:43:50,742:-------------------------------------------------------- INFO(127761665959744)2025-04-23 14:43:50,742:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1z_27_L001_R1_001.fastq.gz INFO(134255242377024)2025-04-23 14:44:02,183:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim INFO(134255242377024)2025-04-23 14:44:02,619:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim.derep INFO(134255242377024)2025-04-23 14:44:03,465:total sequences 13856, passing sequences 13856, failing sequences 0 INFO(134255242377024)2025-04-23 14:44:03,466:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(128486096643904)2025-04-23 14:44:06,139:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim INFO(128486096643904)2025-04-23 14:44:06,193:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim.derep INFO(128486096643904)2025-04-23 14:44:06,683:total sequences 2487, passing sequences 2487, failing sequences 0 INFO(128486096643904)2025-04-23 14:44:06,683:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(128486096643904)2025-04-23 14:44:13,216:deblurring 2487 sequences INFO(127761665959744)2025-04-23 14:44:16,869:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim INFO(127761665959744)2025-04-23 14:44:16,942:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim.derep INFO(138387420268352)2025-04-23 14:44:17,487:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim INFO(138387420268352)2025-04-23 14:44:17,577:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim.derep INFO(127761665959744)2025-04-23 14:44:17,621:total sequences 2092, passing sequences 2092, failing sequences 0 INFO(127761665959744)2025-04-23 14:44:17,621:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(128486096643904)2025-04-23 14:44:17,904:939 unique sequences left following deblurring INFO(128486096643904)2025-04-23 14:44:17,910:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(128486096643904)2025-04-23 14:44:18,204:finished processing file INFO(128486096643904)2025-04-23 14:44:18,204:finished processing per sample fasta files INFO(128486096643904)2025-04-23 14:44:18,204:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5o_45_L001_R1_001.fastq.gz finished INFO(138387420268352)2025-04-23 14:44:18,344:total sequences 3526, passing sequences 3526, failing sequences 0 INFO(138387420268352)2025-04-23 14:44:18,344:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127396261029696)2025-04-23 14:44:19,255:************************* INFO(127396261029696)2025-04-23 14:44:19,256:deblurring started WARNING(127396261029696)2025-04-23 14:44:19,256:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1o_18_L001_R1_001.fastq.gz WARNING(127396261029696)2025-04-23 14:44:19,256:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1o_18_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127396261029696)2025-04-23 14:44:19,256:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127396261029696)2025-04-23 14:44:19,256:deblur worker thread started INFO(127396261029696)2025-04-23 14:44:19,257:processing per sample fasta files INFO(127396261029696)2025-04-23 14:44:19,257:-------------------------------------------------------- INFO(127396261029696)2025-04-23 14:44:19,257:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1o_18_L001_R1_001.fastq.gz INFO(127761665959744)2025-04-23 14:44:23,215:deblurring 2092 sequences INFO(127761665959744)2025-04-23 14:44:25,691:881 unique sequences left following deblurring INFO(127761665959744)2025-04-23 14:44:25,698:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(127761665959744)2025-04-23 14:44:25,919:finished processing file INFO(127761665959744)2025-04-23 14:44:25,920:finished processing per sample fasta files INFO(127761665959744)2025-04-23 14:44:25,920:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1z_27_L001_R1_001.fastq.gz finished INFO(139506634295104)2025-04-23 14:44:26,976:************************* INFO(139506634295104)2025-04-23 14:44:26,976:deblurring started WARNING(139506634295104)2025-04-23 14:44:26,976:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1s_22_L001_R1_001.fastq.gz WARNING(139506634295104)2025-04-23 14:44:26,977:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1s_22_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(139506634295104)2025-04-23 14:44:26,977:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(139506634295104)2025-04-23 14:44:26,977:deblur worker thread started INFO(139506634295104)2025-04-23 14:44:26,977:processing per sample fasta files INFO(139506634295104)2025-04-23 14:44:26,977:-------------------------------------------------------- INFO(139506634295104)2025-04-23 14:44:26,977:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1s_22_L001_R1_001.fastq.gz INFO(138387420268352)2025-04-23 14:44:30,278:deblurring 3526 sequences INFO(138387420268352)2025-04-23 14:44:41,306:1814 unique sequences left following deblurring INFO(138387420268352)2025-04-23 14:44:41,317:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(138387420268352)2025-04-23 14:44:41,984:finished processing file INFO(138387420268352)2025-04-23 14:44:41,986:finished processing per sample fasta files INFO(138387420268352)2025-04-23 14:44:41,986:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1d_8_L001_R1_001.fastq.gz finished INFO(127825188783936)2025-04-23 14:44:43,329:************************* INFO(127825188783936)2025-04-23 14:44:43,329:deblurring started WARNING(127825188783936)2025-04-23 14:44:43,329:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5m_43_L001_R1_001.fastq.gz WARNING(127825188783936)2025-04-23 14:44:43,330:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5m_43_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127825188783936)2025-04-23 14:44:43,330:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127825188783936)2025-04-23 14:44:43,330:deblur worker thread started INFO(127825188783936)2025-04-23 14:44:43,330:processing per sample fasta files INFO(127825188783936)2025-04-23 14:44:43,330:-------------------------------------------------------- INFO(127825188783936)2025-04-23 14:44:43,330:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5m_43_L001_R1_001.fastq.gz INFO(127396261029696)2025-04-23 14:45:00,842:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim INFO(127396261029696)2025-04-23 14:45:00,930:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim.derep INFO(127396261029696)2025-04-23 14:45:01,498:total sequences 4492, passing sequences 4492, failing sequences 0 INFO(127396261029696)2025-04-23 14:45:01,498:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127825188783936)2025-04-23 14:45:07,901:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim INFO(127825188783936)2025-04-23 14:45:07,941:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim.derep INFO(127825188783936)2025-04-23 14:45:08,456:total sequences 2330, passing sequences 2330, failing sequences 0 INFO(127825188783936)2025-04-23 14:45:08,457:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(139506634295104)2025-04-23 14:45:08,568:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim INFO(139506634295104)2025-04-23 14:45:08,672:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim.derep INFO(139506634295104)2025-04-23 14:45:09,253:total sequences 4269, passing sequences 4269, failing sequences 0 INFO(139506634295104)2025-04-23 14:45:09,253:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127825188783936)2025-04-23 14:45:15,697:deblurring 2330 sequences INFO(127825188783936)2025-04-23 14:45:21,610:1445 unique sequences left following deblurring INFO(127825188783936)2025-04-23 14:45:21,620:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(127825188783936)2025-04-23 14:45:22,181:finished processing file INFO(127825188783936)2025-04-23 14:45:22,182:finished processing per sample fasta files INFO(127825188783936)2025-04-23 14:45:22,183:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5m_43_L001_R1_001.fastq.gz finished INFO(134724408641344)2025-04-23 14:45:23,589:************************* INFO(134724408641344)2025-04-23 14:45:23,589:deblurring started WARNING(134724408641344)2025-04-23 14:45:23,590:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ff_39_L001_R1_001.fastq.gz WARNING(134724408641344)2025-04-23 14:45:23,590:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ff_39_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134724408641344)2025-04-23 14:45:23,590:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134724408641344)2025-04-23 14:45:23,590:deblur worker thread started INFO(134724408641344)2025-04-23 14:45:23,590:processing per sample fasta files INFO(134724408641344)2025-04-23 14:45:23,590:-------------------------------------------------------- INFO(134724408641344)2025-04-23 14:45:23,590:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ff_39_L001_R1_001.fastq.gz INFO(127396261029696)2025-04-23 14:45:24,271:deblurring 4492 sequences INFO(139506634295104)2025-04-23 14:45:29,496:deblurring 4269 sequences INFO(127396261029696)2025-04-23 14:45:40,110:2458 unique sequences left following deblurring INFO(127396261029696)2025-04-23 14:45:40,129:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(127396261029696)2025-04-23 14:45:40,833:finished processing file INFO(127396261029696)2025-04-23 14:45:40,834:finished processing per sample fasta files INFO(127396261029696)2025-04-23 14:45:40,835:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1o_18_L001_R1_001.fastq.gz finished INFO(139506634295104)2025-04-23 14:45:41,402:1982 unique sequences left following deblurring INFO(139506634295104)2025-04-23 14:45:41,415:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(124463453095744)2025-04-23 14:45:42,025:************************* INFO(124463453095744)2025-04-23 14:45:42,025:deblurring started WARNING(124463453095744)2025-04-23 14:45:42,025:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5u_50_L001_R1_001.fastq.gz WARNING(124463453095744)2025-04-23 14:45:42,026:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5u_50_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124463453095744)2025-04-23 14:45:42,026:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124463453095744)2025-04-23 14:45:42,026:deblur worker thread started INFO(124463453095744)2025-04-23 14:45:42,026:processing per sample fasta files INFO(124463453095744)2025-04-23 14:45:42,026:-------------------------------------------------------- INFO(124463453095744)2025-04-23 14:45:42,026:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5u_50_L001_R1_001.fastq.gz INFO(139506634295104)2025-04-23 14:45:42,139:finished processing file INFO(139506634295104)2025-04-23 14:45:42,141:finished processing per sample fasta files INFO(139506634295104)2025-04-23 14:45:42,141:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1s_22_L001_R1_001.fastq.gz finished INFO(139854224234304)2025-04-23 14:45:43,650:************************* INFO(139854224234304)2025-04-23 14:45:43,651:deblurring started WARNING(139854224234304)2025-04-23 14:45:43,651:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5f_38_L001_R1_001.fastq.gz WARNING(139854224234304)2025-04-23 14:45:43,651:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5f_38_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(139854224234304)2025-04-23 14:45:43,651:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(139854224234304)2025-04-23 14:45:43,652:deblur worker thread started INFO(139854224234304)2025-04-23 14:45:43,652:processing per sample fasta files INFO(139854224234304)2025-04-23 14:45:43,652:-------------------------------------------------------- INFO(139854224234304)2025-04-23 14:45:43,652:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5f_38_L001_R1_001.fastq.gz INFO(139854224234304)2025-04-23 14:45:45,558:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim INFO(139854224234304)2025-04-23 14:45:45,568:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim.derep INFO(139854224234304)2025-04-23 14:45:46,145:total sequences 292, passing sequences 292, failing sequences 0 INFO(139854224234304)2025-04-23 14:45:46,145:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(139854224234304)2025-04-23 14:45:49,417:deblurring 292 sequences INFO(139854224234304)2025-04-23 14:45:49,505:152 unique sequences left following deblurring INFO(139854224234304)2025-04-23 14:45:49,506:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(139854224234304)2025-04-23 14:45:49,544:finished processing file INFO(139854224234304)2025-04-23 14:45:49,545:finished processing per sample fasta files INFO(139854224234304)2025-04-23 14:45:49,545:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5f_38_L001_R1_001.fastq.gz finished INFO(124187377252160)2025-04-23 14:45:50,685:************************* INFO(124187377252160)2025-04-23 14:45:50,685:deblurring started WARNING(124187377252160)2025-04-23 14:45:50,686:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1J_0_L001_R1_001.fastq.gz WARNING(124187377252160)2025-04-23 14:45:50,686:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1J_0_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124187377252160)2025-04-23 14:45:50,686:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124187377252160)2025-04-23 14:45:50,686:deblur worker thread started INFO(124187377252160)2025-04-23 14:45:50,686:processing per sample fasta files INFO(124187377252160)2025-04-23 14:45:50,687:-------------------------------------------------------- INFO(124187377252160)2025-04-23 14:45:50,687:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1J_0_L001_R1_001.fastq.gz INFO(124187377252160)2025-04-23 14:45:52,798:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim INFO(124187377252160)2025-04-23 14:45:52,832:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim.derep INFO(124187377252160)2025-04-23 14:45:53,855:total sequences 364, passing sequences 364, failing sequences 0 INFO(124187377252160)2025-04-23 14:45:53,856:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124187377252160)2025-04-23 14:45:59,307:deblurring 364 sequences INFO(124187377252160)2025-04-23 14:45:59,450:293 unique sequences left following deblurring INFO(124187377252160)2025-04-23 14:45:59,451:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(124187377252160)2025-04-23 14:45:59,513:finished processing file INFO(124187377252160)2025-04-23 14:45:59,514:finished processing per sample fasta files INFO(124187377252160)2025-04-23 14:45:59,514:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1J_0_L001_R1_001.fastq.gz finished INFO(127276839499584)2025-04-23 14:46:00,564:************************* INFO(127276839499584)2025-04-23 14:46:00,564:deblurring started WARNING(127276839499584)2025-04-23 14:46:00,564:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1h_14_L001_R1_001.fastq.gz WARNING(127276839499584)2025-04-23 14:46:00,564:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1h_14_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127276839499584)2025-04-23 14:46:00,565:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127276839499584)2025-04-23 14:46:00,565:deblur worker thread started INFO(127276839499584)2025-04-23 14:46:00,565:processing per sample fasta files INFO(127276839499584)2025-04-23 14:46:00,565:-------------------------------------------------------- INFO(127276839499584)2025-04-23 14:46:00,565:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1h_14_L001_R1_001.fastq.gz INFO(124463453095744)2025-04-23 14:46:02,192:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim INFO(124463453095744)2025-04-23 14:46:02,228:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim.derep INFO(124463453095744)2025-04-23 14:46:02,752:total sequences 1726, passing sequences 1726, failing sequences 0 INFO(124463453095744)2025-04-23 14:46:02,752:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124463453095744)2025-04-23 14:46:06,635:deblurring 1726 sequences INFO(124463453095744)2025-04-23 14:46:09,628:904 unique sequences left following deblurring INFO(124463453095744)2025-04-23 14:46:09,634:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(124463453095744)2025-04-23 14:46:10,103:finished processing file INFO(124463453095744)2025-04-23 14:46:10,104:finished processing per sample fasta files INFO(124463453095744)2025-04-23 14:46:10,104:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5u_50_L001_R1_001.fastq.gz finished INFO(139011090253632)2025-04-23 14:46:12,449:************************* INFO(139011090253632)2025-04-23 14:46:12,449:deblurring started WARNING(139011090253632)2025-04-23 14:46:12,450:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5q_47_L001_R1_001.fastq.gz WARNING(139011090253632)2025-04-23 14:46:12,450:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5q_47_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(139011090253632)2025-04-23 14:46:12,450:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(139011090253632)2025-04-23 14:46:12,451:deblur worker thread started INFO(139011090253632)2025-04-23 14:46:12,451:processing per sample fasta files INFO(139011090253632)2025-04-23 14:46:12,451:-------------------------------------------------------- INFO(139011090253632)2025-04-23 14:46:12,451:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5q_47_L001_R1_001.fastq.gz INFO(127276839499584)2025-04-23 14:46:23,732:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim INFO(127276839499584)2025-04-23 14:46:23,776:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim.derep INFO(127276839499584)2025-04-23 14:46:24,546:total sequences 1031, passing sequences 1031, failing sequences 0 INFO(127276839499584)2025-04-23 14:46:24,546:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127276839499584)2025-04-23 14:46:27,825:deblurring 1031 sequences INFO(127276839499584)2025-04-23 14:46:28,559:532 unique sequences left following deblurring INFO(127276839499584)2025-04-23 14:46:28,562:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(127276839499584)2025-04-23 14:46:28,685:finished processing file INFO(127276839499584)2025-04-23 14:46:28,685:finished processing per sample fasta files INFO(127276839499584)2025-04-23 14:46:28,685:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1h_14_L001_R1_001.fastq.gz finished INFO(134571682400064)2025-04-23 14:46:29,852:************************* INFO(134571682400064)2025-04-23 14:46:29,853:deblurring started WARNING(134571682400064)2025-04-23 14:46:29,853:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1L_1_L001_R1_001.fastq.gz WARNING(134571682400064)2025-04-23 14:46:29,854:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1L_1_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134571682400064)2025-04-23 14:46:29,854:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134571682400064)2025-04-23 14:46:29,854:deblur worker thread started INFO(134571682400064)2025-04-23 14:46:29,854:processing per sample fasta files INFO(134571682400064)2025-04-23 14:46:29,854:-------------------------------------------------------- INFO(134571682400064)2025-04-23 14:46:29,854:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1L_1_L001_R1_001.fastq.gz INFO(134571682400064)2025-04-23 14:46:39,349:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim INFO(134571682400064)2025-04-23 14:46:39,373:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim.derep INFO(134571682400064)2025-04-23 14:46:39,864:total sequences 1053, passing sequences 1053, failing sequences 0 INFO(134571682400064)2025-04-23 14:46:39,864:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134571682400064)2025-04-23 14:46:42,034:deblurring 1053 sequences INFO(134571682400064)2025-04-23 14:46:42,827:598 unique sequences left following deblurring INFO(134571682400064)2025-04-23 14:46:42,833:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(134571682400064)2025-04-23 14:46:42,990:finished processing file INFO(134571682400064)2025-04-23 14:46:42,991:finished processing per sample fasta files INFO(134571682400064)2025-04-23 14:46:42,991:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1L_1_L001_R1_001.fastq.gz finished INFO(131750355502912)2025-04-23 14:46:44,079:************************* INFO(131750355502912)2025-04-23 14:46:44,079:deblurring started WARNING(131750355502912)2025-04-23 14:46:44,080:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5k_42_L001_R1_001.fastq.gz WARNING(131750355502912)2025-04-23 14:46:44,080:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5k_42_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(131750355502912)2025-04-23 14:46:44,080:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(131750355502912)2025-04-23 14:46:44,080:deblur worker thread started INFO(131750355502912)2025-04-23 14:46:44,080:processing per sample fasta files INFO(131750355502912)2025-04-23 14:46:44,080:-------------------------------------------------------- INFO(131750355502912)2025-04-23 14:46:44,080:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5k_42_L001_R1_001.fastq.gz INFO(139011090253632)2025-04-23 14:46:50,325:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim INFO(139011090253632)2025-04-23 14:46:51,651:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim.derep INFO(139011090253632)2025-04-23 14:46:52,667:total sequences 6897, passing sequences 6897, failing sequences 0 INFO(139011090253632)2025-04-23 14:46:52,667:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131750355502912)2025-04-23 14:46:57,466:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim INFO(131750355502912)2025-04-23 14:46:57,497:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim.derep INFO(134724408641344)2025-04-23 14:46:57,781:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim INFO(134724408641344)2025-04-23 14:46:58,055:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim.derep INFO(131750355502912)2025-04-23 14:46:58,107:total sequences 1255, passing sequences 1255, failing sequences 0 INFO(131750355502912)2025-04-23 14:46:58,108:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134724408641344)2025-04-23 14:46:58,755:total sequences 8154, passing sequences 8154, failing sequences 0 INFO(134724408641344)2025-04-23 14:46:58,755:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131750355502912)2025-04-23 14:47:00,608:deblurring 1255 sequences INFO(131750355502912)2025-04-23 14:47:01,915:783 unique sequences left following deblurring INFO(131750355502912)2025-04-23 14:47:01,919:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(131750355502912)2025-04-23 14:47:02,084:finished processing file INFO(131750355502912)2025-04-23 14:47:02,085:finished processing per sample fasta files INFO(131750355502912)2025-04-23 14:47:02,085:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5k_42_L001_R1_001.fastq.gz finished INFO(126126008846144)2025-04-23 14:47:03,465:************************* INFO(126126008846144)2025-04-23 14:47:03,465:deblurring started WARNING(126126008846144)2025-04-23 14:47:03,466:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1dd_9_L001_R1_001.fastq.gz WARNING(126126008846144)2025-04-23 14:47:03,466:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1dd_9_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(126126008846144)2025-04-23 14:47:03,466:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(126126008846144)2025-04-23 14:47:03,466:deblur worker thread started INFO(126126008846144)2025-04-23 14:47:03,466:processing per sample fasta files INFO(126126008846144)2025-04-23 14:47:03,466:-------------------------------------------------------- INFO(126126008846144)2025-04-23 14:47:03,466:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1dd_9_L001_R1_001.fastq.gz INFO(134255242377024)2025-04-23 14:47:34,760:deblurring 13856 sequences INFO(139011090253632)2025-04-23 14:47:37,617:deblurring 6897 sequences INFO(134724408641344)2025-04-23 14:48:04,173:deblurring 8154 sequences INFO(126126008846144)2025-04-23 14:48:12,048:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim INFO(126126008846144)2025-04-23 14:48:12,170:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim.derep INFO(126126008846144)2025-04-23 14:48:12,993:total sequences 5382, passing sequences 5382, failing sequences 0 INFO(126126008846144)2025-04-23 14:48:12,993:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(139011090253632)2025-04-23 14:48:31,982:4786 unique sequences left following deblurring INFO(139011090253632)2025-04-23 14:48:32,048:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(139011090253632)2025-04-23 14:48:34,197:finished processing file INFO(139011090253632)2025-04-23 14:48:34,200:finished processing per sample fasta files INFO(139011090253632)2025-04-23 14:48:34,200:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5q_47_L001_R1_001.fastq.gz finished INFO(136401386395456)2025-04-23 14:48:35,715:************************* INFO(136401386395456)2025-04-23 14:48:35,716:deblurring started WARNING(136401386395456)2025-04-23 14:48:35,716:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5h_41_L001_R1_001.fastq.gz WARNING(136401386395456)2025-04-23 14:48:35,716:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5h_41_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(136401386395456)2025-04-23 14:48:35,717:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(136401386395456)2025-04-23 14:48:35,717:deblur worker thread started INFO(136401386395456)2025-04-23 14:48:35,717:processing per sample fasta files INFO(136401386395456)2025-04-23 14:48:35,717:-------------------------------------------------------- INFO(136401386395456)2025-04-23 14:48:35,717:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5h_41_L001_R1_001.fastq.gz INFO(126126008846144)2025-04-23 14:48:49,569:deblurring 5382 sequences INFO(134724408641344)2025-04-23 14:48:50,663:3328 unique sequences left following deblurring INFO(134724408641344)2025-04-23 14:48:50,717:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(134724408641344)2025-04-23 14:48:51,966:finished processing file INFO(134724408641344)2025-04-23 14:48:51,969:finished processing per sample fasta files INFO(134724408641344)2025-04-23 14:48:51,969:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ff_39_L001_R1_001.fastq.gz finished INFO(125572725610304)2025-04-23 14:48:53,065:************************* INFO(125572725610304)2025-04-23 14:48:53,065:deblurring started WARNING(125572725610304)2025-04-23 14:48:53,066:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1q_20_L001_R1_001.fastq.gz WARNING(125572725610304)2025-04-23 14:48:53,066:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1q_20_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(125572725610304)2025-04-23 14:48:53,066:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(125572725610304)2025-04-23 14:48:53,066:deblur worker thread started INFO(125572725610304)2025-04-23 14:48:53,066:processing per sample fasta files INFO(125572725610304)2025-04-23 14:48:53,066:-------------------------------------------------------- INFO(125572725610304)2025-04-23 14:48:53,066:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1q_20_L001_R1_001.fastq.gz INFO(126126008846144)2025-04-23 14:49:05,467:2050 unique sequences left following deblurring INFO(126126008846144)2025-04-23 14:49:05,484:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(126126008846144)2025-04-23 14:49:06,069:finished processing file INFO(126126008846144)2025-04-23 14:49:06,073:finished processing per sample fasta files INFO(126126008846144)2025-04-23 14:49:06,073:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1dd_9_L001_R1_001.fastq.gz finished INFO(134255242377024)2025-04-23 14:49:06,660:3387 unique sequences left following deblurring INFO(134255242377024)2025-04-23 14:49:06,704:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(124004218959680)2025-04-23 14:49:07,496:************************* INFO(124004218959680)2025-04-23 14:49:07,496:deblurring started WARNING(124004218959680)2025-04-23 14:49:07,497:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1y_26_L001_R1_001.fastq.gz WARNING(124004218959680)2025-04-23 14:49:07,497:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1y_26_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124004218959680)2025-04-23 14:49:07,497:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124004218959680)2025-04-23 14:49:07,497:deblur worker thread started INFO(124004218959680)2025-04-23 14:49:07,497:processing per sample fasta files INFO(124004218959680)2025-04-23 14:49:07,497:-------------------------------------------------------- INFO(124004218959680)2025-04-23 14:49:07,497:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1y_26_L001_R1_001.fastq.gz INFO(134255242377024)2025-04-23 14:49:08,100:finished processing file INFO(134255242377024)2025-04-23 14:49:08,102:finished processing per sample fasta files INFO(134255242377024)2025-04-23 14:49:08,102:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1p_19_L001_R1_001.fastq.gz finished INFO(131197918910272)2025-04-23 14:49:09,409:************************* INFO(131197918910272)2025-04-23 14:49:09,409:deblurring started WARNING(131197918910272)2025-04-23 14:49:09,410:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5J_28_L001_R1_001.fastq.gz WARNING(131197918910272)2025-04-23 14:49:09,410:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5J_28_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(131197918910272)2025-04-23 14:49:09,410:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(131197918910272)2025-04-23 14:49:09,410:deblur worker thread started INFO(131197918910272)2025-04-23 14:49:09,410:processing per sample fasta files INFO(131197918910272)2025-04-23 14:49:09,410:-------------------------------------------------------- INFO(131197918910272)2025-04-23 14:49:09,410:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5J_28_L001_R1_001.fastq.gz INFO(131197918910272)2025-04-23 14:49:09,427:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5J_28_L001_R1_001.fastq.gz.trim INFO(131197918910272)2025-04-23 14:49:09,431:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5J_28_L001_R1_001.fastq.gz.trim.derep WARNING(131197918910272)2025-04-23 14:49:09,431:file /tmp/tmp6ycitqez/deblur_working_dir/Site5J_28_L001_R1_001.fastq.gz.trim.derep has size 0, continuing WARNING(131197918910272)2025-04-23 14:49:09,431:remove artifacts failed, aborting WARNING(131197918910272)2025-04-23 14:49:09,431:deblurring failed for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5J_28_L001_R1_001.fastq.gz INFO(131197918910272)2025-04-23 14:49:09,432:finished processing per sample fasta files INFO(131197918910272)2025-04-23 14:49:09,432:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5J_28_L001_R1_001.fastq.gz finished INFO(125632985245504)2025-04-23 14:49:10,495:************************* INFO(125632985245504)2025-04-23 14:49:10,495:deblurring started WARNING(125632985245504)2025-04-23 14:49:10,495:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5L_29_L001_R1_001.fastq.gz WARNING(125632985245504)2025-04-23 14:49:10,496:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5L_29_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(125632985245504)2025-04-23 14:49:10,496:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(125632985245504)2025-04-23 14:49:10,496:deblur worker thread started INFO(125632985245504)2025-04-23 14:49:10,496:processing per sample fasta files INFO(125632985245504)2025-04-23 14:49:10,496:-------------------------------------------------------- INFO(125632985245504)2025-04-23 14:49:10,496:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5L_29_L001_R1_001.fastq.gz INFO(125572725610304)2025-04-23 14:49:22,764:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim INFO(125572725610304)2025-04-23 14:49:22,789:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim.derep INFO(125572725610304)2025-04-23 14:49:23,319:total sequences 965, passing sequences 965, failing sequences 0 INFO(125572725610304)2025-04-23 14:49:23,319:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(125572725610304)2025-04-23 14:49:25,187:deblurring 965 sequences INFO(125572725610304)2025-04-23 14:49:26,004:536 unique sequences left following deblurring INFO(125572725610304)2025-04-23 14:49:26,008:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(125572725610304)2025-04-23 14:49:26,149:finished processing file INFO(125572725610304)2025-04-23 14:49:26,149:finished processing per sample fasta files INFO(125572725610304)2025-04-23 14:49:26,150:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1q_20_L001_R1_001.fastq.gz finished INFO(132283168909120)2025-04-23 14:49:27,182:************************* INFO(132283168909120)2025-04-23 14:49:27,182:deblurring started WARNING(132283168909120)2025-04-23 14:49:27,183:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5b_32_L001_R1_001.fastq.gz WARNING(132283168909120)2025-04-23 14:49:27,183:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5b_32_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(132283168909120)2025-04-23 14:49:27,183:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(132283168909120)2025-04-23 14:49:27,183:deblur worker thread started INFO(132283168909120)2025-04-23 14:49:27,183:processing per sample fasta files INFO(132283168909120)2025-04-23 14:49:27,183:-------------------------------------------------------- INFO(132283168909120)2025-04-23 14:49:27,183:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5b_32_L001_R1_001.fastq.gz INFO(124004218959680)2025-04-23 14:49:35,970:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim INFO(124004218959680)2025-04-23 14:49:36,045:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim.derep INFO(124004218959680)2025-04-23 14:49:36,620:total sequences 3287, passing sequences 3287, failing sequences 0 INFO(124004218959680)2025-04-23 14:49:36,620:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(125632985245504)2025-04-23 14:49:45,376:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim INFO(125632985245504)2025-04-23 14:49:45,467:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim.derep INFO(125632985245504)2025-04-23 14:49:46,050:total sequences 3817, passing sequences 3817, failing sequences 0 INFO(125632985245504)2025-04-23 14:49:46,050:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124004218959680)2025-04-23 14:49:47,344:deblurring 3287 sequences INFO(136401386395456)2025-04-23 14:49:48,865:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim INFO(136401386395456)2025-04-23 14:49:48,922:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim.derep INFO(136401386395456)2025-04-23 14:49:49,410:total sequences 1546, passing sequences 1546, failing sequences 0 INFO(136401386395456)2025-04-23 14:49:49,411:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(136401386395456)2025-04-23 14:49:52,946:deblurring 1546 sequences INFO(124004218959680)2025-04-23 14:49:53,520:1392 unique sequences left following deblurring INFO(124004218959680)2025-04-23 14:49:53,529:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(124004218959680)2025-04-23 14:49:53,908:finished processing file INFO(124004218959680)2025-04-23 14:49:53,909:finished processing per sample fasta files INFO(124004218959680)2025-04-23 14:49:53,909:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1y_26_L001_R1_001.fastq.gz finished INFO(136401386395456)2025-04-23 14:49:54,011:511 unique sequences left following deblurring INFO(136401386395456)2025-04-23 14:49:54,015:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(136401386395456)2025-04-23 14:49:54,180:finished processing file INFO(136401386395456)2025-04-23 14:49:54,181:finished processing per sample fasta files INFO(136401386395456)2025-04-23 14:49:54,181:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5h_41_L001_R1_001.fastq.gz finished INFO(129157799372608)2025-04-23 14:49:55,123:************************* INFO(129157799372608)2025-04-23 14:49:55,124:deblurring started WARNING(129157799372608)2025-04-23 14:49:55,124:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5e_36_L001_R1_001.fastq.gz WARNING(129157799372608)2025-04-23 14:49:55,124:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5e_36_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129157799372608)2025-04-23 14:49:55,124:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129157799372608)2025-04-23 14:49:55,124:deblur worker thread started INFO(129157799372608)2025-04-23 14:49:55,125:processing per sample fasta files INFO(129157799372608)2025-04-23 14:49:55,125:-------------------------------------------------------- INFO(129157799372608)2025-04-23 14:49:55,125:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5e_36_L001_R1_001.fastq.gz INFO(134774455101248)2025-04-23 14:49:55,292:************************* INFO(134774455101248)2025-04-23 14:49:55,293:deblurring started WARNING(134774455101248)2025-04-23 14:49:55,294:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1g_13_L001_R1_001.fastq.gz WARNING(134774455101248)2025-04-23 14:49:55,294:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1g_13_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134774455101248)2025-04-23 14:49:55,294:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134774455101248)2025-04-23 14:49:55,294:deblur worker thread started INFO(134774455101248)2025-04-23 14:49:55,294:processing per sample fasta files INFO(134774455101248)2025-04-23 14:49:55,295:-------------------------------------------------------- INFO(134774455101248)2025-04-23 14:49:55,295:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1g_13_L001_R1_001.fastq.gz INFO(125632985245504)2025-04-23 14:49:59,957:deblurring 3817 sequences INFO(132283168909120)2025-04-23 14:50:03,366:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim INFO(132283168909120)2025-04-23 14:50:03,415:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim.derep INFO(132283168909120)2025-04-23 14:50:03,926:total sequences 2458, passing sequences 2458, failing sequences 0 INFO(132283168909120)2025-04-23 14:50:03,926:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(132283168909120)2025-04-23 14:50:10,172:deblurring 2458 sequences INFO(125632985245504)2025-04-23 14:50:11,737:2318 unique sequences left following deblurring INFO(125632985245504)2025-04-23 14:50:11,751:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(125632985245504)2025-04-23 14:50:12,422:finished processing file INFO(125632985245504)2025-04-23 14:50:12,423:finished processing per sample fasta files INFO(125632985245504)2025-04-23 14:50:12,423:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5L_29_L001_R1_001.fastq.gz finished INFO(123239032973120)2025-04-23 14:50:13,450:************************* INFO(123239032973120)2025-04-23 14:50:13,450:deblurring started WARNING(123239032973120)2025-04-23 14:50:13,451:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5bb_33_L001_R1_001.fastq.gz WARNING(123239032973120)2025-04-23 14:50:13,451:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5bb_33_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123239032973120)2025-04-23 14:50:13,451:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123239032973120)2025-04-23 14:50:13,451:deblur worker thread started INFO(123239032973120)2025-04-23 14:50:13,451:processing per sample fasta files INFO(123239032973120)2025-04-23 14:50:13,451:-------------------------------------------------------- INFO(123239032973120)2025-04-23 14:50:13,451:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5bb_33_L001_R1_001.fastq.gz INFO(132283168909120)2025-04-23 14:50:13,790:1022 unique sequences left following deblurring INFO(132283168909120)2025-04-23 14:50:13,796:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(132283168909120)2025-04-23 14:50:14,038:finished processing file INFO(132283168909120)2025-04-23 14:50:14,039:finished processing per sample fasta files INFO(132283168909120)2025-04-23 14:50:14,039:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5b_32_L001_R1_001.fastq.gz finished INFO(127502347372352)2025-04-23 14:50:15,076:************************* INFO(127502347372352)2025-04-23 14:50:15,077:deblurring started WARNING(127502347372352)2025-04-23 14:50:15,077:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1U_2_L001_R1_001.fastq.gz WARNING(127502347372352)2025-04-23 14:50:15,077:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1U_2_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127502347372352)2025-04-23 14:50:15,077:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127502347372352)2025-04-23 14:50:15,078:deblur worker thread started INFO(127502347372352)2025-04-23 14:50:15,078:processing per sample fasta files INFO(127502347372352)2025-04-23 14:50:15,078:-------------------------------------------------------- INFO(127502347372352)2025-04-23 14:50:15,078:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1U_2_L001_R1_001.fastq.gz INFO(127502347372352)2025-04-23 14:50:22,429:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim INFO(127502347372352)2025-04-23 14:50:22,467:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim.derep INFO(127502347372352)2025-04-23 14:50:22,951:total sequences 1527, passing sequences 1527, failing sequences 0 INFO(127502347372352)2025-04-23 14:50:22,951:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127502347372352)2025-04-23 14:50:26,152:deblurring 1527 sequences INFO(127502347372352)2025-04-23 14:50:28,575:1111 unique sequences left following deblurring INFO(127502347372352)2025-04-23 14:50:28,586:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(127502347372352)2025-04-23 14:50:28,849:finished processing file INFO(127502347372352)2025-04-23 14:50:28,849:finished processing per sample fasta files INFO(127502347372352)2025-04-23 14:50:28,849:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1U_2_L001_R1_001.fastq.gz finished INFO(135398680573760)2025-04-23 14:50:29,869:************************* INFO(135398680573760)2025-04-23 14:50:29,869:deblurring started WARNING(135398680573760)2025-04-23 14:50:29,869:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1n_17_L001_R1_001.fastq.gz WARNING(135398680573760)2025-04-23 14:50:29,869:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1n_17_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(135398680573760)2025-04-23 14:50:29,869:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(135398680573760)2025-04-23 14:50:29,869:deblur worker thread started INFO(135398680573760)2025-04-23 14:50:29,869:processing per sample fasta files INFO(135398680573760)2025-04-23 14:50:29,870:-------------------------------------------------------- INFO(135398680573760)2025-04-23 14:50:29,870:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1n_17_L001_R1_001.fastq.gz INFO(134774455101248)2025-04-23 14:50:32,931:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim INFO(134774455101248)2025-04-23 14:50:33,014:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim.derep INFO(134774455101248)2025-04-23 14:50:33,562:total sequences 3187, passing sequences 3187, failing sequences 0 INFO(134774455101248)2025-04-23 14:50:33,562:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134774455101248)2025-04-23 14:50:44,044:deblurring 3187 sequences INFO(134774455101248)2025-04-23 14:50:49,722:1183 unique sequences left following deblurring INFO(134774455101248)2025-04-23 14:50:49,732:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(134774455101248)2025-04-23 14:50:50,058:finished processing file INFO(134774455101248)2025-04-23 14:50:50,059:finished processing per sample fasta files INFO(134774455101248)2025-04-23 14:50:50,059:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1g_13_L001_R1_001.fastq.gz finished INFO(126003844204352)2025-04-23 14:50:51,075:************************* INFO(126003844204352)2025-04-23 14:50:51,076:deblurring started WARNING(126003844204352)2025-04-23 14:50:51,076:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1k_15_L001_R1_001.fastq.gz WARNING(126003844204352)2025-04-23 14:50:51,076:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1k_15_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(126003844204352)2025-04-23 14:50:51,077:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(126003844204352)2025-04-23 14:50:51,077:deblur worker thread started INFO(126003844204352)2025-04-23 14:50:51,077:processing per sample fasta files INFO(126003844204352)2025-04-23 14:50:51,077:-------------------------------------------------------- INFO(126003844204352)2025-04-23 14:50:51,077:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1k_15_L001_R1_001.fastq.gz INFO(129157799372608)2025-04-23 14:50:58,643:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim INFO(129157799372608)2025-04-23 14:50:58,777:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim.derep INFO(129157799372608)2025-04-23 14:50:59,303:total sequences 3017, passing sequences 3017, failing sequences 0 INFO(129157799372608)2025-04-23 14:50:59,303:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(129157799372608)2025-04-23 14:51:08,852:deblurring 3017 sequences INFO(126003844204352)2025-04-23 14:51:11,043:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim INFO(126003844204352)2025-04-23 14:51:11,120:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim.derep INFO(126003844204352)2025-04-23 14:51:11,684:total sequences 2521, passing sequences 2521, failing sequences 0 INFO(126003844204352)2025-04-23 14:51:11,684:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(135398680573760)2025-04-23 14:51:12,496:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim INFO(129157799372608)2025-04-23 14:51:12,547:999 unique sequences left following deblurring INFO(129157799372608)2025-04-23 14:51:12,554:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(135398680573760)2025-04-23 14:51:12,583:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim.derep INFO(129157799372608)2025-04-23 14:51:12,813:finished processing file INFO(129157799372608)2025-04-23 14:51:12,813:finished processing per sample fasta files INFO(129157799372608)2025-04-23 14:51:12,814:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5e_36_L001_R1_001.fastq.gz finished INFO(135398680573760)2025-04-23 14:51:13,262:total sequences 4681, passing sequences 4681, failing sequences 0 INFO(135398680573760)2025-04-23 14:51:13,263:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127185943734080)2025-04-23 14:51:13,883:************************* INFO(127185943734080)2025-04-23 14:51:13,883:deblurring started WARNING(127185943734080)2025-04-23 14:51:13,884:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5a_30_L001_R1_001.fastq.gz WARNING(127185943734080)2025-04-23 14:51:13,884:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5a_30_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127185943734080)2025-04-23 14:51:13,884:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127185943734080)2025-04-23 14:51:13,884:deblur worker thread started INFO(127185943734080)2025-04-23 14:51:13,884:processing per sample fasta files INFO(127185943734080)2025-04-23 14:51:13,884:-------------------------------------------------------- INFO(127185943734080)2025-04-23 14:51:13,884:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5a_30_L001_R1_001.fastq.gz INFO(126003844204352)2025-04-23 14:51:18,213:deblurring 2521 sequences INFO(126003844204352)2025-04-23 14:51:22,012:1140 unique sequences left following deblurring INFO(126003844204352)2025-04-23 14:51:22,020:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(126003844204352)2025-04-23 14:51:22,321:finished processing file INFO(126003844204352)2025-04-23 14:51:22,322:finished processing per sample fasta files INFO(126003844204352)2025-04-23 14:51:22,322:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1k_15_L001_R1_001.fastq.gz finished INFO(123239032973120)2025-04-23 14:51:22,527:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim INFO(123239032973120)2025-04-23 14:51:22,769:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim.derep INFO(133523533674304)2025-04-23 14:51:23,451:************************* INFO(133523533674304)2025-04-23 14:51:23,452:deblurring started WARNING(133523533674304)2025-04-23 14:51:23,452:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5z_53_L001_R1_001.fastq.gz WARNING(133523533674304)2025-04-23 14:51:23,452:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5z_53_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133523533674304)2025-04-23 14:51:23,452:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133523533674304)2025-04-23 14:51:23,452:deblur worker thread started INFO(133523533674304)2025-04-23 14:51:23,452:processing per sample fasta files INFO(133523533674304)2025-04-23 14:51:23,452:-------------------------------------------------------- INFO(133523533674304)2025-04-23 14:51:23,452:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5z_53_L001_R1_001.fastq.gz INFO(123239032973120)2025-04-23 14:51:23,475:total sequences 7234, passing sequences 7234, failing sequences 0 INFO(123239032973120)2025-04-23 14:51:23,475:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(135398680573760)2025-04-23 14:51:33,931:deblurring 4681 sequences INFO(127185943734080)2025-04-23 14:51:42,173:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim INFO(127185943734080)2025-04-23 14:51:42,195:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim.derep INFO(127185943734080)2025-04-23 14:51:42,697:total sequences 902, passing sequences 902, failing sequences 0 INFO(127185943734080)2025-04-23 14:51:42,698:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127185943734080)2025-04-23 14:51:44,352:deblurring 902 sequences INFO(127185943734080)2025-04-23 14:51:44,948:495 unique sequences left following deblurring INFO(127185943734080)2025-04-23 14:51:44,950:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(127185943734080)2025-04-23 14:51:45,084:finished processing file INFO(127185943734080)2025-04-23 14:51:45,084:finished processing per sample fasta files INFO(127185943734080)2025-04-23 14:51:45,084:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5a_30_L001_R1_001.fastq.gz finished INFO(136860889409344)2025-04-23 14:51:46,316:************************* INFO(136860889409344)2025-04-23 14:51:46,316:deblurring started WARNING(136860889409344)2025-04-23 14:51:46,316:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1t_23_L001_R1_001.fastq.gz WARNING(136860889409344)2025-04-23 14:51:46,316:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1t_23_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(136860889409344)2025-04-23 14:51:46,317:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(136860889409344)2025-04-23 14:51:46,317:deblur worker thread started INFO(136860889409344)2025-04-23 14:51:46,317:processing per sample fasta files INFO(136860889409344)2025-04-23 14:51:46,317:-------------------------------------------------------- INFO(136860889409344)2025-04-23 14:51:46,317:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1t_23_L001_R1_001.fastq.gz INFO(135398680573760)2025-04-23 14:51:49,275:2322 unique sequences left following deblurring INFO(135398680573760)2025-04-23 14:51:49,294:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(135398680573760)2025-04-23 14:51:49,928:finished processing file INFO(135398680573760)2025-04-23 14:51:49,930:finished processing per sample fasta files INFO(135398680573760)2025-04-23 14:51:49,930:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1n_17_L001_R1_001.fastq.gz finished INFO(128893682001728)2025-04-23 14:51:50,993:************************* INFO(128893682001728)2025-04-23 14:51:50,994:deblurring started WARNING(128893682001728)2025-04-23 14:51:50,994:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1ee_11_L001_R1_001.fastq.gz WARNING(128893682001728)2025-04-23 14:51:50,994:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1ee_11_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(128893682001728)2025-04-23 14:51:50,995:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(128893682001728)2025-04-23 14:51:50,995:deblur worker thread started INFO(128893682001728)2025-04-23 14:51:50,995:processing per sample fasta files INFO(128893682001728)2025-04-23 14:51:50,995:-------------------------------------------------------- INFO(128893682001728)2025-04-23 14:51:50,995:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1ee_11_L001_R1_001.fastq.gz INFO(123239032973120)2025-04-23 14:52:09,989:deblurring 7234 sequences INFO(136860889409344)2025-04-23 14:52:21,405:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim INFO(136860889409344)2025-04-23 14:52:21,490:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim.derep INFO(136860889409344)2025-04-23 14:52:22,067:total sequences 4668, passing sequences 4668, failing sequences 0 INFO(136860889409344)2025-04-23 14:52:22,067:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(128893682001728)2025-04-23 14:52:30,798:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim INFO(128893682001728)2025-04-23 14:52:30,881:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim.derep INFO(128893682001728)2025-04-23 14:52:31,470:total sequences 3407, passing sequences 3407, failing sequences 0 INFO(128893682001728)2025-04-23 14:52:31,470:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123239032973120)2025-04-23 14:52:41,697:2772 unique sequences left following deblurring INFO(123239032973120)2025-04-23 14:52:41,725:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(128893682001728)2025-04-23 14:52:42,462:deblurring 3407 sequences INFO(123239032973120)2025-04-23 14:52:42,654:finished processing file INFO(123239032973120)2025-04-23 14:52:42,658:finished processing per sample fasta files INFO(123239032973120)2025-04-23 14:52:42,658:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5bb_33_L001_R1_001.fastq.gz finished INFO(136860889409344)2025-04-23 14:52:42,902:deblurring 4668 sequences INFO(138143536674624)2025-04-23 14:52:43,811:************************* INFO(138143536674624)2025-04-23 14:52:43,811:deblurring started WARNING(138143536674624)2025-04-23 14:52:43,811:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5g_40_L001_R1_001.fastq.gz WARNING(138143536674624)2025-04-23 14:52:43,812:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5g_40_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138143536674624)2025-04-23 14:52:43,812:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138143536674624)2025-04-23 14:52:43,812:deblur worker thread started INFO(138143536674624)2025-04-23 14:52:43,812:processing per sample fasta files INFO(138143536674624)2025-04-23 14:52:43,812:-------------------------------------------------------- INFO(138143536674624)2025-04-23 14:52:43,812:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5g_40_L001_R1_001.fastq.gz INFO(128893682001728)2025-04-23 14:52:51,325:1904 unique sequences left following deblurring INFO(128893682001728)2025-04-23 14:52:51,338:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(128893682001728)2025-04-23 14:52:51,882:finished processing file INFO(128893682001728)2025-04-23 14:52:51,884:finished processing per sample fasta files INFO(128893682001728)2025-04-23 14:52:51,884:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1ee_11_L001_R1_001.fastq.gz finished INFO(128239072634688)2025-04-23 14:52:52,913:************************* INFO(128239072634688)2025-04-23 14:52:52,913:deblurring started WARNING(128239072634688)2025-04-23 14:52:52,914:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5n_44_L001_R1_001.fastq.gz WARNING(128239072634688)2025-04-23 14:52:52,914:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5n_44_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(128239072634688)2025-04-23 14:52:52,914:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(128239072634688)2025-04-23 14:52:52,914:deblur worker thread started INFO(128239072634688)2025-04-23 14:52:52,914:processing per sample fasta files INFO(128239072634688)2025-04-23 14:52:52,914:-------------------------------------------------------- INFO(128239072634688)2025-04-23 14:52:52,914:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5n_44_L001_R1_001.fastq.gz INFO(133523533674304)2025-04-23 14:52:56,887:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim INFO(133523533674304)2025-04-23 14:52:57,249:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim.derep INFO(133523533674304)2025-04-23 14:52:58,254:total sequences 12415, passing sequences 12415, failing sequences 0 INFO(133523533674304)2025-04-23 14:52:58,254:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(136860889409344)2025-04-23 14:52:58,477:2324 unique sequences left following deblurring INFO(136860889409344)2025-04-23 14:52:58,514:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(136860889409344)2025-04-23 14:52:59,213:finished processing file INFO(136860889409344)2025-04-23 14:52:59,215:finished processing per sample fasta files INFO(136860889409344)2025-04-23 14:52:59,215:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1t_23_L001_R1_001.fastq.gz finished INFO(129711244711744)2025-04-23 14:53:00,365:************************* INFO(129711244711744)2025-04-23 14:53:00,365:deblurring started WARNING(129711244711744)2025-04-23 14:53:00,366:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1c_6_L001_R1_001.fastq.gz WARNING(129711244711744)2025-04-23 14:53:00,366:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1c_6_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129711244711744)2025-04-23 14:53:00,366:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129711244711744)2025-04-23 14:53:00,366:deblur worker thread started INFO(129711244711744)2025-04-23 14:53:00,366:processing per sample fasta files INFO(129711244711744)2025-04-23 14:53:00,366:-------------------------------------------------------- INFO(129711244711744)2025-04-23 14:53:00,366:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1c_6_L001_R1_001.fastq.gz INFO(138143536674624)2025-04-23 14:53:03,453:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim INFO(138143536674624)2025-04-23 14:53:03,560:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim.derep INFO(138143536674624)2025-04-23 14:53:04,162:total sequences 5221, passing sequences 5221, failing sequences 0 INFO(138143536674624)2025-04-23 14:53:04,163:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(128239072634688)2025-04-23 14:53:12,792:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim INFO(128239072634688)2025-04-23 14:53:12,844:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim.derep INFO(128239072634688)2025-04-23 14:53:13,410:total sequences 2366, passing sequences 2366, failing sequences 0 INFO(128239072634688)2025-04-23 14:53:13,410:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(128239072634688)2025-04-23 14:53:19,421:deblurring 2366 sequences INFO(128239072634688)2025-04-23 14:53:23,486:1270 unique sequences left following deblurring INFO(128239072634688)2025-04-23 14:53:23,505:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(129711244711744)2025-04-23 14:53:23,540:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim INFO(129711244711744)2025-04-23 14:53:23,588:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim.derep INFO(128239072634688)2025-04-23 14:53:24,132:finished processing file INFO(128239072634688)2025-04-23 14:53:24,132:finished processing per sample fasta files INFO(128239072634688)2025-04-23 14:53:24,132:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5n_44_L001_R1_001.fastq.gz finished INFO(129711244711744)2025-04-23 14:53:24,191:total sequences 2341, passing sequences 2341, failing sequences 0 INFO(129711244711744)2025-04-23 14:53:24,191:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(135362046404416)2025-04-23 14:53:25,412:************************* INFO(135362046404416)2025-04-23 14:53:25,412:deblurring started WARNING(135362046404416)2025-04-23 14:53:25,412:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1f_12_L001_R1_001.fastq.gz WARNING(135362046404416)2025-04-23 14:53:25,412:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1f_12_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(135362046404416)2025-04-23 14:53:25,412:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(135362046404416)2025-04-23 14:53:25,413:deblur worker thread started INFO(135362046404416)2025-04-23 14:53:25,413:processing per sample fasta files INFO(135362046404416)2025-04-23 14:53:25,413:-------------------------------------------------------- INFO(135362046404416)2025-04-23 14:53:25,413:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1f_12_L001_R1_001.fastq.gz INFO(138143536674624)2025-04-23 14:53:27,456:deblurring 5221 sequences INFO(129711244711744)2025-04-23 14:53:30,870:deblurring 2341 sequences INFO(129711244711744)2025-04-23 14:53:34,905:1258 unique sequences left following deblurring INFO(129711244711744)2025-04-23 14:53:34,917:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(129711244711744)2025-04-23 14:53:35,307:finished processing file INFO(129711244711744)2025-04-23 14:53:35,308:finished processing per sample fasta files INFO(129711244711744)2025-04-23 14:53:35,308:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1c_6_L001_R1_001.fastq.gz finished INFO(138250698340160)2025-04-23 14:53:36,431:************************* INFO(138250698340160)2025-04-23 14:53:36,431:deblurring started WARNING(138250698340160)2025-04-23 14:53:36,432:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ee_37_L001_R1_001.fastq.gz WARNING(138250698340160)2025-04-23 14:53:36,432:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ee_37_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138250698340160)2025-04-23 14:53:36,432:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138250698340160)2025-04-23 14:53:36,432:deblur worker thread started INFO(138250698340160)2025-04-23 14:53:36,432:processing per sample fasta files INFO(138250698340160)2025-04-23 14:53:36,432:-------------------------------------------------------- INFO(138250698340160)2025-04-23 14:53:36,432:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ee_37_L001_R1_001.fastq.gz INFO(138143536674624)2025-04-23 14:53:44,884:2509 unique sequences left following deblurring INFO(138143536674624)2025-04-23 14:53:44,902:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(138143536674624)2025-04-23 14:53:45,736:finished processing file INFO(138143536674624)2025-04-23 14:53:45,738:finished processing per sample fasta files INFO(138143536674624)2025-04-23 14:53:45,738:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5g_40_L001_R1_001.fastq.gz finished INFO(131827973175104)2025-04-23 14:53:46,922:************************* INFO(131827973175104)2025-04-23 14:53:46,922:deblurring started WARNING(131827973175104)2025-04-23 14:53:46,922:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5r_48_L001_R1_001.fastq.gz WARNING(131827973175104)2025-04-23 14:53:46,922:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5r_48_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(131827973175104)2025-04-23 14:53:46,922:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(131827973175104)2025-04-23 14:53:46,923:deblur worker thread started INFO(131827973175104)2025-04-23 14:53:46,923:processing per sample fasta files INFO(131827973175104)2025-04-23 14:53:46,923:-------------------------------------------------------- INFO(131827973175104)2025-04-23 14:53:46,923:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5r_48_L001_R1_001.fastq.gz INFO(135362046404416)2025-04-23 14:54:18,700:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim INFO(135362046404416)2025-04-23 14:54:18,754:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim.derep INFO(135362046404416)2025-04-23 14:54:19,250:total sequences 1867, passing sequences 1867, failing sequences 0 INFO(135362046404416)2025-04-23 14:54:19,250:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131827973175104)2025-04-23 14:54:22,648:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim INFO(131827973175104)2025-04-23 14:54:22,716:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim.derep INFO(131827973175104)2025-04-23 14:54:23,233:total sequences 2928, passing sequences 2928, failing sequences 0 INFO(131827973175104)2025-04-23 14:54:23,233:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(135362046404416)2025-04-23 14:54:24,050:deblurring 1867 sequences INFO(135362046404416)2025-04-23 14:54:25,439:526 unique sequences left following deblurring INFO(135362046404416)2025-04-23 14:54:25,443:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(135362046404416)2025-04-23 14:54:25,696:finished processing file INFO(135362046404416)2025-04-23 14:54:25,697:finished processing per sample fasta files INFO(135362046404416)2025-04-23 14:54:25,697:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1f_12_L001_R1_001.fastq.gz finished INFO(131827973175104)2025-04-23 14:54:31,593:deblurring 2928 sequences INFO(138250698340160)2025-04-23 14:54:32,991:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim INFO(138250698340160)2025-04-23 14:54:33,060:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim.derep INFO(138250698340160)2025-04-23 14:54:33,573:total sequences 3216, passing sequences 3216, failing sequences 0 INFO(138250698340160)2025-04-23 14:54:33,574:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131827973175104)2025-04-23 14:54:38,763:1667 unique sequences left following deblurring INFO(131827973175104)2025-04-23 14:54:38,776:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(131827973175104)2025-04-23 14:54:39,269:finished processing file INFO(131827973175104)2025-04-23 14:54:39,270:finished processing per sample fasta files INFO(131827973175104)2025-04-23 14:54:39,270:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5r_48_L001_R1_001.fastq.gz finished INFO(127728237328192)2025-04-23 14:54:40,276:************************* INFO(127728237328192)2025-04-23 14:54:40,276:deblurring started WARNING(127728237328192)2025-04-23 14:54:40,277:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1v_24_L001_R1_001.fastq.gz WARNING(127728237328192)2025-04-23 14:54:40,277:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1v_24_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127728237328192)2025-04-23 14:54:40,277:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127728237328192)2025-04-23 14:54:40,277:deblur worker thread started INFO(127728237328192)2025-04-23 14:54:40,277:processing per sample fasta files INFO(127728237328192)2025-04-23 14:54:40,277:-------------------------------------------------------- INFO(127728237328192)2025-04-23 14:54:40,277:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1v_24_L001_R1_001.fastq.gz INFO(138250698340160)2025-04-23 14:54:43,805:deblurring 3216 sequences INFO(138250698340160)2025-04-23 14:54:49,793:1427 unique sequences left following deblurring INFO(138250698340160)2025-04-23 14:54:49,803:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(138250698340160)2025-04-23 14:54:50,150:finished processing file INFO(138250698340160)2025-04-23 14:54:50,151:finished processing per sample fasta files INFO(138250698340160)2025-04-23 14:54:50,152:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5ee_37_L001_R1_001.fastq.gz finished INFO(134530342922048)2025-04-23 14:54:51,161:************************* INFO(134530342922048)2025-04-23 14:54:51,161:deblurring started WARNING(134530342922048)2025-04-23 14:54:51,161:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5p_46_L001_R1_001.fastq.gz WARNING(134530342922048)2025-04-23 14:54:51,161:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5p_46_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134530342922048)2025-04-23 14:54:51,161:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134530342922048)2025-04-23 14:54:51,162:deblur worker thread started INFO(134530342922048)2025-04-23 14:54:51,162:processing per sample fasta files INFO(134530342922048)2025-04-23 14:54:51,162:-------------------------------------------------------- INFO(134530342922048)2025-04-23 14:54:51,162:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5p_46_L001_R1_001.fastq.gz INFO(133523533674304)2025-04-23 14:55:06,542:deblurring 12415 sequences INFO(127728237328192)2025-04-23 14:55:09,445:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim INFO(127728237328192)2025-04-23 14:55:09,496:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim.derep INFO(127728237328192)2025-04-23 14:55:09,988:total sequences 2467, passing sequences 2467, failing sequences 0 INFO(127728237328192)2025-04-23 14:55:09,988:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134530342922048)2025-04-23 14:55:15,143:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim INFO(134530342922048)2025-04-23 14:55:15,196:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim.derep INFO(134530342922048)2025-04-23 14:55:15,743:total sequences 3193, passing sequences 3193, failing sequences 0 INFO(134530342922048)2025-04-23 14:55:15,743:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127728237328192)2025-04-23 14:55:15,976:deblurring 2467 sequences INFO(127728237328192)2025-04-23 14:55:19,725:1239 unique sequences left following deblurring INFO(127728237328192)2025-04-23 14:55:19,733:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(127728237328192)2025-04-23 14:55:20,051:finished processing file INFO(127728237328192)2025-04-23 14:55:20,052:finished processing per sample fasta files INFO(127728237328192)2025-04-23 14:55:20,052:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1v_24_L001_R1_001.fastq.gz finished INFO(134530342922048)2025-04-23 14:55:24,905:deblurring 3193 sequences INFO(134530342922048)2025-04-23 14:55:32,118:2027 unique sequences left following deblurring INFO(134530342922048)2025-04-23 14:55:32,130:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(134530342922048)2025-04-23 14:55:32,681:finished processing file INFO(134530342922048)2025-04-23 14:55:32,682:finished processing per sample fasta files INFO(134530342922048)2025-04-23 14:55:32,682:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5p_46_L001_R1_001.fastq.gz finished INFO(133523533674304)2025-04-23 14:57:06,946:7155 unique sequences left following deblurring INFO(133523533674304)2025-04-23 14:57:07,015:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(133523533674304)2025-04-23 14:57:09,237:finished processing file INFO(133523533674304)2025-04-23 14:57:09,244:finished processing per sample fasta files INFO(133523533674304)2025-04-23 14:57:09,246:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site5z_53_L001_R1_001.fastq.gz finished INFO(124299157862208)2025-04-23 14:57:10,272:************************* INFO(124299157862208)2025-04-23 14:57:10,272:deblurring started WARNING(124299157862208)2025-04-23 14:57:10,273:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1bb_5_L001_R1_001.fastq.gz WARNING(124299157862208)2025-04-23 14:57:10,273:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1bb_5_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp6ycitqez', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp6ycitqez/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124299157862208)2025-04-23 14:57:10,273:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124299157862208)2025-04-23 14:57:10,273:deblur worker thread started INFO(124299157862208)2025-04-23 14:57:10,273:processing per sample fasta files INFO(124299157862208)2025-04-23 14:57:10,273:-------------------------------------------------------- INFO(124299157862208)2025-04-23 14:57:10,273:launch_workflow for file /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1bb_5_L001_R1_001.fastq.gz INFO(124299157862208)2025-04-23 14:57:35,580:dereplicate seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim INFO(124299157862208)2025-04-23 14:57:35,605:remove_artifacts_seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim.derep INFO(124299157862208)2025-04-23 14:57:35,979:total sequences 1030, passing sequences 1030, failing sequences 0 INFO(124299157862208)2025-04-23 14:57:35,979:multiple_sequence_alignment seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124299157862208)2025-04-23 14:57:37,467:deblurring 1030 sequences INFO(124299157862208)2025-04-23 14:57:38,049:506 unique sequences left following deblurring INFO(124299157862208)2025-04-23 14:57:38,052:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp6ycitqez/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp6ycitqez/deblur_working_dir INFO(124299157862208)2025-04-23 14:57:38,164:finished processing file INFO(124299157862208)2025-04-23 14:57:38,165:finished processing per sample fasta files INFO(124299157862208)2025-04-23 14:57:38,165:worker thread for /tmp/qiime2/sam/data/c4819cbf-8c2b-4fcb-8578-70d23647c172/data/Site1bb_5_L001_R1_001.fastq.gz finished INFO(127372641085248)2025-04-23 14:57:38,321:create_otu_table for 52 samples, into output table /tmp/tmp6ycitqez/all.biom INFO(127372641085248)2025-04-23 14:57:40,997:for output biom table loaded 52 samples, 20785 unique sequences INFO(127372641085248)2025-04-23 14:57:41,039:keeping 5670 (out of 20785 sequences) with >=10 reads INFO(127372641085248)2025-04-23 14:57:41,312:saved to biom file /tmp/tmp6ycitqez/all.biom INFO(127372641085248)2025-04-23 14:57:41,319:saved sequence fasta file to /tmp/tmp6ycitqez/all.seqs.fa INFO(127372641085248)2025-04-23 14:57:41,328:getting 16s sequences from the biom table INFO(127372641085248)2025-04-23 14:57:41,328:remove_artifacts_seqs file /tmp/tmp6ycitqez/all.seqs.fa INFO(127372641085248)2025-04-23 14:58:24,178:total sequences 5670, passing sequences 706, failing sequences 4964 INFO(127372641085248)2025-04-23 14:58:24,254:wrote artifact only filtered biom table to /tmp/tmp6ycitqez/reference-non-hit.biom INFO(127372641085248)2025-04-23 14:58:24,260:saved biom table sequences to fasta file /tmp/tmp6ycitqez/reference-non-hit.seqs.fa WARNING(127372641085248)2025-04-23 14:58:24,266:removed 2 samples with reads per sample<1 INFO(127372641085248)2025-04-23 14:58:24,280:wrote 16s filtered biom table to /tmp/tmp6ycitqez/reference-hit.biom INFO(127372641085248)2025-04-23 14:58:24,282:saved biom table sequences to fasta file /tmp/tmp6ycitqez/reference-hit.seqs.fa INFO(127372641085248)2025-04-23 14:58:24,282:Keeping temp files INFO(127372641085248)2025-04-23 14:58:24,282:deblur workflow finished INFO(127372641085248)2025-04-23 14:58:24,282:output saved to /tmp/tmp6ycitqez/all.biom INFO(127372641085248)2025-04-23 14:58:24,282:------------------ INFO(127852991805248)2025-04-23 15:58:30,921:************************* INFO(127852991805248)2025-04-23 15:58:30,922:deblurring started WARNING(127852991805248)2025-04-23 15:58:30,922:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data WARNING(127852991805248)2025-04-23 15:58:30,922:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': (), 'neg_ref_fp': (), 'neg_ref_db_fp': (), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 4, 'is_worker_thread': False, 'logger': } INFO(127852991805248)2025-04-23 15:58:30,922:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127852991805248)2025-04-23 15:58:30,922:deblur main program started INFO(127852991805248)2025-04-23 15:58:30,922:processing directory /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data INFO(127852991805248)2025-04-23 15:58:30,923:building negative db sortmerna index files INFO(127852991805248)2025-04-23 15:58:30,923:build_index_sortmerna files ['/home/sam/programs/miniforge3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/deblur/support_files/artifacts.fa'] to dir /tmp/tmp7pd06scn/deblur_working_dir INFO(127852991805248)2025-04-23 15:58:30,960:building positive db sortmerna index files INFO(127852991805248)2025-04-23 15:58:30,960:build_index_sortmerna files ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',) to dir /tmp/tmp7pd06scn/deblur_working_dir INFO(127852991805248)2025-04-23 17:17:07,790:parallel processing per sample fasta files INFO(127852991805248)2025-04-23 17:17:07,790:parallel deblur started for 54 inputs INFO(125904557569856)2025-04-23 17:17:08,644:************************* INFO(125904557569856)2025-04-23 17:17:08,645:deblurring started WARNING(125904557569856)2025-04-23 17:17:08,645:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1r_21_L001_R1_001.fastq.gz WARNING(125904557569856)2025-04-23 17:17:08,645:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1r_21_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(125904557569856)2025-04-23 17:17:08,645:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(125904557569856)2025-04-23 17:17:08,645:deblur worker thread started INFO(125904557569856)2025-04-23 17:17:08,645:processing per sample fasta files INFO(125904557569856)2025-04-23 17:17:08,645:-------------------------------------------------------- INFO(125904557569856)2025-04-23 17:17:08,645:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1r_21_L001_R1_001.fastq.gz INFO(132029805905728)2025-04-23 17:17:08,672:************************* INFO(132029805905728)2025-04-23 17:17:08,672:deblurring started WARNING(132029805905728)2025-04-23 17:17:08,672:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5aa_31_L001_R1_001.fastq.gz WARNING(132029805905728)2025-04-23 17:17:08,672:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5aa_31_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(132029805905728)2025-04-23 17:17:08,672:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(132029805905728)2025-04-23 17:17:08,673:deblur worker thread started INFO(132029805905728)2025-04-23 17:17:08,673:processing per sample fasta files INFO(132029805905728)2025-04-23 17:17:08,673:-------------------------------------------------------- INFO(132029805905728)2025-04-23 17:17:08,673:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5aa_31_L001_R1_001.fastq.gz INFO(123345197004608)2025-04-23 17:17:08,709:************************* INFO(123345197004608)2025-04-23 17:17:08,709:deblurring started WARNING(123345197004608)2025-04-23 17:17:08,710:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1m_16_L001_R1_001.fastq.gz WARNING(123345197004608)2025-04-23 17:17:08,710:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1m_16_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123345197004608)2025-04-23 17:17:08,710:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123345197004608)2025-04-23 17:17:08,711:deblur worker thread started INFO(123345197004608)2025-04-23 17:17:08,711:processing per sample fasta files INFO(123345197004608)2025-04-23 17:17:08,711:-------------------------------------------------------- INFO(123345197004608)2025-04-23 17:17:08,711:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1m_16_L001_R1_001.fastq.gz INFO(135265047758656)2025-04-23 17:17:08,771:************************* INFO(135265047758656)2025-04-23 17:17:08,771:deblurring started WARNING(135265047758656)2025-04-23 17:17:08,771:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1e_10_L001_R1_001.fastq.gz WARNING(135265047758656)2025-04-23 17:17:08,771:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1e_10_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(135265047758656)2025-04-23 17:17:08,771:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(135265047758656)2025-04-23 17:17:08,771:deblur worker thread started INFO(135265047758656)2025-04-23 17:17:08,771:processing per sample fasta files INFO(135265047758656)2025-04-23 17:17:08,772:-------------------------------------------------------- INFO(135265047758656)2025-04-23 17:17:08,772:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1e_10_L001_R1_001.fastq.gz INFO(135265047758656)2025-04-23 17:17:13,770:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim INFO(135265047758656)2025-04-23 17:17:13,782:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim.derep INFO(135265047758656)2025-04-23 17:17:14,224:total sequences 543, passing sequences 543, failing sequences 0 INFO(135265047758656)2025-04-23 17:17:14,224:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(135265047758656)2025-04-23 17:17:15,146:deblurring 543 sequences INFO(135265047758656)2025-04-23 17:17:15,404:360 unique sequences left following deblurring INFO(135265047758656)2025-04-23 17:17:15,406:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(135265047758656)2025-04-23 17:17:15,487:finished processing file INFO(135265047758656)2025-04-23 17:17:15,487:finished processing per sample fasta files INFO(135265047758656)2025-04-23 17:17:15,487:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1e_10_L001_R1_001.fastq.gz finished INFO(140000881837888)2025-04-23 17:17:16,535:************************* INFO(140000881837888)2025-04-23 17:17:16,535:deblurring started WARNING(140000881837888)2025-04-23 17:17:16,535:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1a_3_L001_R1_001.fastq.gz WARNING(140000881837888)2025-04-23 17:17:16,535:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1a_3_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(140000881837888)2025-04-23 17:17:16,536:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(140000881837888)2025-04-23 17:17:16,536:deblur worker thread started INFO(140000881837888)2025-04-23 17:17:16,536:processing per sample fasta files INFO(140000881837888)2025-04-23 17:17:16,536:-------------------------------------------------------- INFO(140000881837888)2025-04-23 17:17:16,536:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1a_3_L001_R1_001.fastq.gz INFO(125904557569856)2025-04-23 17:17:35,894:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim INFO(125904557569856)2025-04-23 17:17:35,958:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim.derep INFO(125904557569856)2025-04-23 17:17:36,504:total sequences 2945, passing sequences 2945, failing sequences 0 INFO(125904557569856)2025-04-23 17:17:36,505:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123345197004608)2025-04-23 17:17:36,572:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim INFO(123345197004608)2025-04-23 17:17:36,658:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim.derep INFO(123345197004608)2025-04-23 17:17:37,270:total sequences 3401, passing sequences 3401, failing sequences 0 INFO(123345197004608)2025-04-23 17:17:37,270:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(125904557569856)2025-04-23 17:17:45,045:deblurring 2945 sequences INFO(123345197004608)2025-04-23 17:17:48,782:deblurring 3401 sequences INFO(125904557569856)2025-04-23 17:17:50,584:1352 unique sequences left following deblurring INFO(125904557569856)2025-04-23 17:17:50,591:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(125904557569856)2025-04-23 17:17:50,963:finished processing file INFO(125904557569856)2025-04-23 17:17:50,965:finished processing per sample fasta files INFO(125904557569856)2025-04-23 17:17:50,965:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1r_21_L001_R1_001.fastq.gz finished INFO(133221802813248)2025-04-23 17:17:52,026:************************* INFO(133221802813248)2025-04-23 17:17:52,027:deblurring started WARNING(133221802813248)2025-04-23 17:17:52,027:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1p_19_L001_R1_001.fastq.gz WARNING(133221802813248)2025-04-23 17:17:52,027:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1p_19_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133221802813248)2025-04-23 17:17:52,028:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133221802813248)2025-04-23 17:17:52,028:deblur worker thread started INFO(133221802813248)2025-04-23 17:17:52,028:processing per sample fasta files INFO(133221802813248)2025-04-23 17:17:52,028:-------------------------------------------------------- INFO(133221802813248)2025-04-23 17:17:52,028:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1p_19_L001_R1_001.fastq.gz INFO(140000881837888)2025-04-23 17:17:54,093:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim INFO(140000881837888)2025-04-23 17:17:54,137:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim.derep INFO(140000881837888)2025-04-23 17:17:54,861:total sequences 2178, passing sequences 2178, failing sequences 0 INFO(140000881837888)2025-04-23 17:17:54,861:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123345197004608)2025-04-23 17:17:56,509:1726 unique sequences left following deblurring INFO(123345197004608)2025-04-23 17:17:56,522:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(123345197004608)2025-04-23 17:17:57,050:finished processing file INFO(123345197004608)2025-04-23 17:17:57,051:finished processing per sample fasta files INFO(123345197004608)2025-04-23 17:17:57,051:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1m_16_L001_R1_001.fastq.gz finished INFO(138884182091584)2025-04-23 17:17:58,232:************************* INFO(138884182091584)2025-04-23 17:17:58,232:deblurring started WARNING(138884182091584)2025-04-23 17:17:58,233:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5cc_35_L001_R1_001.fastq.gz WARNING(138884182091584)2025-04-23 17:17:58,233:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5cc_35_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138884182091584)2025-04-23 17:17:58,233:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138884182091584)2025-04-23 17:17:58,233:deblur worker thread started INFO(138884182091584)2025-04-23 17:17:58,233:processing per sample fasta files INFO(138884182091584)2025-04-23 17:17:58,233:-------------------------------------------------------- INFO(138884182091584)2025-04-23 17:17:58,233:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5cc_35_L001_R1_001.fastq.gz INFO(132029805905728)2025-04-23 17:18:00,755:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim INFO(140000881837888)2025-04-23 17:18:00,882:deblurring 2178 sequences INFO(132029805905728)2025-04-23 17:18:00,924:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim.derep INFO(132029805905728)2025-04-23 17:18:01,709:total sequences 5700, passing sequences 5700, failing sequences 0 INFO(132029805905728)2025-04-23 17:18:01,709:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(140000881837888)2025-04-23 17:18:04,421:1142 unique sequences left following deblurring INFO(140000881837888)2025-04-23 17:18:04,429:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(140000881837888)2025-04-23 17:18:04,762:finished processing file INFO(140000881837888)2025-04-23 17:18:04,763:finished processing per sample fasta files INFO(140000881837888)2025-04-23 17:18:04,764:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1a_3_L001_R1_001.fastq.gz finished INFO(138633102026560)2025-04-23 17:18:05,855:************************* INFO(138633102026560)2025-04-23 17:18:05,856:deblurring started WARNING(138633102026560)2025-04-23 17:18:05,856:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5s_49_L001_R1_001.fastq.gz WARNING(138633102026560)2025-04-23 17:18:05,856:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5s_49_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138633102026560)2025-04-23 17:18:05,856:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138633102026560)2025-04-23 17:18:05,857:deblur worker thread started INFO(138633102026560)2025-04-23 17:18:05,857:processing per sample fasta files INFO(138633102026560)2025-04-23 17:18:05,857:-------------------------------------------------------- INFO(138633102026560)2025-04-23 17:18:05,857:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5s_49_L001_R1_001.fastq.gz INFO(138633102026560)2025-04-23 17:18:28,583:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim INFO(138633102026560)2025-04-23 17:18:28,635:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim.derep INFO(138633102026560)2025-04-23 17:18:29,220:total sequences 2652, passing sequences 2652, failing sequences 0 INFO(138633102026560)2025-04-23 17:18:29,220:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(132029805905728)2025-04-23 17:18:32,204:deblurring 5700 sequences INFO(138633102026560)2025-04-23 17:18:36,537:deblurring 2652 sequences INFO(138633102026560)2025-04-23 17:18:41,477:1468 unique sequences left following deblurring INFO(138633102026560)2025-04-23 17:18:41,485:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(138633102026560)2025-04-23 17:18:41,921:finished processing file INFO(138633102026560)2025-04-23 17:18:41,922:finished processing per sample fasta files INFO(138633102026560)2025-04-23 17:18:41,922:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5s_49_L001_R1_001.fastq.gz finished INFO(126118829729600)2025-04-23 17:18:43,215:************************* INFO(126118829729600)2025-04-23 17:18:43,215:deblurring started WARNING(126118829729600)2025-04-23 17:18:43,216:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1w_25_L001_R1_001.fastq.gz WARNING(126118829729600)2025-04-23 17:18:43,216:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1w_25_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(126118829729600)2025-04-23 17:18:43,216:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(126118829729600)2025-04-23 17:18:43,216:deblur worker thread started INFO(126118829729600)2025-04-23 17:18:43,217:processing per sample fasta files INFO(126118829729600)2025-04-23 17:18:43,217:-------------------------------------------------------- INFO(126118829729600)2025-04-23 17:18:43,217:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1w_25_L001_R1_001.fastq.gz INFO(132029805905728)2025-04-23 17:18:51,000:2306 unique sequences left following deblurring INFO(132029805905728)2025-04-23 17:18:51,021:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(132029805905728)2025-04-23 17:18:51,672:finished processing file INFO(132029805905728)2025-04-23 17:18:51,674:finished processing per sample fasta files INFO(132029805905728)2025-04-23 17:18:51,674:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5aa_31_L001_R1_001.fastq.gz finished INFO(136195825928000)2025-04-23 17:18:52,775:************************* INFO(136195825928000)2025-04-23 17:18:52,775:deblurring started WARNING(136195825928000)2025-04-23 17:18:52,776:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1cc_7_L001_R1_001.fastq.gz WARNING(136195825928000)2025-04-23 17:18:52,776:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1cc_7_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(136195825928000)2025-04-23 17:18:52,776:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(136195825928000)2025-04-23 17:18:52,776:deblur worker thread started INFO(136195825928000)2025-04-23 17:18:52,776:processing per sample fasta files INFO(136195825928000)2025-04-23 17:18:52,776:-------------------------------------------------------- INFO(136195825928000)2025-04-23 17:18:52,776:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1cc_7_L001_R1_001.fastq.gz INFO(138884182091584)2025-04-23 17:19:15,472:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim INFO(138884182091584)2025-04-23 17:19:15,716:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim.derep INFO(138884182091584)2025-04-23 17:19:16,467:total sequences 7549, passing sequences 7549, failing sequences 0 INFO(138884182091584)2025-04-23 17:19:16,468:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(126118829729600)2025-04-23 17:19:18,727:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim INFO(126118829729600)2025-04-23 17:19:18,799:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim.derep INFO(126118829729600)2025-04-23 17:19:19,374:total sequences 2838, passing sequences 2838, failing sequences 0 INFO(126118829729600)2025-04-23 17:19:19,374:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(126118829729600)2025-04-23 17:19:27,869:deblurring 2838 sequences INFO(126118829729600)2025-04-23 17:19:32,433:1157 unique sequences left following deblurring INFO(126118829729600)2025-04-23 17:19:32,441:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(126118829729600)2025-04-23 17:19:32,751:finished processing file INFO(126118829729600)2025-04-23 17:19:32,752:finished processing per sample fasta files INFO(126118829729600)2025-04-23 17:19:32,752:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1w_25_L001_R1_001.fastq.gz finished INFO(131080645404480)2025-04-23 17:19:33,906:************************* INFO(131080645404480)2025-04-23 17:19:33,906:deblurring started WARNING(131080645404480)2025-04-23 17:19:33,907:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1b_4_L001_R1_001.fastq.gz WARNING(131080645404480)2025-04-23 17:19:33,907:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1b_4_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(131080645404480)2025-04-23 17:19:33,907:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(131080645404480)2025-04-23 17:19:33,907:deblur worker thread started INFO(131080645404480)2025-04-23 17:19:33,907:processing per sample fasta files INFO(131080645404480)2025-04-23 17:19:33,907:-------------------------------------------------------- INFO(131080645404480)2025-04-23 17:19:33,907:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1b_4_L001_R1_001.fastq.gz INFO(136195825928000)2025-04-23 17:19:57,222:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim INFO(136195825928000)2025-04-23 17:19:57,331:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim.derep INFO(136195825928000)2025-04-23 17:19:57,953:total sequences 4718, passing sequences 4718, failing sequences 0 INFO(136195825928000)2025-04-23 17:19:57,954:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131080645404480)2025-04-23 17:20:01,942:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim INFO(131080645404480)2025-04-23 17:20:02,023:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim.derep INFO(131080645404480)2025-04-23 17:20:02,707:total sequences 3405, passing sequences 3405, failing sequences 0 INFO(131080645404480)2025-04-23 17:20:02,710:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(138884182091584)2025-04-23 17:20:10,774:deblurring 7549 sequences INFO(131080645404480)2025-04-23 17:20:14,458:deblurring 3405 sequences INFO(136195825928000)2025-04-23 17:20:20,386:deblurring 4718 sequences INFO(131080645404480)2025-04-23 17:20:23,728:1977 unique sequences left following deblurring INFO(131080645404480)2025-04-23 17:20:23,741:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(131080645404480)2025-04-23 17:20:24,375:finished processing file INFO(131080645404480)2025-04-23 17:20:24,376:finished processing per sample fasta files INFO(131080645404480)2025-04-23 17:20:24,376:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1b_4_L001_R1_001.fastq.gz finished INFO(129603877504832)2025-04-23 17:20:25,492:************************* INFO(129603877504832)2025-04-23 17:20:25,493:deblurring started WARNING(129603877504832)2025-04-23 17:20:25,493:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5v_51_L001_R1_001.fastq.gz WARNING(129603877504832)2025-04-23 17:20:25,494:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5v_51_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129603877504832)2025-04-23 17:20:25,494:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129603877504832)2025-04-23 17:20:25,494:deblur worker thread started INFO(129603877504832)2025-04-23 17:20:25,494:processing per sample fasta files INFO(129603877504832)2025-04-23 17:20:25,494:-------------------------------------------------------- INFO(129603877504832)2025-04-23 17:20:25,494:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5v_51_L001_R1_001.fastq.gz INFO(136195825928000)2025-04-23 17:20:33,836:1864 unique sequences left following deblurring INFO(136195825928000)2025-04-23 17:20:33,855:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(136195825928000)2025-04-23 17:20:34,444:finished processing file INFO(136195825928000)2025-04-23 17:20:34,445:finished processing per sample fasta files INFO(136195825928000)2025-04-23 17:20:34,446:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1cc_7_L001_R1_001.fastq.gz finished INFO(128472716810048)2025-04-23 17:20:35,755:************************* INFO(128472716810048)2025-04-23 17:20:35,755:deblurring started WARNING(128472716810048)2025-04-23 17:20:35,756:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5c_34_L001_R1_001.fastq.gz WARNING(128472716810048)2025-04-23 17:20:35,756:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5c_34_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(128472716810048)2025-04-23 17:20:35,756:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(128472716810048)2025-04-23 17:20:35,756:deblur worker thread started INFO(128472716810048)2025-04-23 17:20:35,757:processing per sample fasta files INFO(128472716810048)2025-04-23 17:20:35,757:-------------------------------------------------------- INFO(128472716810048)2025-04-23 17:20:35,757:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5c_34_L001_R1_001.fastq.gz INFO(129603877504832)2025-04-23 17:20:40,765:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim INFO(129603877504832)2025-04-23 17:20:40,792:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim.derep INFO(129603877504832)2025-04-23 17:20:41,316:total sequences 1168, passing sequences 1168, failing sequences 0 INFO(129603877504832)2025-04-23 17:20:41,316:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(129603877504832)2025-04-23 17:20:43,551:deblurring 1168 sequences INFO(129603877504832)2025-04-23 17:20:44,426:482 unique sequences left following deblurring INFO(129603877504832)2025-04-23 17:20:44,429:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(129603877504832)2025-04-23 17:20:44,548:finished processing file INFO(129603877504832)2025-04-23 17:20:44,549:finished processing per sample fasta files INFO(129603877504832)2025-04-23 17:20:44,549:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5v_51_L001_R1_001.fastq.gz finished INFO(131482683103040)2025-04-23 17:20:45,594:************************* INFO(131482683103040)2025-04-23 17:20:45,594:deblurring started WARNING(131482683103040)2025-04-23 17:20:45,595:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1d_8_L001_R1_001.fastq.gz WARNING(131482683103040)2025-04-23 17:20:45,595:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1d_8_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(131482683103040)2025-04-23 17:20:45,595:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(131482683103040)2025-04-23 17:20:45,595:deblur worker thread started INFO(131482683103040)2025-04-23 17:20:45,595:processing per sample fasta files INFO(131482683103040)2025-04-23 17:20:45,595:-------------------------------------------------------- INFO(131482683103040)2025-04-23 17:20:45,595:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1d_8_L001_R1_001.fastq.gz INFO(128472716810048)2025-04-23 17:20:47,187:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim INFO(138884182091584)2025-04-23 17:20:47,197:2965 unique sequences left following deblurring INFO(128472716810048)2025-04-23 17:20:47,215:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim.derep INFO(138884182091584)2025-04-23 17:20:47,229:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(128472716810048)2025-04-23 17:20:47,753:total sequences 1165, passing sequences 1165, failing sequences 0 INFO(128472716810048)2025-04-23 17:20:47,753:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(138884182091584)2025-04-23 17:20:48,241:finished processing file INFO(138884182091584)2025-04-23 17:20:48,243:finished processing per sample fasta files INFO(138884182091584)2025-04-23 17:20:48,244:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5cc_35_L001_R1_001.fastq.gz finished INFO(137180860254016)2025-04-23 17:20:49,354:************************* INFO(137180860254016)2025-04-23 17:20:49,355:deblurring started WARNING(137180860254016)2025-04-23 17:20:49,355:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5w_52_L001_R1_001.fastq.gz WARNING(137180860254016)2025-04-23 17:20:49,355:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5w_52_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(137180860254016)2025-04-23 17:20:49,355:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(137180860254016)2025-04-23 17:20:49,356:deblur worker thread started INFO(137180860254016)2025-04-23 17:20:49,356:processing per sample fasta files INFO(137180860254016)2025-04-23 17:20:49,356:-------------------------------------------------------- INFO(137180860254016)2025-04-23 17:20:49,356:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5w_52_L001_R1_001.fastq.gz INFO(137180860254016)2025-04-23 17:20:49,363:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5w_52_L001_R1_001.fastq.gz.trim INFO(137180860254016)2025-04-23 17:20:49,369:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5w_52_L001_R1_001.fastq.gz.trim.derep WARNING(137180860254016)2025-04-23 17:20:49,369:file /tmp/tmp7pd06scn/deblur_working_dir/Site5w_52_L001_R1_001.fastq.gz.trim.derep has size 0, continuing WARNING(137180860254016)2025-04-23 17:20:49,369:remove artifacts failed, aborting WARNING(137180860254016)2025-04-23 17:20:49,370:deblurring failed for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5w_52_L001_R1_001.fastq.gz INFO(137180860254016)2025-04-23 17:20:49,370:finished processing per sample fasta files INFO(137180860254016)2025-04-23 17:20:49,370:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5w_52_L001_R1_001.fastq.gz finished INFO(128472716810048)2025-04-23 17:20:50,078:deblurring 1165 sequences INFO(123633495000896)2025-04-23 17:20:50,516:************************* INFO(123633495000896)2025-04-23 17:20:50,516:deblurring started WARNING(123633495000896)2025-04-23 17:20:50,516:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5o_45_L001_R1_001.fastq.gz WARNING(123633495000896)2025-04-23 17:20:50,516:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5o_45_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123633495000896)2025-04-23 17:20:50,516:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123633495000896)2025-04-23 17:20:50,517:deblur worker thread started INFO(123633495000896)2025-04-23 17:20:50,517:processing per sample fasta files INFO(123633495000896)2025-04-23 17:20:50,517:-------------------------------------------------------- INFO(123633495000896)2025-04-23 17:20:50,517:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5o_45_L001_R1_001.fastq.gz INFO(128472716810048)2025-04-23 17:20:51,282:741 unique sequences left following deblurring INFO(128472716810048)2025-04-23 17:20:51,286:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(128472716810048)2025-04-23 17:20:51,486:finished processing file INFO(128472716810048)2025-04-23 17:20:51,487:finished processing per sample fasta files INFO(128472716810048)2025-04-23 17:20:51,487:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5c_34_L001_R1_001.fastq.gz finished INFO(128144113129280)2025-04-23 17:20:52,562:************************* INFO(128144113129280)2025-04-23 17:20:52,562:deblurring started WARNING(128144113129280)2025-04-23 17:20:52,563:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1z_27_L001_R1_001.fastq.gz WARNING(128144113129280)2025-04-23 17:20:52,563:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1z_27_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(128144113129280)2025-04-23 17:20:52,563:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(128144113129280)2025-04-23 17:20:52,563:deblur worker thread started INFO(128144113129280)2025-04-23 17:20:52,563:processing per sample fasta files INFO(128144113129280)2025-04-23 17:20:52,563:-------------------------------------------------------- INFO(128144113129280)2025-04-23 17:20:52,563:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1z_27_L001_R1_001.fastq.gz INFO(133221802813248)2025-04-23 17:21:04,337:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim INFO(133221802813248)2025-04-23 17:21:04,794:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim.derep INFO(133221802813248)2025-04-23 17:21:05,697:total sequences 13856, passing sequences 13856, failing sequences 0 INFO(133221802813248)2025-04-23 17:21:05,697:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123633495000896)2025-04-23 17:21:10,173:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim INFO(123633495000896)2025-04-23 17:21:10,233:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim.derep INFO(123633495000896)2025-04-23 17:21:10,783:total sequences 2487, passing sequences 2487, failing sequences 0 INFO(123633495000896)2025-04-23 17:21:10,784:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131482683103040)2025-04-23 17:21:15,745:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim INFO(131482683103040)2025-04-23 17:21:15,823:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim.derep INFO(131482683103040)2025-04-23 17:21:16,417:total sequences 3526, passing sequences 3526, failing sequences 0 INFO(131482683103040)2025-04-23 17:21:16,417:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123633495000896)2025-04-23 17:21:17,656:deblurring 2487 sequences INFO(128144113129280)2025-04-23 17:21:18,490:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim INFO(128144113129280)2025-04-23 17:21:18,547:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim.derep INFO(128144113129280)2025-04-23 17:21:19,102:total sequences 2092, passing sequences 2092, failing sequences 0 INFO(128144113129280)2025-04-23 17:21:19,102:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123633495000896)2025-04-23 17:21:21,261:939 unique sequences left following deblurring INFO(123633495000896)2025-04-23 17:21:21,267:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(123633495000896)2025-04-23 17:21:21,524:finished processing file INFO(123633495000896)2025-04-23 17:21:21,525:finished processing per sample fasta files INFO(123633495000896)2025-04-23 17:21:21,525:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5o_45_L001_R1_001.fastq.gz finished INFO(125650096244544)2025-04-23 17:21:22,644:************************* INFO(125650096244544)2025-04-23 17:21:22,645:deblurring started WARNING(125650096244544)2025-04-23 17:21:22,645:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1o_18_L001_R1_001.fastq.gz WARNING(125650096244544)2025-04-23 17:21:22,645:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1o_18_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(125650096244544)2025-04-23 17:21:22,645:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(125650096244544)2025-04-23 17:21:22,645:deblur worker thread started INFO(125650096244544)2025-04-23 17:21:22,646:processing per sample fasta files INFO(125650096244544)2025-04-23 17:21:22,646:-------------------------------------------------------- INFO(125650096244544)2025-04-23 17:21:22,646:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1o_18_L001_R1_001.fastq.gz INFO(128144113129280)2025-04-23 17:21:24,507:deblurring 2092 sequences INFO(128144113129280)2025-04-23 17:21:27,248:881 unique sequences left following deblurring INFO(128144113129280)2025-04-23 17:21:27,255:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(128144113129280)2025-04-23 17:21:27,505:finished processing file INFO(128144113129280)2025-04-23 17:21:27,506:finished processing per sample fasta files INFO(128144113129280)2025-04-23 17:21:27,506:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1z_27_L001_R1_001.fastq.gz finished INFO(131482683103040)2025-04-23 17:21:28,592:deblurring 3526 sequences INFO(131704173057856)2025-04-23 17:21:28,639:************************* INFO(131704173057856)2025-04-23 17:21:28,639:deblurring started WARNING(131704173057856)2025-04-23 17:21:28,639:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1s_22_L001_R1_001.fastq.gz WARNING(131704173057856)2025-04-23 17:21:28,640:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1s_22_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(131704173057856)2025-04-23 17:21:28,640:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(131704173057856)2025-04-23 17:21:28,640:deblur worker thread started INFO(131704173057856)2025-04-23 17:21:28,640:processing per sample fasta files INFO(131704173057856)2025-04-23 17:21:28,640:-------------------------------------------------------- INFO(131704173057856)2025-04-23 17:21:28,640:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1s_22_L001_R1_001.fastq.gz INFO(131482683103040)2025-04-23 17:21:37,477:1814 unique sequences left following deblurring INFO(131482683103040)2025-04-23 17:21:37,490:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(131482683103040)2025-04-23 17:21:38,024:finished processing file INFO(131482683103040)2025-04-23 17:21:38,025:finished processing per sample fasta files INFO(131482683103040)2025-04-23 17:21:38,025:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1d_8_L001_R1_001.fastq.gz finished INFO(131867454871360)2025-04-23 17:21:39,245:************************* INFO(131867454871360)2025-04-23 17:21:39,245:deblurring started WARNING(131867454871360)2025-04-23 17:21:39,245:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5m_43_L001_R1_001.fastq.gz WARNING(131867454871360)2025-04-23 17:21:39,245:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5m_43_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(131867454871360)2025-04-23 17:21:39,246:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(131867454871360)2025-04-23 17:21:39,246:deblur worker thread started INFO(131867454871360)2025-04-23 17:21:39,246:processing per sample fasta files INFO(131867454871360)2025-04-23 17:21:39,246:-------------------------------------------------------- INFO(131867454871360)2025-04-23 17:21:39,246:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5m_43_L001_R1_001.fastq.gz INFO(131867454871360)2025-04-23 17:22:00,228:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim INFO(131867454871360)2025-04-23 17:22:00,277:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim.derep INFO(125650096244544)2025-04-23 17:22:00,370:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim INFO(125650096244544)2025-04-23 17:22:00,464:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim.derep INFO(131867454871360)2025-04-23 17:22:00,845:total sequences 2330, passing sequences 2330, failing sequences 0 INFO(131867454871360)2025-04-23 17:22:00,846:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(125650096244544)2025-04-23 17:22:01,120:total sequences 4492, passing sequences 4492, failing sequences 0 INFO(125650096244544)2025-04-23 17:22:01,121:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131704173057856)2025-04-23 17:22:04,801:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim INFO(131704173057856)2025-04-23 17:22:04,907:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim.derep INFO(131704173057856)2025-04-23 17:22:05,603:total sequences 4269, passing sequences 4269, failing sequences 0 INFO(131704173057856)2025-04-23 17:22:05,603:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131867454871360)2025-04-23 17:22:07,084:deblurring 2330 sequences INFO(131867454871360)2025-04-23 17:22:12,043:1445 unique sequences left following deblurring INFO(131867454871360)2025-04-23 17:22:12,052:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(131867454871360)2025-04-23 17:22:12,456:finished processing file INFO(131867454871360)2025-04-23 17:22:12,457:finished processing per sample fasta files INFO(131867454871360)2025-04-23 17:22:12,457:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5m_43_L001_R1_001.fastq.gz finished INFO(137997316335424)2025-04-23 17:22:13,559:************************* INFO(137997316335424)2025-04-23 17:22:13,560:deblurring started WARNING(137997316335424)2025-04-23 17:22:13,560:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5ff_39_L001_R1_001.fastq.gz WARNING(137997316335424)2025-04-23 17:22:13,560:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5ff_39_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(137997316335424)2025-04-23 17:22:13,561:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(137997316335424)2025-04-23 17:22:13,561:deblur worker thread started INFO(137997316335424)2025-04-23 17:22:13,561:processing per sample fasta files INFO(137997316335424)2025-04-23 17:22:13,561:-------------------------------------------------------- INFO(137997316335424)2025-04-23 17:22:13,561:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5ff_39_L001_R1_001.fastq.gz INFO(125650096244544)2025-04-23 17:22:20,246:deblurring 4492 sequences INFO(131704173057856)2025-04-23 17:22:23,073:deblurring 4269 sequences INFO(131704173057856)2025-04-23 17:22:34,717:1982 unique sequences left following deblurring INFO(131704173057856)2025-04-23 17:22:34,731:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(131704173057856)2025-04-23 17:22:35,369:finished processing file INFO(131704173057856)2025-04-23 17:22:35,370:finished processing per sample fasta files INFO(131704173057856)2025-04-23 17:22:35,370:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1s_22_L001_R1_001.fastq.gz finished INFO(125650096244544)2025-04-23 17:22:36,219:2458 unique sequences left following deblurring INFO(125650096244544)2025-04-23 17:22:36,240:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(125345002940224)2025-04-23 17:22:36,482:************************* INFO(125345002940224)2025-04-23 17:22:36,482:deblurring started WARNING(125345002940224)2025-04-23 17:22:36,483:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5f_38_L001_R1_001.fastq.gz WARNING(125345002940224)2025-04-23 17:22:36,483:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5f_38_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(125345002940224)2025-04-23 17:22:36,483:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(125345002940224)2025-04-23 17:22:36,483:deblur worker thread started INFO(125345002940224)2025-04-23 17:22:36,483:processing per sample fasta files INFO(125345002940224)2025-04-23 17:22:36,483:-------------------------------------------------------- INFO(125345002940224)2025-04-23 17:22:36,483:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5f_38_L001_R1_001.fastq.gz INFO(125650096244544)2025-04-23 17:22:37,038:finished processing file INFO(125650096244544)2025-04-23 17:22:37,039:finished processing per sample fasta files INFO(125650096244544)2025-04-23 17:22:37,040:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1o_18_L001_R1_001.fastq.gz finished INFO(125345002940224)2025-04-23 17:22:38,055:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim INFO(125345002940224)2025-04-23 17:22:38,065:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim.derep INFO(130215944988480)2025-04-23 17:22:38,216:************************* INFO(130215944988480)2025-04-23 17:22:38,217:deblurring started WARNING(130215944988480)2025-04-23 17:22:38,217:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5u_50_L001_R1_001.fastq.gz WARNING(130215944988480)2025-04-23 17:22:38,218:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5u_50_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(130215944988480)2025-04-23 17:22:38,218:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(130215944988480)2025-04-23 17:22:38,218:deblur worker thread started INFO(130215944988480)2025-04-23 17:22:38,219:processing per sample fasta files INFO(130215944988480)2025-04-23 17:22:38,219:-------------------------------------------------------- INFO(130215944988480)2025-04-23 17:22:38,220:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5u_50_L001_R1_001.fastq.gz INFO(125345002940224)2025-04-23 17:22:38,559:total sequences 292, passing sequences 292, failing sequences 0 INFO(125345002940224)2025-04-23 17:22:38,559:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(125345002940224)2025-04-23 17:22:41,601:deblurring 292 sequences INFO(125345002940224)2025-04-23 17:22:41,662:152 unique sequences left following deblurring INFO(125345002940224)2025-04-23 17:22:41,663:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(125345002940224)2025-04-23 17:22:41,696:finished processing file INFO(125345002940224)2025-04-23 17:22:41,697:finished processing per sample fasta files INFO(125345002940224)2025-04-23 17:22:41,697:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5f_38_L001_R1_001.fastq.gz finished INFO(124382927382336)2025-04-23 17:22:42,732:************************* INFO(124382927382336)2025-04-23 17:22:42,733:deblurring started WARNING(124382927382336)2025-04-23 17:22:42,733:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1J_0_L001_R1_001.fastq.gz WARNING(124382927382336)2025-04-23 17:22:42,733:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1J_0_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124382927382336)2025-04-23 17:22:42,734:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124382927382336)2025-04-23 17:22:42,734:deblur worker thread started INFO(124382927382336)2025-04-23 17:22:42,734:processing per sample fasta files INFO(124382927382336)2025-04-23 17:22:42,734:-------------------------------------------------------- INFO(124382927382336)2025-04-23 17:22:42,734:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1J_0_L001_R1_001.fastq.gz INFO(124382927382336)2025-04-23 17:22:44,236:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim INFO(124382927382336)2025-04-23 17:22:44,249:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim.derep INFO(124382927382336)2025-04-23 17:22:44,713:total sequences 364, passing sequences 364, failing sequences 0 INFO(124382927382336)2025-04-23 17:22:44,713:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124382927382336)2025-04-23 17:22:49,172:deblurring 364 sequences INFO(124382927382336)2025-04-23 17:22:49,305:293 unique sequences left following deblurring INFO(124382927382336)2025-04-23 17:22:49,306:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(124382927382336)2025-04-23 17:22:49,368:finished processing file INFO(124382927382336)2025-04-23 17:22:49,369:finished processing per sample fasta files INFO(124382927382336)2025-04-23 17:22:49,369:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1J_0_L001_R1_001.fastq.gz finished INFO(136815583885120)2025-04-23 17:22:50,503:************************* INFO(136815583885120)2025-04-23 17:22:50,503:deblurring started WARNING(136815583885120)2025-04-23 17:22:50,504:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1h_14_L001_R1_001.fastq.gz WARNING(136815583885120)2025-04-23 17:22:50,504:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1h_14_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(136815583885120)2025-04-23 17:22:50,504:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(136815583885120)2025-04-23 17:22:50,504:deblur worker thread started INFO(136815583885120)2025-04-23 17:22:50,504:processing per sample fasta files INFO(136815583885120)2025-04-23 17:22:50,505:-------------------------------------------------------- INFO(136815583885120)2025-04-23 17:22:50,505:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1h_14_L001_R1_001.fastq.gz INFO(130215944988480)2025-04-23 17:22:53,744:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim INFO(130215944988480)2025-04-23 17:22:53,787:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim.derep INFO(130215944988480)2025-04-23 17:22:54,347:total sequences 1726, passing sequences 1726, failing sequences 0 INFO(130215944988480)2025-04-23 17:22:54,348:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(130215944988480)2025-04-23 17:22:57,785:deblurring 1726 sequences INFO(130215944988480)2025-04-23 17:22:59,701:904 unique sequences left following deblurring INFO(130215944988480)2025-04-23 17:22:59,707:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(130215944988480)2025-04-23 17:22:59,965:finished processing file INFO(130215944988480)2025-04-23 17:22:59,965:finished processing per sample fasta files INFO(130215944988480)2025-04-23 17:22:59,965:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5u_50_L001_R1_001.fastq.gz finished INFO(127306341181248)2025-04-23 17:23:01,102:************************* INFO(127306341181248)2025-04-23 17:23:01,103:deblurring started WARNING(127306341181248)2025-04-23 17:23:01,103:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5q_47_L001_R1_001.fastq.gz WARNING(127306341181248)2025-04-23 17:23:01,103:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5q_47_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127306341181248)2025-04-23 17:23:01,103:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127306341181248)2025-04-23 17:23:01,104:deblur worker thread started INFO(127306341181248)2025-04-23 17:23:01,104:processing per sample fasta files INFO(127306341181248)2025-04-23 17:23:01,104:-------------------------------------------------------- INFO(127306341181248)2025-04-23 17:23:01,104:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5q_47_L001_R1_001.fastq.gz INFO(136815583885120)2025-04-23 17:23:03,319:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim INFO(136815583885120)2025-04-23 17:23:03,344:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim.derep INFO(136815583885120)2025-04-23 17:23:03,880:total sequences 1031, passing sequences 1031, failing sequences 0 INFO(136815583885120)2025-04-23 17:23:03,880:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(136815583885120)2025-04-23 17:23:05,692:deblurring 1031 sequences INFO(136815583885120)2025-04-23 17:23:06,489:532 unique sequences left following deblurring INFO(136815583885120)2025-04-23 17:23:06,492:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(136815583885120)2025-04-23 17:23:06,626:finished processing file INFO(136815583885120)2025-04-23 17:23:06,626:finished processing per sample fasta files INFO(136815583885120)2025-04-23 17:23:06,627:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1h_14_L001_R1_001.fastq.gz finished INFO(127428005377856)2025-04-23 17:23:07,725:************************* INFO(127428005377856)2025-04-23 17:23:07,726:deblurring started WARNING(127428005377856)2025-04-23 17:23:07,726:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1L_1_L001_R1_001.fastq.gz WARNING(127428005377856)2025-04-23 17:23:07,727:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1L_1_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127428005377856)2025-04-23 17:23:07,727:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127428005377856)2025-04-23 17:23:07,727:deblur worker thread started INFO(127428005377856)2025-04-23 17:23:07,727:processing per sample fasta files INFO(127428005377856)2025-04-23 17:23:07,727:-------------------------------------------------------- INFO(127428005377856)2025-04-23 17:23:07,727:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1L_1_L001_R1_001.fastq.gz INFO(127428005377856)2025-04-23 17:23:16,515:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim INFO(127428005377856)2025-04-23 17:23:16,542:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim.derep INFO(127428005377856)2025-04-23 17:23:17,049:total sequences 1053, passing sequences 1053, failing sequences 0 INFO(127428005377856)2025-04-23 17:23:17,049:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127428005377856)2025-04-23 17:23:18,995:deblurring 1053 sequences INFO(127428005377856)2025-04-23 17:23:19,799:598 unique sequences left following deblurring INFO(127428005377856)2025-04-23 17:23:19,803:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(127428005377856)2025-04-23 17:23:19,961:finished processing file INFO(127428005377856)2025-04-23 17:23:19,962:finished processing per sample fasta files INFO(127428005377856)2025-04-23 17:23:19,962:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1L_1_L001_R1_001.fastq.gz finished INFO(124584640313152)2025-04-23 17:23:21,125:************************* INFO(124584640313152)2025-04-23 17:23:21,126:deblurring started WARNING(124584640313152)2025-04-23 17:23:21,126:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5k_42_L001_R1_001.fastq.gz WARNING(124584640313152)2025-04-23 17:23:21,126:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5k_42_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124584640313152)2025-04-23 17:23:21,126:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124584640313152)2025-04-23 17:23:21,126:deblur worker thread started INFO(124584640313152)2025-04-23 17:23:21,126:processing per sample fasta files INFO(124584640313152)2025-04-23 17:23:21,126:-------------------------------------------------------- INFO(124584640313152)2025-04-23 17:23:21,126:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5k_42_L001_R1_001.fastq.gz INFO(127306341181248)2025-04-23 17:23:29,062:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim INFO(127306341181248)2025-04-23 17:23:29,228:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim.derep INFO(137997316335424)2025-04-23 17:23:29,801:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim INFO(127306341181248)2025-04-23 17:23:29,881:total sequences 6897, passing sequences 6897, failing sequences 0 INFO(127306341181248)2025-04-23 17:23:29,881:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(137997316335424)2025-04-23 17:23:30,007:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim.derep INFO(137997316335424)2025-04-23 17:23:30,758:total sequences 8154, passing sequences 8154, failing sequences 0 INFO(137997316335424)2025-04-23 17:23:30,759:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124584640313152)2025-04-23 17:23:32,143:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim INFO(124584640313152)2025-04-23 17:23:32,172:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim.derep INFO(124584640313152)2025-04-23 17:23:32,694:total sequences 1255, passing sequences 1255, failing sequences 0 INFO(124584640313152)2025-04-23 17:23:32,694:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124584640313152)2025-04-23 17:23:35,174:deblurring 1255 sequences INFO(124584640313152)2025-04-23 17:23:36,555:783 unique sequences left following deblurring INFO(124584640313152)2025-04-23 17:23:36,559:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(124584640313152)2025-04-23 17:23:36,749:finished processing file INFO(124584640313152)2025-04-23 17:23:36,749:finished processing per sample fasta files INFO(124584640313152)2025-04-23 17:23:36,749:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5k_42_L001_R1_001.fastq.gz finished INFO(125424809985856)2025-04-23 17:23:37,974:************************* INFO(125424809985856)2025-04-23 17:23:37,974:deblurring started WARNING(125424809985856)2025-04-23 17:23:37,975:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1dd_9_L001_R1_001.fastq.gz WARNING(125424809985856)2025-04-23 17:23:37,975:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1dd_9_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(125424809985856)2025-04-23 17:23:37,975:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(125424809985856)2025-04-23 17:23:37,975:deblur worker thread started INFO(125424809985856)2025-04-23 17:23:37,975:processing per sample fasta files INFO(125424809985856)2025-04-23 17:23:37,975:-------------------------------------------------------- INFO(125424809985856)2025-04-23 17:23:37,975:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1dd_9_L001_R1_001.fastq.gz INFO(133221802813248)2025-04-23 17:24:13,628:deblurring 13856 sequences INFO(127306341181248)2025-04-23 17:24:14,472:deblurring 6897 sequences INFO(137997316335424)2025-04-23 17:24:34,432:deblurring 8154 sequences INFO(125424809985856)2025-04-23 17:24:39,795:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim INFO(125424809985856)2025-04-23 17:24:39,956:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim.derep INFO(125424809985856)2025-04-23 17:24:40,707:total sequences 5382, passing sequences 5382, failing sequences 0 INFO(125424809985856)2025-04-23 17:24:40,708:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127306341181248)2025-04-23 17:25:05,734:4786 unique sequences left following deblurring INFO(127306341181248)2025-04-23 17:25:05,784:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(127306341181248)2025-04-23 17:25:07,601:finished processing file INFO(127306341181248)2025-04-23 17:25:07,608:finished processing per sample fasta files INFO(127306341181248)2025-04-23 17:25:07,609:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5q_47_L001_R1_001.fastq.gz finished INFO(137492927280960)2025-04-23 17:25:08,923:************************* INFO(137492927280960)2025-04-23 17:25:08,923:deblurring started WARNING(137492927280960)2025-04-23 17:25:08,923:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5h_41_L001_R1_001.fastq.gz WARNING(137492927280960)2025-04-23 17:25:08,924:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5h_41_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(137492927280960)2025-04-23 17:25:08,924:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(137492927280960)2025-04-23 17:25:08,924:deblur worker thread started INFO(137492927280960)2025-04-23 17:25:08,924:processing per sample fasta files INFO(137492927280960)2025-04-23 17:25:08,924:-------------------------------------------------------- INFO(137492927280960)2025-04-23 17:25:08,924:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5h_41_L001_R1_001.fastq.gz INFO(125424809985856)2025-04-23 17:25:10,034:deblurring 5382 sequences INFO(137997316335424)2025-04-23 17:25:15,833:3328 unique sequences left following deblurring INFO(137997316335424)2025-04-23 17:25:15,872:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(137997316335424)2025-04-23 17:25:17,069:finished processing file INFO(137997316335424)2025-04-23 17:25:17,071:finished processing per sample fasta files INFO(137997316335424)2025-04-23 17:25:17,072:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5ff_39_L001_R1_001.fastq.gz finished INFO(132083828160320)2025-04-23 17:25:18,276:************************* INFO(132083828160320)2025-04-23 17:25:18,277:deblurring started WARNING(132083828160320)2025-04-23 17:25:18,277:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1q_20_L001_R1_001.fastq.gz WARNING(132083828160320)2025-04-23 17:25:18,277:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1q_20_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(132083828160320)2025-04-23 17:25:18,277:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(132083828160320)2025-04-23 17:25:18,277:deblur worker thread started INFO(132083828160320)2025-04-23 17:25:18,277:processing per sample fasta files INFO(132083828160320)2025-04-23 17:25:18,277:-------------------------------------------------------- INFO(132083828160320)2025-04-23 17:25:18,277:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1q_20_L001_R1_001.fastq.gz INFO(125424809985856)2025-04-23 17:25:26,211:2050 unique sequences left following deblurring INFO(125424809985856)2025-04-23 17:25:26,229:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(125424809985856)2025-04-23 17:25:26,881:finished processing file INFO(125424809985856)2025-04-23 17:25:26,883:finished processing per sample fasta files INFO(125424809985856)2025-04-23 17:25:26,883:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1dd_9_L001_R1_001.fastq.gz finished INFO(139479262914368)2025-04-23 17:25:28,081:************************* INFO(139479262914368)2025-04-23 17:25:28,083:deblurring started WARNING(139479262914368)2025-04-23 17:25:28,084:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1y_26_L001_R1_001.fastq.gz WARNING(139479262914368)2025-04-23 17:25:28,084:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1y_26_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(139479262914368)2025-04-23 17:25:28,084:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(139479262914368)2025-04-23 17:25:28,084:deblur worker thread started INFO(139479262914368)2025-04-23 17:25:28,084:processing per sample fasta files INFO(139479262914368)2025-04-23 17:25:28,085:-------------------------------------------------------- INFO(139479262914368)2025-04-23 17:25:28,085:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1y_26_L001_R1_001.fastq.gz INFO(133221802813248)2025-04-23 17:25:37,245:3387 unique sequences left following deblurring INFO(133221802813248)2025-04-23 17:25:37,286:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(133221802813248)2025-04-23 17:25:38,468:finished processing file INFO(133221802813248)2025-04-23 17:25:38,471:finished processing per sample fasta files INFO(133221802813248)2025-04-23 17:25:38,471:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1p_19_L001_R1_001.fastq.gz finished INFO(128985470793536)2025-04-23 17:25:39,798:************************* INFO(128985470793536)2025-04-23 17:25:39,798:deblurring started WARNING(128985470793536)2025-04-23 17:25:39,799:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5J_28_L001_R1_001.fastq.gz WARNING(128985470793536)2025-04-23 17:25:39,799:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5J_28_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(128985470793536)2025-04-23 17:25:39,799:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(128985470793536)2025-04-23 17:25:39,799:deblur worker thread started INFO(128985470793536)2025-04-23 17:25:39,799:processing per sample fasta files INFO(128985470793536)2025-04-23 17:25:39,799:-------------------------------------------------------- INFO(128985470793536)2025-04-23 17:25:39,799:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5J_28_L001_R1_001.fastq.gz INFO(128985470793536)2025-04-23 17:25:39,815:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5J_28_L001_R1_001.fastq.gz.trim INFO(128985470793536)2025-04-23 17:25:39,819:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5J_28_L001_R1_001.fastq.gz.trim.derep WARNING(128985470793536)2025-04-23 17:25:39,819:file /tmp/tmp7pd06scn/deblur_working_dir/Site5J_28_L001_R1_001.fastq.gz.trim.derep has size 0, continuing WARNING(128985470793536)2025-04-23 17:25:39,819:remove artifacts failed, aborting WARNING(128985470793536)2025-04-23 17:25:39,819:deblurring failed for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5J_28_L001_R1_001.fastq.gz INFO(128985470793536)2025-04-23 17:25:39,819:finished processing per sample fasta files INFO(128985470793536)2025-04-23 17:25:39,819:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5J_28_L001_R1_001.fastq.gz finished INFO(124407370970944)2025-04-23 17:25:41,014:************************* INFO(124407370970944)2025-04-23 17:25:41,014:deblurring started WARNING(124407370970944)2025-04-23 17:25:41,014:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5L_29_L001_R1_001.fastq.gz WARNING(124407370970944)2025-04-23 17:25:41,014:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5L_29_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124407370970944)2025-04-23 17:25:41,015:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124407370970944)2025-04-23 17:25:41,015:deblur worker thread started INFO(124407370970944)2025-04-23 17:25:41,015:processing per sample fasta files INFO(124407370970944)2025-04-23 17:25:41,015:-------------------------------------------------------- INFO(124407370970944)2025-04-23 17:25:41,015:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5L_29_L001_R1_001.fastq.gz INFO(132083828160320)2025-04-23 17:25:47,696:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim INFO(132083828160320)2025-04-23 17:25:47,722:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim.derep INFO(132083828160320)2025-04-23 17:25:48,416:total sequences 965, passing sequences 965, failing sequences 0 INFO(132083828160320)2025-04-23 17:25:48,416:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(132083828160320)2025-04-23 17:25:50,972:deblurring 965 sequences INFO(132083828160320)2025-04-23 17:25:51,801:536 unique sequences left following deblurring INFO(132083828160320)2025-04-23 17:25:51,804:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(132083828160320)2025-04-23 17:25:51,963:finished processing file INFO(132083828160320)2025-04-23 17:25:51,963:finished processing per sample fasta files INFO(132083828160320)2025-04-23 17:25:51,964:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1q_20_L001_R1_001.fastq.gz finished INFO(136958164571968)2025-04-23 17:25:53,387:************************* INFO(136958164571968)2025-04-23 17:25:53,387:deblurring started WARNING(136958164571968)2025-04-23 17:25:53,388:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5b_32_L001_R1_001.fastq.gz WARNING(136958164571968)2025-04-23 17:25:53,388:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5b_32_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(136958164571968)2025-04-23 17:25:53,388:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(136958164571968)2025-04-23 17:25:53,388:deblur worker thread started INFO(136958164571968)2025-04-23 17:25:53,388:processing per sample fasta files INFO(136958164571968)2025-04-23 17:25:53,388:-------------------------------------------------------- INFO(136958164571968)2025-04-23 17:25:53,388:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5b_32_L001_R1_001.fastq.gz INFO(139479262914368)2025-04-23 17:26:02,341:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim INFO(139479262914368)2025-04-23 17:26:02,468:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim.derep INFO(139479262914368)2025-04-23 17:26:03,245:total sequences 3287, passing sequences 3287, failing sequences 0 INFO(139479262914368)2025-04-23 17:26:03,246:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(139479262914368)2025-04-23 17:26:17,358:deblurring 3287 sequences INFO(139479262914368)2025-04-23 17:26:26,078:1392 unique sequences left following deblurring INFO(139479262914368)2025-04-23 17:26:26,087:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(139479262914368)2025-04-23 17:26:26,700:finished processing file INFO(139479262914368)2025-04-23 17:26:26,701:finished processing per sample fasta files INFO(139479262914368)2025-04-23 17:26:26,701:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1y_26_L001_R1_001.fastq.gz finished INFO(124407370970944)2025-04-23 17:26:26,850:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim INFO(124407370970944)2025-04-23 17:26:26,971:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim.derep INFO(124407370970944)2025-04-23 17:26:27,707:total sequences 3817, passing sequences 3817, failing sequences 0 INFO(124407370970944)2025-04-23 17:26:27,707:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(136336643827520)2025-04-23 17:26:28,202:************************* INFO(136336643827520)2025-04-23 17:26:28,203:deblurring started WARNING(136336643827520)2025-04-23 17:26:28,204:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5e_36_L001_R1_001.fastq.gz WARNING(136336643827520)2025-04-23 17:26:28,204:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5e_36_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(136336643827520)2025-04-23 17:26:28,204:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(136336643827520)2025-04-23 17:26:28,204:deblur worker thread started INFO(136336643827520)2025-04-23 17:26:28,204:processing per sample fasta files INFO(136336643827520)2025-04-23 17:26:28,204:-------------------------------------------------------- INFO(136336643827520)2025-04-23 17:26:28,204:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5e_36_L001_R1_001.fastq.gz INFO(137492927280960)2025-04-23 17:26:32,529:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim INFO(137492927280960)2025-04-23 17:26:32,618:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim.derep INFO(137492927280960)2025-04-23 17:26:33,359:total sequences 1546, passing sequences 1546, failing sequences 0 INFO(137492927280960)2025-04-23 17:26:33,359:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(137492927280960)2025-04-23 17:26:38,804:deblurring 1546 sequences INFO(137492927280960)2025-04-23 17:26:40,426:511 unique sequences left following deblurring INFO(137492927280960)2025-04-23 17:26:40,435:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(137492927280960)2025-04-23 17:26:40,705:finished processing file INFO(137492927280960)2025-04-23 17:26:40,706:finished processing per sample fasta files INFO(137492927280960)2025-04-23 17:26:40,706:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5h_41_L001_R1_001.fastq.gz finished INFO(134768327079744)2025-04-23 17:26:42,382:************************* INFO(134768327079744)2025-04-23 17:26:42,383:deblurring started WARNING(134768327079744)2025-04-23 17:26:42,383:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1g_13_L001_R1_001.fastq.gz WARNING(134768327079744)2025-04-23 17:26:42,383:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1g_13_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134768327079744)2025-04-23 17:26:42,383:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134768327079744)2025-04-23 17:26:42,383:deblur worker thread started INFO(134768327079744)2025-04-23 17:26:42,383:processing per sample fasta files INFO(134768327079744)2025-04-23 17:26:42,383:-------------------------------------------------------- INFO(134768327079744)2025-04-23 17:26:42,383:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1g_13_L001_R1_001.fastq.gz INFO(136958164571968)2025-04-23 17:26:45,478:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim INFO(136958164571968)2025-04-23 17:26:45,557:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim.derep INFO(124407370970944)2025-04-23 17:26:45,999:deblurring 3817 sequences INFO(136958164571968)2025-04-23 17:26:46,249:total sequences 2458, passing sequences 2458, failing sequences 0 INFO(136958164571968)2025-04-23 17:26:46,249:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(136958164571968)2025-04-23 17:26:54,416:deblurring 2458 sequences INFO(136958164571968)2025-04-23 17:26:58,833:1022 unique sequences left following deblurring INFO(136958164571968)2025-04-23 17:26:58,844:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(136958164571968)2025-04-23 17:26:59,263:finished processing file INFO(136958164571968)2025-04-23 17:26:59,264:finished processing per sample fasta files INFO(136958164571968)2025-04-23 17:26:59,266:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5b_32_L001_R1_001.fastq.gz finished INFO(133274237781824)2025-04-23 17:27:00,645:************************* INFO(133274237781824)2025-04-23 17:27:00,645:deblurring started WARNING(133274237781824)2025-04-23 17:27:00,645:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1U_2_L001_R1_001.fastq.gz WARNING(133274237781824)2025-04-23 17:27:00,645:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1U_2_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133274237781824)2025-04-23 17:27:00,645:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133274237781824)2025-04-23 17:27:00,645:deblur worker thread started INFO(133274237781824)2025-04-23 17:27:00,645:processing per sample fasta files INFO(133274237781824)2025-04-23 17:27:00,646:-------------------------------------------------------- INFO(133274237781824)2025-04-23 17:27:00,646:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1U_2_L001_R1_001.fastq.gz INFO(124407370970944)2025-04-23 17:27:00,991:2318 unique sequences left following deblurring INFO(124407370970944)2025-04-23 17:27:01,004:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(124407370970944)2025-04-23 17:27:02,115:finished processing file INFO(124407370970944)2025-04-23 17:27:02,118:finished processing per sample fasta files INFO(124407370970944)2025-04-23 17:27:02,118:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5L_29_L001_R1_001.fastq.gz finished INFO(133876082685760)2025-04-23 17:27:03,729:************************* INFO(133876082685760)2025-04-23 17:27:03,730:deblurring started WARNING(133876082685760)2025-04-23 17:27:03,730:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5bb_33_L001_R1_001.fastq.gz WARNING(133876082685760)2025-04-23 17:27:03,730:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5bb_33_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133876082685760)2025-04-23 17:27:03,730:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133876082685760)2025-04-23 17:27:03,730:deblur worker thread started INFO(133876082685760)2025-04-23 17:27:03,730:processing per sample fasta files INFO(133876082685760)2025-04-23 17:27:03,730:-------------------------------------------------------- INFO(133876082685760)2025-04-23 17:27:03,730:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5bb_33_L001_R1_001.fastq.gz INFO(133274237781824)2025-04-23 17:27:11,615:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim INFO(133274237781824)2025-04-23 17:27:11,672:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim.derep INFO(133274237781824)2025-04-23 17:27:12,610:total sequences 1527, passing sequences 1527, failing sequences 0 INFO(133274237781824)2025-04-23 17:27:12,611:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(133274237781824)2025-04-23 17:27:16,473:deblurring 1527 sequences INFO(133274237781824)2025-04-23 17:27:20,259:1111 unique sequences left following deblurring INFO(133274237781824)2025-04-23 17:27:20,276:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(133274237781824)2025-04-23 17:27:20,721:finished processing file INFO(133274237781824)2025-04-23 17:27:20,721:finished processing per sample fasta files INFO(133274237781824)2025-04-23 17:27:20,722:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1U_2_L001_R1_001.fastq.gz finished INFO(123347009705792)2025-04-23 17:27:22,378:************************* INFO(123347009705792)2025-04-23 17:27:22,378:deblurring started WARNING(123347009705792)2025-04-23 17:27:22,378:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1n_17_L001_R1_001.fastq.gz WARNING(123347009705792)2025-04-23 17:27:22,379:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1n_17_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123347009705792)2025-04-23 17:27:22,379:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123347009705792)2025-04-23 17:27:22,379:deblur worker thread started INFO(123347009705792)2025-04-23 17:27:22,379:processing per sample fasta files INFO(123347009705792)2025-04-23 17:27:22,379:-------------------------------------------------------- INFO(123347009705792)2025-04-23 17:27:22,379:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1n_17_L001_R1_001.fastq.gz INFO(134768327079744)2025-04-23 17:27:34,750:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim INFO(134768327079744)2025-04-23 17:27:34,862:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim.derep INFO(134768327079744)2025-04-23 17:27:35,707:total sequences 3187, passing sequences 3187, failing sequences 0 INFO(134768327079744)2025-04-23 17:27:35,707:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134768327079744)2025-04-23 17:27:48,421:deblurring 3187 sequences INFO(134768327079744)2025-04-23 17:27:53,699:1183 unique sequences left following deblurring INFO(134768327079744)2025-04-23 17:27:53,706:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(134768327079744)2025-04-23 17:27:54,151:finished processing file INFO(134768327079744)2025-04-23 17:27:54,152:finished processing per sample fasta files INFO(134768327079744)2025-04-23 17:27:54,152:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1g_13_L001_R1_001.fastq.gz finished INFO(127969365702464)2025-04-23 17:27:55,430:************************* INFO(127969365702464)2025-04-23 17:27:55,430:deblurring started WARNING(127969365702464)2025-04-23 17:27:55,431:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1k_15_L001_R1_001.fastq.gz WARNING(127969365702464)2025-04-23 17:27:55,431:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1k_15_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127969365702464)2025-04-23 17:27:55,431:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127969365702464)2025-04-23 17:27:55,431:deblur worker thread started INFO(127969365702464)2025-04-23 17:27:55,431:processing per sample fasta files INFO(127969365702464)2025-04-23 17:27:55,432:-------------------------------------------------------- INFO(127969365702464)2025-04-23 17:27:55,432:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1k_15_L001_R1_001.fastq.gz INFO(136336643827520)2025-04-23 17:27:56,270:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim INFO(136336643827520)2025-04-23 17:27:56,429:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim.derep INFO(136336643827520)2025-04-23 17:27:57,074:total sequences 3017, passing sequences 3017, failing sequences 0 INFO(136336643827520)2025-04-23 17:27:57,075:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(136336643827520)2025-04-23 17:28:07,263:deblurring 3017 sequences INFO(136336643827520)2025-04-23 17:28:11,761:999 unique sequences left following deblurring INFO(136336643827520)2025-04-23 17:28:11,769:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(136336643827520)2025-04-23 17:28:12,093:finished processing file INFO(136336643827520)2025-04-23 17:28:12,093:finished processing per sample fasta files INFO(136336643827520)2025-04-23 17:28:12,094:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5e_36_L001_R1_001.fastq.gz finished INFO(139115922859840)2025-04-23 17:28:13,258:************************* INFO(139115922859840)2025-04-23 17:28:13,258:deblurring started WARNING(139115922859840)2025-04-23 17:28:13,258:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5a_30_L001_R1_001.fastq.gz WARNING(139115922859840)2025-04-23 17:28:13,259:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5a_30_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(139115922859840)2025-04-23 17:28:13,259:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(139115922859840)2025-04-23 17:28:13,259:deblur worker thread started INFO(139115922859840)2025-04-23 17:28:13,259:processing per sample fasta files INFO(139115922859840)2025-04-23 17:28:13,259:-------------------------------------------------------- INFO(139115922859840)2025-04-23 17:28:13,259:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5a_30_L001_R1_001.fastq.gz INFO(123347009705792)2025-04-23 17:28:15,315:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim INFO(123347009705792)2025-04-23 17:28:15,427:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim.derep INFO(123347009705792)2025-04-23 17:28:16,175:total sequences 4681, passing sequences 4681, failing sequences 0 INFO(123347009705792)2025-04-23 17:28:16,175:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127969365702464)2025-04-23 17:28:17,679:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim INFO(127969365702464)2025-04-23 17:28:17,742:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim.derep INFO(127969365702464)2025-04-23 17:28:18,317:total sequences 2521, passing sequences 2521, failing sequences 0 INFO(127969365702464)2025-04-23 17:28:18,317:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(127969365702464)2025-04-23 17:28:24,776:deblurring 2521 sequences INFO(127969365702464)2025-04-23 17:28:28,646:1140 unique sequences left following deblurring INFO(127969365702464)2025-04-23 17:28:28,654:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(127969365702464)2025-04-23 17:28:28,984:finished processing file INFO(127969365702464)2025-04-23 17:28:28,985:finished processing per sample fasta files INFO(127969365702464)2025-04-23 17:28:28,985:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1k_15_L001_R1_001.fastq.gz finished INFO(133876082685760)2025-04-23 17:28:29,677:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim INFO(133876082685760)2025-04-23 17:28:29,926:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim.derep INFO(126744653825856)2025-04-23 17:28:30,174:************************* INFO(126744653825856)2025-04-23 17:28:30,175:deblurring started WARNING(126744653825856)2025-04-23 17:28:30,175:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5z_53_L001_R1_001.fastq.gz WARNING(126744653825856)2025-04-23 17:28:30,175:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5z_53_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(126744653825856)2025-04-23 17:28:30,175:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(126744653825856)2025-04-23 17:28:30,175:deblur worker thread started INFO(126744653825856)2025-04-23 17:28:30,176:processing per sample fasta files INFO(126744653825856)2025-04-23 17:28:30,176:-------------------------------------------------------- INFO(126744653825856)2025-04-23 17:28:30,176:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5z_53_L001_R1_001.fastq.gz INFO(133876082685760)2025-04-23 17:28:30,708:total sequences 7234, passing sequences 7234, failing sequences 0 INFO(133876082685760)2025-04-23 17:28:30,708:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123347009705792)2025-04-23 17:28:39,516:deblurring 4681 sequences INFO(139115922859840)2025-04-23 17:28:43,894:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim INFO(139115922859840)2025-04-23 17:28:43,917:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim.derep INFO(139115922859840)2025-04-23 17:28:44,456:total sequences 902, passing sequences 902, failing sequences 0 INFO(139115922859840)2025-04-23 17:28:44,456:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(139115922859840)2025-04-23 17:28:46,259:deblurring 902 sequences INFO(139115922859840)2025-04-23 17:28:46,885:495 unique sequences left following deblurring INFO(139115922859840)2025-04-23 17:28:46,889:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(139115922859840)2025-04-23 17:28:47,012:finished processing file INFO(139115922859840)2025-04-23 17:28:47,013:finished processing per sample fasta files INFO(139115922859840)2025-04-23 17:28:47,013:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5a_30_L001_R1_001.fastq.gz finished INFO(124527352571712)2025-04-23 17:28:48,129:************************* INFO(124527352571712)2025-04-23 17:28:48,129:deblurring started WARNING(124527352571712)2025-04-23 17:28:48,130:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1t_23_L001_R1_001.fastq.gz WARNING(124527352571712)2025-04-23 17:28:48,130:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1t_23_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124527352571712)2025-04-23 17:28:48,130:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124527352571712)2025-04-23 17:28:48,130:deblur worker thread started INFO(124527352571712)2025-04-23 17:28:48,130:processing per sample fasta files INFO(124527352571712)2025-04-23 17:28:48,130:-------------------------------------------------------- INFO(124527352571712)2025-04-23 17:28:48,130:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1t_23_L001_R1_001.fastq.gz INFO(123347009705792)2025-04-23 17:28:55,303:2322 unique sequences left following deblurring INFO(123347009705792)2025-04-23 17:28:55,325:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(123347009705792)2025-04-23 17:28:56,055:finished processing file INFO(123347009705792)2025-04-23 17:28:56,056:finished processing per sample fasta files INFO(123347009705792)2025-04-23 17:28:56,057:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1n_17_L001_R1_001.fastq.gz finished INFO(123518203545408)2025-04-23 17:28:57,266:************************* INFO(123518203545408)2025-04-23 17:28:57,266:deblurring started WARNING(123518203545408)2025-04-23 17:28:57,267:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1ee_11_L001_R1_001.fastq.gz WARNING(123518203545408)2025-04-23 17:28:57,267:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1ee_11_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123518203545408)2025-04-23 17:28:57,267:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123518203545408)2025-04-23 17:28:57,267:deblur worker thread started INFO(123518203545408)2025-04-23 17:28:57,267:processing per sample fasta files INFO(123518203545408)2025-04-23 17:28:57,268:-------------------------------------------------------- INFO(123518203545408)2025-04-23 17:28:57,268:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1ee_11_L001_R1_001.fastq.gz INFO(133876082685760)2025-04-23 17:29:22,196:deblurring 7234 sequences INFO(124527352571712)2025-04-23 17:29:25,832:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim INFO(124527352571712)2025-04-23 17:29:25,918:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim.derep INFO(124527352571712)2025-04-23 17:29:26,512:total sequences 4668, passing sequences 4668, failing sequences 0 INFO(124527352571712)2025-04-23 17:29:26,512:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123518203545408)2025-04-23 17:29:38,099:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim INFO(123518203545408)2025-04-23 17:29:38,173:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim.derep INFO(123518203545408)2025-04-23 17:29:38,745:total sequences 3407, passing sequences 3407, failing sequences 0 INFO(123518203545408)2025-04-23 17:29:38,745:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124527352571712)2025-04-23 17:29:46,020:deblurring 4668 sequences INFO(123518203545408)2025-04-23 17:29:49,134:deblurring 3407 sequences INFO(133876082685760)2025-04-23 17:29:52,373:2772 unique sequences left following deblurring INFO(133876082685760)2025-04-23 17:29:52,403:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(133876082685760)2025-04-23 17:29:53,258:finished processing file INFO(133876082685760)2025-04-23 17:29:53,260:finished processing per sample fasta files INFO(133876082685760)2025-04-23 17:29:53,261:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5bb_33_L001_R1_001.fastq.gz finished INFO(134997626480448)2025-04-23 17:29:54,269:************************* INFO(134997626480448)2025-04-23 17:29:54,269:deblurring started WARNING(134997626480448)2025-04-23 17:29:54,270:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5g_40_L001_R1_001.fastq.gz WARNING(134997626480448)2025-04-23 17:29:54,270:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5g_40_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134997626480448)2025-04-23 17:29:54,270:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134997626480448)2025-04-23 17:29:54,270:deblur worker thread started INFO(134997626480448)2025-04-23 17:29:54,270:processing per sample fasta files INFO(134997626480448)2025-04-23 17:29:54,270:-------------------------------------------------------- INFO(134997626480448)2025-04-23 17:29:54,270:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5g_40_L001_R1_001.fastq.gz INFO(123518203545408)2025-04-23 17:29:57,447:1904 unique sequences left following deblurring INFO(123518203545408)2025-04-23 17:29:57,459:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(123518203545408)2025-04-23 17:29:58,003:finished processing file INFO(123518203545408)2025-04-23 17:29:58,004:finished processing per sample fasta files INFO(123518203545408)2025-04-23 17:29:58,004:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1ee_11_L001_R1_001.fastq.gz finished INFO(131553108268864)2025-04-23 17:29:59,032:************************* INFO(131553108268864)2025-04-23 17:29:59,033:deblurring started WARNING(131553108268864)2025-04-23 17:29:59,034:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5n_44_L001_R1_001.fastq.gz WARNING(131553108268864)2025-04-23 17:29:59,034:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5n_44_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(131553108268864)2025-04-23 17:29:59,034:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(131553108268864)2025-04-23 17:29:59,034:deblur worker thread started INFO(131553108268864)2025-04-23 17:29:59,035:processing per sample fasta files INFO(131553108268864)2025-04-23 17:29:59,035:-------------------------------------------------------- INFO(131553108268864)2025-04-23 17:29:59,036:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5n_44_L001_R1_001.fastq.gz INFO(124527352571712)2025-04-23 17:29:59,882:2324 unique sequences left following deblurring INFO(124527352571712)2025-04-23 17:29:59,899:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(124527352571712)2025-04-23 17:30:00,600:finished processing file INFO(124527352571712)2025-04-23 17:30:00,601:finished processing per sample fasta files INFO(124527352571712)2025-04-23 17:30:00,601:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1t_23_L001_R1_001.fastq.gz finished INFO(129565663840064)2025-04-23 17:30:01,610:************************* INFO(129565663840064)2025-04-23 17:30:01,610:deblurring started WARNING(129565663840064)2025-04-23 17:30:01,611:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1c_6_L001_R1_001.fastq.gz WARNING(129565663840064)2025-04-23 17:30:01,611:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1c_6_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129565663840064)2025-04-23 17:30:01,611:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129565663840064)2025-04-23 17:30:01,611:deblur worker thread started INFO(129565663840064)2025-04-23 17:30:01,611:processing per sample fasta files INFO(129565663840064)2025-04-23 17:30:01,612:-------------------------------------------------------- INFO(129565663840064)2025-04-23 17:30:01,612:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1c_6_L001_R1_001.fastq.gz INFO(126744653825856)2025-04-23 17:30:06,626:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim INFO(126744653825856)2025-04-23 17:30:06,965:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim.derep INFO(126744653825856)2025-04-23 17:30:07,748:total sequences 12415, passing sequences 12415, failing sequences 0 INFO(126744653825856)2025-04-23 17:30:07,748:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134997626480448)2025-04-23 17:30:12,085:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim INFO(134997626480448)2025-04-23 17:30:12,180:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim.derep INFO(134997626480448)2025-04-23 17:30:12,729:total sequences 5221, passing sequences 5221, failing sequences 0 INFO(134997626480448)2025-04-23 17:30:12,729:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131553108268864)2025-04-23 17:30:18,466:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim INFO(131553108268864)2025-04-23 17:30:18,513:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim.derep INFO(131553108268864)2025-04-23 17:30:19,025:total sequences 2366, passing sequences 2366, failing sequences 0 INFO(131553108268864)2025-04-23 17:30:19,026:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(129565663840064)2025-04-23 17:30:23,420:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim INFO(129565663840064)2025-04-23 17:30:23,468:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim.derep INFO(129565663840064)2025-04-23 17:30:23,981:total sequences 2341, passing sequences 2341, failing sequences 0 INFO(129565663840064)2025-04-23 17:30:23,981:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131553108268864)2025-04-23 17:30:24,918:deblurring 2366 sequences INFO(131553108268864)2025-04-23 17:30:28,802:1270 unique sequences left following deblurring INFO(131553108268864)2025-04-23 17:30:28,813:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(131553108268864)2025-04-23 17:30:29,133:finished processing file INFO(131553108268864)2025-04-23 17:30:29,134:finished processing per sample fasta files INFO(131553108268864)2025-04-23 17:30:29,134:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5n_44_L001_R1_001.fastq.gz finished INFO(129565663840064)2025-04-23 17:30:29,662:deblurring 2341 sequences INFO(134003263326016)2025-04-23 17:30:30,223:************************* INFO(134003263326016)2025-04-23 17:30:30,223:deblurring started WARNING(134003263326016)2025-04-23 17:30:30,224:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1f_12_L001_R1_001.fastq.gz WARNING(134003263326016)2025-04-23 17:30:30,224:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1f_12_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134003263326016)2025-04-23 17:30:30,224:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134003263326016)2025-04-23 17:30:30,224:deblur worker thread started INFO(134003263326016)2025-04-23 17:30:30,224:processing per sample fasta files INFO(134003263326016)2025-04-23 17:30:30,225:-------------------------------------------------------- INFO(134003263326016)2025-04-23 17:30:30,225:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1f_12_L001_R1_001.fastq.gz INFO(129565663840064)2025-04-23 17:30:33,276:1258 unique sequences left following deblurring INFO(129565663840064)2025-04-23 17:30:33,285:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(129565663840064)2025-04-23 17:30:33,634:finished processing file INFO(129565663840064)2025-04-23 17:30:33,634:finished processing per sample fasta files INFO(129565663840064)2025-04-23 17:30:33,635:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1c_6_L001_R1_001.fastq.gz finished INFO(134967693526848)2025-04-23 17:30:34,722:************************* INFO(134967693526848)2025-04-23 17:30:34,722:deblurring started WARNING(134967693526848)2025-04-23 17:30:34,723:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5ee_37_L001_R1_001.fastq.gz WARNING(134967693526848)2025-04-23 17:30:34,723:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5ee_37_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134967693526848)2025-04-23 17:30:34,723:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134967693526848)2025-04-23 17:30:34,724:deblur worker thread started INFO(134967693526848)2025-04-23 17:30:34,724:processing per sample fasta files INFO(134967693526848)2025-04-23 17:30:34,724:-------------------------------------------------------- INFO(134967693526848)2025-04-23 17:30:34,724:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5ee_37_L001_R1_001.fastq.gz INFO(134997626480448)2025-04-23 17:30:35,184:deblurring 5221 sequences INFO(134997626480448)2025-04-23 17:30:52,537:2509 unique sequences left following deblurring INFO(134997626480448)2025-04-23 17:30:52,553:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(134997626480448)2025-04-23 17:30:53,288:finished processing file INFO(134997626480448)2025-04-23 17:30:53,289:finished processing per sample fasta files INFO(134997626480448)2025-04-23 17:30:53,290:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5g_40_L001_R1_001.fastq.gz finished INFO(133502781634368)2025-04-23 17:30:54,318:************************* INFO(133502781634368)2025-04-23 17:30:54,318:deblurring started WARNING(133502781634368)2025-04-23 17:30:54,318:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5r_48_L001_R1_001.fastq.gz WARNING(133502781634368)2025-04-23 17:30:54,319:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5r_48_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133502781634368)2025-04-23 17:30:54,319:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133502781634368)2025-04-23 17:30:54,319:deblur worker thread started INFO(133502781634368)2025-04-23 17:30:54,319:processing per sample fasta files INFO(133502781634368)2025-04-23 17:30:54,319:-------------------------------------------------------- INFO(133502781634368)2025-04-23 17:30:54,319:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5r_48_L001_R1_001.fastq.gz INFO(134003263326016)2025-04-23 17:31:18,082:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim INFO(134003263326016)2025-04-23 17:31:18,138:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim.derep INFO(134003263326016)2025-04-23 17:31:18,625:total sequences 1867, passing sequences 1867, failing sequences 0 INFO(134003263326016)2025-04-23 17:31:18,626:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134003263326016)2025-04-23 17:31:22,948:deblurring 1867 sequences INFO(134003263326016)2025-04-23 17:31:24,222:526 unique sequences left following deblurring INFO(134003263326016)2025-04-23 17:31:24,226:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(134003263326016)2025-04-23 17:31:24,407:finished processing file INFO(134003263326016)2025-04-23 17:31:24,408:finished processing per sample fasta files INFO(134003263326016)2025-04-23 17:31:24,408:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1f_12_L001_R1_001.fastq.gz finished INFO(133502781634368)2025-04-23 17:31:27,430:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim INFO(133502781634368)2025-04-23 17:31:27,491:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim.derep INFO(133502781634368)2025-04-23 17:31:27,955:total sequences 2928, passing sequences 2928, failing sequences 0 INFO(133502781634368)2025-04-23 17:31:27,955:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134967693526848)2025-04-23 17:31:28,997:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim INFO(134967693526848)2025-04-23 17:31:29,061:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim.derep INFO(134967693526848)2025-04-23 17:31:29,584:total sequences 3216, passing sequences 3216, failing sequences 0 INFO(134967693526848)2025-04-23 17:31:29,584:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(133502781634368)2025-04-23 17:31:35,770:deblurring 2928 sequences INFO(134967693526848)2025-04-23 17:31:38,628:deblurring 3216 sequences INFO(133502781634368)2025-04-23 17:31:41,502:1667 unique sequences left following deblurring INFO(133502781634368)2025-04-23 17:31:41,514:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(133502781634368)2025-04-23 17:31:41,936:finished processing file INFO(133502781634368)2025-04-23 17:31:41,937:finished processing per sample fasta files INFO(133502781634368)2025-04-23 17:31:41,937:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5r_48_L001_R1_001.fastq.gz finished INFO(136901772511040)2025-04-23 17:31:42,920:************************* INFO(136901772511040)2025-04-23 17:31:42,920:deblurring started WARNING(136901772511040)2025-04-23 17:31:42,920:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1v_24_L001_R1_001.fastq.gz WARNING(136901772511040)2025-04-23 17:31:42,921:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1v_24_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(136901772511040)2025-04-23 17:31:42,921:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(136901772511040)2025-04-23 17:31:42,921:deblur worker thread started INFO(136901772511040)2025-04-23 17:31:42,921:processing per sample fasta files INFO(136901772511040)2025-04-23 17:31:42,921:-------------------------------------------------------- INFO(136901772511040)2025-04-23 17:31:42,921:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1v_24_L001_R1_001.fastq.gz INFO(134967693526848)2025-04-23 17:31:44,174:1427 unique sequences left following deblurring INFO(134967693526848)2025-04-23 17:31:44,184:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(134967693526848)2025-04-23 17:31:44,531:finished processing file INFO(134967693526848)2025-04-23 17:31:44,532:finished processing per sample fasta files INFO(134967693526848)2025-04-23 17:31:44,532:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5ee_37_L001_R1_001.fastq.gz finished INFO(133079341619008)2025-04-23 17:31:45,480:************************* INFO(133079341619008)2025-04-23 17:31:45,481:deblurring started WARNING(133079341619008)2025-04-23 17:31:45,481:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5p_46_L001_R1_001.fastq.gz WARNING(133079341619008)2025-04-23 17:31:45,481:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5p_46_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133079341619008)2025-04-23 17:31:45,481:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133079341619008)2025-04-23 17:31:45,481:deblur worker thread started INFO(133079341619008)2025-04-23 17:31:45,481:processing per sample fasta files INFO(133079341619008)2025-04-23 17:31:45,481:-------------------------------------------------------- INFO(133079341619008)2025-04-23 17:31:45,481:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5p_46_L001_R1_001.fastq.gz INFO(126744653825856)2025-04-23 17:32:06,134:deblurring 12415 sequences INFO(133079341619008)2025-04-23 17:32:08,167:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim INFO(133079341619008)2025-04-23 17:32:08,216:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim.derep INFO(133079341619008)2025-04-23 17:32:08,731:total sequences 3193, passing sequences 3193, failing sequences 0 INFO(133079341619008)2025-04-23 17:32:08,732:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(136901772511040)2025-04-23 17:32:10,761:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim INFO(136901772511040)2025-04-23 17:32:10,806:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim.derep INFO(136901772511040)2025-04-23 17:32:11,247:total sequences 2467, passing sequences 2467, failing sequences 0 INFO(136901772511040)2025-04-23 17:32:11,247:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(136901772511040)2025-04-23 17:32:16,953:deblurring 2467 sequences INFO(133079341619008)2025-04-23 17:32:17,468:deblurring 3193 sequences INFO(136901772511040)2025-04-23 17:32:20,527:1239 unique sequences left following deblurring INFO(136901772511040)2025-04-23 17:32:20,535:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(136901772511040)2025-04-23 17:32:20,856:finished processing file INFO(136901772511040)2025-04-23 17:32:20,857:finished processing per sample fasta files INFO(136901772511040)2025-04-23 17:32:20,857:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1v_24_L001_R1_001.fastq.gz finished INFO(133079341619008)2025-04-23 17:32:24,846:2027 unique sequences left following deblurring INFO(133079341619008)2025-04-23 17:32:24,858:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(133079341619008)2025-04-23 17:32:25,387:finished processing file INFO(133079341619008)2025-04-23 17:32:25,388:finished processing per sample fasta files INFO(133079341619008)2025-04-23 17:32:25,388:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5p_46_L001_R1_001.fastq.gz finished INFO(126744653825856)2025-04-23 17:33:50,591:7155 unique sequences left following deblurring INFO(126744653825856)2025-04-23 17:33:50,646:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(126744653825856)2025-04-23 17:33:52,697:finished processing file INFO(126744653825856)2025-04-23 17:33:52,701:finished processing per sample fasta files INFO(126744653825856)2025-04-23 17:33:52,701:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site5z_53_L001_R1_001.fastq.gz finished INFO(123300769777472)2025-04-23 17:33:53,482:************************* INFO(123300769777472)2025-04-23 17:33:53,482:deblurring started WARNING(123300769777472)2025-04-23 17:33:53,483:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1bb_5_L001_R1_001.fastq.gz WARNING(123300769777472)2025-04-23 17:33:53,483:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1bb_5_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmp7pd06scn', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmp7pd06scn/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123300769777472)2025-04-23 17:33:53,483:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123300769777472)2025-04-23 17:33:53,483:deblur worker thread started INFO(123300769777472)2025-04-23 17:33:53,483:processing per sample fasta files INFO(123300769777472)2025-04-23 17:33:53,483:-------------------------------------------------------- INFO(123300769777472)2025-04-23 17:33:53,483:launch_workflow for file /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1bb_5_L001_R1_001.fastq.gz INFO(123300769777472)2025-04-23 17:34:15,080:dereplicate seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim INFO(123300769777472)2025-04-23 17:34:15,104:remove_artifacts_seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim.derep INFO(123300769777472)2025-04-23 17:34:15,493:total sequences 1030, passing sequences 1030, failing sequences 0 INFO(123300769777472)2025-04-23 17:34:15,493:multiple_sequence_alignment seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123300769777472)2025-04-23 17:34:16,938:deblurring 1030 sequences INFO(123300769777472)2025-04-23 17:34:17,498:506 unique sequences left following deblurring INFO(123300769777472)2025-04-23 17:34:17,500:remove_chimeras_denovo_from_seqs seqs file /tmp/tmp7pd06scn/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmp7pd06scn/deblur_working_dir INFO(123300769777472)2025-04-23 17:34:17,613:finished processing file INFO(123300769777472)2025-04-23 17:34:17,613:finished processing per sample fasta files INFO(123300769777472)2025-04-23 17:34:17,613:worker thread for /tmp/qiime2/sam/data/041e2329-191c-4ec0-8faa-6291ed03a117/data/Site1bb_5_L001_R1_001.fastq.gz finished INFO(127852991805248)2025-04-23 17:34:17,790:create_otu_table for 52 samples, into output table /tmp/tmp7pd06scn/all.biom INFO(127852991805248)2025-04-23 17:34:20,387:for output biom table loaded 52 samples, 20785 unique sequences INFO(127852991805248)2025-04-23 17:34:20,418:keeping 5670 (out of 20785 sequences) with >=10 reads INFO(127852991805248)2025-04-23 17:34:20,592:saved to biom file /tmp/tmp7pd06scn/all.biom INFO(127852991805248)2025-04-23 17:34:20,597:saved sequence fasta file to /tmp/tmp7pd06scn/all.seqs.fa INFO(127852991805248)2025-04-23 17:34:20,601:getting 16s sequences from the biom table INFO(127852991805248)2025-04-23 17:34:20,602:remove_artifacts_seqs file /tmp/tmp7pd06scn/all.seqs.fa INFO(127852991805248)2025-04-23 17:34:57,076:total sequences 5670, passing sequences 706, failing sequences 4964 INFO(127852991805248)2025-04-23 17:34:57,136:wrote artifact only filtered biom table to /tmp/tmp7pd06scn/reference-non-hit.biom INFO(127852991805248)2025-04-23 17:34:57,142:saved biom table sequences to fasta file /tmp/tmp7pd06scn/reference-non-hit.seqs.fa WARNING(127852991805248)2025-04-23 17:34:57,146:removed 2 samples with reads per sample<1 INFO(127852991805248)2025-04-23 17:34:57,154:wrote 16s filtered biom table to /tmp/tmp7pd06scn/reference-hit.biom INFO(127852991805248)2025-04-23 17:34:57,155:saved biom table sequences to fasta file /tmp/tmp7pd06scn/reference-hit.seqs.fa INFO(127852991805248)2025-04-23 17:34:57,155:Keeping temp files INFO(127852991805248)2025-04-23 17:34:57,156:deblur workflow finished INFO(127852991805248)2025-04-23 17:34:57,156:output saved to /tmp/tmp7pd06scn/all.biom INFO(127852991805248)2025-04-23 17:34:57,156:------------------ INFO(124786264745792)2025-04-24 08:12:27,394:************************* INFO(124786264745792)2025-04-24 08:12:27,395:deblurring started WARNING(124786264745792)2025-04-24 08:12:27,395:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data WARNING(124786264745792)2025-04-24 08:12:27,395:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': (), 'neg_ref_fp': (), 'neg_ref_db_fp': (), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 4, 'is_worker_thread': False, 'logger': } INFO(124786264745792)2025-04-24 08:12:27,395:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124786264745792)2025-04-24 08:12:27,395:deblur main program started INFO(124786264745792)2025-04-24 08:12:27,396:processing directory /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data INFO(124786264745792)2025-04-24 08:12:27,397:building negative db sortmerna index files INFO(124786264745792)2025-04-24 08:12:27,397:build_index_sortmerna files ['/home/sam/programs/miniforge3/envs/qiime2-amplicon-2024.10/lib/python3.10/site-packages/deblur/support_files/artifacts.fa'] to dir /tmp/tmpc40oidxs/deblur_working_dir INFO(124786264745792)2025-04-24 08:12:27,440:building positive db sortmerna index files INFO(124786264745792)2025-04-24 08:12:27,440:build_index_sortmerna files ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',) to dir /tmp/tmpc40oidxs/deblur_working_dir INFO(124786264745792)2025-04-24 09:29:56,898:parallel processing per sample fasta files INFO(124786264745792)2025-04-24 09:29:56,898:parallel deblur started for 54 inputs INFO(126771576620864)2025-04-24 09:29:57,825:************************* INFO(126771576620864)2025-04-24 09:29:57,826:deblurring started WARNING(126771576620864)2025-04-24 09:29:57,826:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5aa_31_L001_R1_001.fastq.gz WARNING(126771576620864)2025-04-24 09:29:57,826:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5aa_31_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(126771576620864)2025-04-24 09:29:57,826:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(126771576620864)2025-04-24 09:29:57,826:deblur worker thread started INFO(126771576620864)2025-04-24 09:29:57,826:processing per sample fasta files INFO(126771576620864)2025-04-24 09:29:57,826:-------------------------------------------------------- INFO(126771576620864)2025-04-24 09:29:57,827:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5aa_31_L001_R1_001.fastq.gz INFO(126556384212800)2025-04-24 09:29:57,834:************************* INFO(126556384212800)2025-04-24 09:29:57,834:deblurring started INFO(139213418084160)2025-04-24 09:29:57,834:************************* INFO(139213418084160)2025-04-24 09:29:57,834:deblurring started WARNING(139213418084160)2025-04-24 09:29:57,834:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1r_21_L001_R1_001.fastq.gz WARNING(139213418084160)2025-04-24 09:29:57,835:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1r_21_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(139213418084160)2025-04-24 09:29:57,835:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(139213418084160)2025-04-24 09:29:57,835:deblur worker thread started INFO(139213418084160)2025-04-24 09:29:57,835:processing per sample fasta files INFO(139213418084160)2025-04-24 09:29:57,835:-------------------------------------------------------- INFO(139213418084160)2025-04-24 09:29:57,835:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1r_21_L001_R1_001.fastq.gz WARNING(126556384212800)2025-04-24 09:29:57,836:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1m_16_L001_R1_001.fastq.gz WARNING(126556384212800)2025-04-24 09:29:57,836:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1m_16_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(126556384212800)2025-04-24 09:29:57,836:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(126556384212800)2025-04-24 09:29:57,836:deblur worker thread started INFO(126556384212800)2025-04-24 09:29:57,836:processing per sample fasta files INFO(126556384212800)2025-04-24 09:29:57,836:-------------------------------------------------------- INFO(126556384212800)2025-04-24 09:29:57,836:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1m_16_L001_R1_001.fastq.gz INFO(130950116775744)2025-04-24 09:29:57,840:************************* INFO(130950116775744)2025-04-24 09:29:57,840:deblurring started WARNING(130950116775744)2025-04-24 09:29:57,840:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1e_10_L001_R1_001.fastq.gz WARNING(130950116775744)2025-04-24 09:29:57,840:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1e_10_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(130950116775744)2025-04-24 09:29:57,841:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(130950116775744)2025-04-24 09:29:57,841:deblur worker thread started INFO(130950116775744)2025-04-24 09:29:57,841:processing per sample fasta files INFO(130950116775744)2025-04-24 09:29:57,841:-------------------------------------------------------- INFO(130950116775744)2025-04-24 09:29:57,841:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1e_10_L001_R1_001.fastq.gz INFO(130950116775744)2025-04-24 09:30:02,648:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim INFO(130950116775744)2025-04-24 09:30:02,665:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim.derep INFO(130950116775744)2025-04-24 09:30:03,139:total sequences 543, passing sequences 543, failing sequences 0 INFO(130950116775744)2025-04-24 09:30:03,140:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(130950116775744)2025-04-24 09:30:04,080:deblurring 543 sequences INFO(130950116775744)2025-04-24 09:30:04,329:360 unique sequences left following deblurring INFO(130950116775744)2025-04-24 09:30:04,331:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1e_10_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(130950116775744)2025-04-24 09:30:04,413:finished processing file INFO(130950116775744)2025-04-24 09:30:04,414:finished processing per sample fasta files INFO(130950116775744)2025-04-24 09:30:04,414:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1e_10_L001_R1_001.fastq.gz finished INFO(131307696498496)2025-04-24 09:30:05,448:************************* INFO(131307696498496)2025-04-24 09:30:05,448:deblurring started WARNING(131307696498496)2025-04-24 09:30:05,449:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1a_3_L001_R1_001.fastq.gz WARNING(131307696498496)2025-04-24 09:30:05,449:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1a_3_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(131307696498496)2025-04-24 09:30:05,449:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(131307696498496)2025-04-24 09:30:05,449:deblur worker thread started INFO(131307696498496)2025-04-24 09:30:05,449:processing per sample fasta files INFO(131307696498496)2025-04-24 09:30:05,449:-------------------------------------------------------- INFO(131307696498496)2025-04-24 09:30:05,449:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1a_3_L001_R1_001.fastq.gz INFO(139213418084160)2025-04-24 09:30:25,656:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim INFO(139213418084160)2025-04-24 09:30:25,719:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim.derep INFO(126556384212800)2025-04-24 09:30:25,967:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim INFO(126556384212800)2025-04-24 09:30:26,067:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim.derep INFO(139213418084160)2025-04-24 09:30:26,301:total sequences 2945, passing sequences 2945, failing sequences 0 INFO(139213418084160)2025-04-24 09:30:26,302:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(126556384212800)2025-04-24 09:30:26,649:total sequences 3401, passing sequences 3401, failing sequences 0 INFO(126556384212800)2025-04-24 09:30:26,649:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(139213418084160)2025-04-24 09:30:34,431:deblurring 2945 sequences INFO(126556384212800)2025-04-24 09:30:37,089:deblurring 3401 sequences INFO(139213418084160)2025-04-24 09:30:39,842:1352 unique sequences left following deblurring INFO(139213418084160)2025-04-24 09:30:39,851:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1r_21_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(139213418084160)2025-04-24 09:30:40,214:finished processing file INFO(139213418084160)2025-04-24 09:30:40,215:finished processing per sample fasta files INFO(139213418084160)2025-04-24 09:30:40,216:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1r_21_L001_R1_001.fastq.gz finished INFO(136066510059328)2025-04-24 09:30:41,231:************************* INFO(136066510059328)2025-04-24 09:30:41,231:deblurring started WARNING(136066510059328)2025-04-24 09:30:41,232:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1p_19_L001_R1_001.fastq.gz WARNING(136066510059328)2025-04-24 09:30:41,232:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1p_19_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(136066510059328)2025-04-24 09:30:41,232:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(136066510059328)2025-04-24 09:30:41,232:deblur worker thread started INFO(136066510059328)2025-04-24 09:30:41,232:processing per sample fasta files INFO(136066510059328)2025-04-24 09:30:41,232:-------------------------------------------------------- INFO(136066510059328)2025-04-24 09:30:41,232:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1p_19_L001_R1_001.fastq.gz INFO(131307696498496)2025-04-24 09:30:43,370:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim INFO(131307696498496)2025-04-24 09:30:43,503:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim.derep INFO(131307696498496)2025-04-24 09:30:44,274:total sequences 2178, passing sequences 2178, failing sequences 0 INFO(131307696498496)2025-04-24 09:30:44,274:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(126556384212800)2025-04-24 09:30:45,647:1726 unique sequences left following deblurring INFO(126556384212800)2025-04-24 09:30:45,660:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1m_16_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(126556384212800)2025-04-24 09:30:46,166:finished processing file INFO(126556384212800)2025-04-24 09:30:46,167:finished processing per sample fasta files INFO(126556384212800)2025-04-24 09:30:46,167:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1m_16_L001_R1_001.fastq.gz finished INFO(131722423277376)2025-04-24 09:30:47,219:************************* INFO(131722423277376)2025-04-24 09:30:47,220:deblurring started WARNING(131722423277376)2025-04-24 09:30:47,220:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5cc_35_L001_R1_001.fastq.gz WARNING(131722423277376)2025-04-24 09:30:47,220:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5cc_35_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(131722423277376)2025-04-24 09:30:47,220:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(131722423277376)2025-04-24 09:30:47,221:deblur worker thread started INFO(131722423277376)2025-04-24 09:30:47,221:processing per sample fasta files INFO(131722423277376)2025-04-24 09:30:47,221:-------------------------------------------------------- INFO(131722423277376)2025-04-24 09:30:47,221:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5cc_35_L001_R1_001.fastq.gz INFO(131307696498496)2025-04-24 09:30:49,765:deblurring 2178 sequences INFO(126771576620864)2025-04-24 09:30:51,107:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim INFO(126771576620864)2025-04-24 09:30:51,248:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim.derep INFO(126771576620864)2025-04-24 09:30:51,886:total sequences 5700, passing sequences 5700, failing sequences 0 INFO(126771576620864)2025-04-24 09:30:51,886:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131307696498496)2025-04-24 09:30:52,976:1142 unique sequences left following deblurring INFO(131307696498496)2025-04-24 09:30:52,984:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1a_3_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(131307696498496)2025-04-24 09:30:53,288:finished processing file INFO(131307696498496)2025-04-24 09:30:53,288:finished processing per sample fasta files INFO(131307696498496)2025-04-24 09:30:53,289:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1a_3_L001_R1_001.fastq.gz finished INFO(130738187773760)2025-04-24 09:30:54,453:************************* INFO(130738187773760)2025-04-24 09:30:54,453:deblurring started WARNING(130738187773760)2025-04-24 09:30:54,453:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5s_49_L001_R1_001.fastq.gz WARNING(130738187773760)2025-04-24 09:30:54,454:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5s_49_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(130738187773760)2025-04-24 09:30:54,454:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(130738187773760)2025-04-24 09:30:54,454:deblur worker thread started INFO(130738187773760)2025-04-24 09:30:54,454:processing per sample fasta files INFO(130738187773760)2025-04-24 09:30:54,454:-------------------------------------------------------- INFO(130738187773760)2025-04-24 09:30:54,454:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5s_49_L001_R1_001.fastq.gz INFO(130738187773760)2025-04-24 09:31:17,412:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim INFO(130738187773760)2025-04-24 09:31:17,465:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim.derep INFO(130738187773760)2025-04-24 09:31:18,037:total sequences 2652, passing sequences 2652, failing sequences 0 INFO(130738187773760)2025-04-24 09:31:18,038:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(126771576620864)2025-04-24 09:31:21,371:deblurring 5700 sequences INFO(130738187773760)2025-04-24 09:31:25,293:deblurring 2652 sequences INFO(130738187773760)2025-04-24 09:31:30,649:1468 unique sequences left following deblurring INFO(130738187773760)2025-04-24 09:31:30,660:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5s_49_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(130738187773760)2025-04-24 09:31:31,123:finished processing file INFO(130738187773760)2025-04-24 09:31:31,124:finished processing per sample fasta files INFO(130738187773760)2025-04-24 09:31:31,124:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5s_49_L001_R1_001.fastq.gz finished INFO(134177902278464)2025-04-24 09:31:32,202:************************* INFO(134177902278464)2025-04-24 09:31:32,203:deblurring started WARNING(134177902278464)2025-04-24 09:31:32,203:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1w_25_L001_R1_001.fastq.gz WARNING(134177902278464)2025-04-24 09:31:32,203:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1w_25_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134177902278464)2025-04-24 09:31:32,203:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134177902278464)2025-04-24 09:31:32,204:deblur worker thread started INFO(134177902278464)2025-04-24 09:31:32,204:processing per sample fasta files INFO(134177902278464)2025-04-24 09:31:32,204:-------------------------------------------------------- INFO(134177902278464)2025-04-24 09:31:32,204:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1w_25_L001_R1_001.fastq.gz INFO(126771576620864)2025-04-24 09:31:40,441:2306 unique sequences left following deblurring INFO(126771576620864)2025-04-24 09:31:40,459:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5aa_31_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(126771576620864)2025-04-24 09:31:41,136:finished processing file INFO(126771576620864)2025-04-24 09:31:41,138:finished processing per sample fasta files INFO(126771576620864)2025-04-24 09:31:41,138:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5aa_31_L001_R1_001.fastq.gz finished INFO(134848413230912)2025-04-24 09:31:42,350:************************* INFO(134848413230912)2025-04-24 09:31:42,350:deblurring started WARNING(134848413230912)2025-04-24 09:31:42,351:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1cc_7_L001_R1_001.fastq.gz WARNING(134848413230912)2025-04-24 09:31:42,351:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1cc_7_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134848413230912)2025-04-24 09:31:42,351:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134848413230912)2025-04-24 09:31:42,351:deblur worker thread started INFO(134848413230912)2025-04-24 09:31:42,351:processing per sample fasta files INFO(134848413230912)2025-04-24 09:31:42,351:-------------------------------------------------------- INFO(134848413230912)2025-04-24 09:31:42,351:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1cc_7_L001_R1_001.fastq.gz INFO(131722423277376)2025-04-24 09:32:03,022:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim INFO(131722423277376)2025-04-24 09:32:03,238:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim.derep INFO(131722423277376)2025-04-24 09:32:03,952:total sequences 7549, passing sequences 7549, failing sequences 0 INFO(131722423277376)2025-04-24 09:32:03,952:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134177902278464)2025-04-24 09:32:09,089:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim INFO(134177902278464)2025-04-24 09:32:09,160:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim.derep INFO(134177902278464)2025-04-24 09:32:09,708:total sequences 2838, passing sequences 2838, failing sequences 0 INFO(134177902278464)2025-04-24 09:32:09,708:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134177902278464)2025-04-24 09:32:18,351:deblurring 2838 sequences INFO(134177902278464)2025-04-24 09:32:23,262:1157 unique sequences left following deblurring INFO(134177902278464)2025-04-24 09:32:23,271:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1w_25_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(134177902278464)2025-04-24 09:32:23,591:finished processing file INFO(134177902278464)2025-04-24 09:32:23,592:finished processing per sample fasta files INFO(134177902278464)2025-04-24 09:32:23,592:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1w_25_L001_R1_001.fastq.gz finished INFO(125917109634880)2025-04-24 09:32:24,661:************************* INFO(125917109634880)2025-04-24 09:32:24,661:deblurring started WARNING(125917109634880)2025-04-24 09:32:24,662:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1b_4_L001_R1_001.fastq.gz WARNING(125917109634880)2025-04-24 09:32:24,662:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1b_4_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(125917109634880)2025-04-24 09:32:24,662:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(125917109634880)2025-04-24 09:32:24,662:deblur worker thread started INFO(125917109634880)2025-04-24 09:32:24,662:processing per sample fasta files INFO(125917109634880)2025-04-24 09:32:24,662:-------------------------------------------------------- INFO(125917109634880)2025-04-24 09:32:24,662:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1b_4_L001_R1_001.fastq.gz INFO(134848413230912)2025-04-24 09:32:48,404:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim INFO(134848413230912)2025-04-24 09:32:48,517:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim.derep INFO(134848413230912)2025-04-24 09:32:49,308:total sequences 4718, passing sequences 4718, failing sequences 0 INFO(134848413230912)2025-04-24 09:32:49,308:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(125917109634880)2025-04-24 09:32:53,292:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim INFO(125917109634880)2025-04-24 09:32:53,363:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim.derep INFO(125917109634880)2025-04-24 09:32:53,930:total sequences 3405, passing sequences 3405, failing sequences 0 INFO(125917109634880)2025-04-24 09:32:53,930:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131722423277376)2025-04-24 09:32:57,453:deblurring 7549 sequences INFO(125917109634880)2025-04-24 09:33:05,428:deblurring 3405 sequences INFO(134848413230912)2025-04-24 09:33:11,086:deblurring 4718 sequences INFO(125917109634880)2025-04-24 09:33:14,742:1977 unique sequences left following deblurring INFO(125917109634880)2025-04-24 09:33:14,757:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1b_4_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(125917109634880)2025-04-24 09:33:15,331:finished processing file INFO(125917109634880)2025-04-24 09:33:15,332:finished processing per sample fasta files INFO(125917109634880)2025-04-24 09:33:15,333:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1b_4_L001_R1_001.fastq.gz finished INFO(124263052330816)2025-04-24 09:33:16,464:************************* INFO(124263052330816)2025-04-24 09:33:16,464:deblurring started WARNING(124263052330816)2025-04-24 09:33:16,465:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5v_51_L001_R1_001.fastq.gz WARNING(124263052330816)2025-04-24 09:33:16,465:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5v_51_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124263052330816)2025-04-24 09:33:16,465:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124263052330816)2025-04-24 09:33:16,465:deblur worker thread started INFO(124263052330816)2025-04-24 09:33:16,465:processing per sample fasta files INFO(124263052330816)2025-04-24 09:33:16,466:-------------------------------------------------------- INFO(124263052330816)2025-04-24 09:33:16,466:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5v_51_L001_R1_001.fastq.gz INFO(134848413230912)2025-04-24 09:33:24,812:1864 unique sequences left following deblurring INFO(134848413230912)2025-04-24 09:33:24,828:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1cc_7_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(134848413230912)2025-04-24 09:33:25,393:finished processing file INFO(134848413230912)2025-04-24 09:33:25,394:finished processing per sample fasta files INFO(134848413230912)2025-04-24 09:33:25,395:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1cc_7_L001_R1_001.fastq.gz finished INFO(124399102048064)2025-04-24 09:33:26,543:************************* INFO(124399102048064)2025-04-24 09:33:26,543:deblurring started WARNING(124399102048064)2025-04-24 09:33:26,544:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5c_34_L001_R1_001.fastq.gz WARNING(124399102048064)2025-04-24 09:33:26,544:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5c_34_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124399102048064)2025-04-24 09:33:26,544:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124399102048064)2025-04-24 09:33:26,544:deblur worker thread started INFO(124399102048064)2025-04-24 09:33:26,544:processing per sample fasta files INFO(124399102048064)2025-04-24 09:33:26,544:-------------------------------------------------------- INFO(124399102048064)2025-04-24 09:33:26,544:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5c_34_L001_R1_001.fastq.gz INFO(124263052330816)2025-04-24 09:33:32,008:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim INFO(124263052330816)2025-04-24 09:33:32,040:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim.derep INFO(124263052330816)2025-04-24 09:33:32,541:total sequences 1168, passing sequences 1168, failing sequences 0 INFO(124263052330816)2025-04-24 09:33:32,541:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131722423277376)2025-04-24 09:33:34,558:2965 unique sequences left following deblurring INFO(131722423277376)2025-04-24 09:33:34,588:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5cc_35_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(124263052330816)2025-04-24 09:33:34,661:deblurring 1168 sequences INFO(124263052330816)2025-04-24 09:33:35,453:482 unique sequences left following deblurring INFO(124263052330816)2025-04-24 09:33:35,457:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5v_51_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(131722423277376)2025-04-24 09:33:35,505:finished processing file INFO(131722423277376)2025-04-24 09:33:35,507:finished processing per sample fasta files INFO(131722423277376)2025-04-24 09:33:35,508:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5cc_35_L001_R1_001.fastq.gz finished INFO(124263052330816)2025-04-24 09:33:35,584:finished processing file INFO(124263052330816)2025-04-24 09:33:35,584:finished processing per sample fasta files INFO(124263052330816)2025-04-24 09:33:35,584:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5v_51_L001_R1_001.fastq.gz finished INFO(128777516447552)2025-04-24 09:33:36,695:************************* INFO(128777516447552)2025-04-24 09:33:36,695:deblurring started WARNING(128777516447552)2025-04-24 09:33:36,695:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5w_52_L001_R1_001.fastq.gz WARNING(128777516447552)2025-04-24 09:33:36,696:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5w_52_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(128777516447552)2025-04-24 09:33:36,696:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(128777516447552)2025-04-24 09:33:36,696:deblur worker thread started INFO(128777516447552)2025-04-24 09:33:36,696:processing per sample fasta files INFO(128777516447552)2025-04-24 09:33:36,696:-------------------------------------------------------- INFO(128777516447552)2025-04-24 09:33:36,696:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5w_52_L001_R1_001.fastq.gz INFO(128777516447552)2025-04-24 09:33:36,703:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5w_52_L001_R1_001.fastq.gz.trim INFO(128777516447552)2025-04-24 09:33:36,707:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5w_52_L001_R1_001.fastq.gz.trim.derep WARNING(128777516447552)2025-04-24 09:33:36,707:file /tmp/tmpc40oidxs/deblur_working_dir/Site5w_52_L001_R1_001.fastq.gz.trim.derep has size 0, continuing WARNING(128777516447552)2025-04-24 09:33:36,709:remove artifacts failed, aborting WARNING(128777516447552)2025-04-24 09:33:36,709:deblurring failed for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5w_52_L001_R1_001.fastq.gz INFO(128777516447552)2025-04-24 09:33:36,709:finished processing per sample fasta files INFO(128777516447552)2025-04-24 09:33:36,709:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5w_52_L001_R1_001.fastq.gz finished INFO(125818049382208)2025-04-24 09:33:36,745:************************* INFO(125818049382208)2025-04-24 09:33:36,745:deblurring started WARNING(125818049382208)2025-04-24 09:33:36,746:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1d_8_L001_R1_001.fastq.gz WARNING(125818049382208)2025-04-24 09:33:36,746:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1d_8_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(125818049382208)2025-04-24 09:33:36,746:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(125818049382208)2025-04-24 09:33:36,746:deblur worker thread started INFO(125818049382208)2025-04-24 09:33:36,746:processing per sample fasta files INFO(125818049382208)2025-04-24 09:33:36,746:-------------------------------------------------------- INFO(125818049382208)2025-04-24 09:33:36,746:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1d_8_L001_R1_001.fastq.gz INFO(138704924739392)2025-04-24 09:33:37,799:************************* INFO(138704924739392)2025-04-24 09:33:37,800:deblurring started WARNING(138704924739392)2025-04-24 09:33:37,801:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5o_45_L001_R1_001.fastq.gz WARNING(138704924739392)2025-04-24 09:33:37,801:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5o_45_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(138704924739392)2025-04-24 09:33:37,801:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(138704924739392)2025-04-24 09:33:37,801:deblur worker thread started INFO(138704924739392)2025-04-24 09:33:37,801:processing per sample fasta files INFO(138704924739392)2025-04-24 09:33:37,801:-------------------------------------------------------- INFO(138704924739392)2025-04-24 09:33:37,801:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5o_45_L001_R1_001.fastq.gz INFO(124399102048064)2025-04-24 09:33:38,202:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim INFO(124399102048064)2025-04-24 09:33:38,228:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim.derep INFO(124399102048064)2025-04-24 09:33:38,691:total sequences 1165, passing sequences 1165, failing sequences 0 INFO(124399102048064)2025-04-24 09:33:38,692:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124399102048064)2025-04-24 09:33:40,949:deblurring 1165 sequences INFO(124399102048064)2025-04-24 09:33:42,113:741 unique sequences left following deblurring INFO(124399102048064)2025-04-24 09:33:42,117:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5c_34_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(124399102048064)2025-04-24 09:33:42,294:finished processing file INFO(124399102048064)2025-04-24 09:33:42,295:finished processing per sample fasta files INFO(124399102048064)2025-04-24 09:33:42,295:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5c_34_L001_R1_001.fastq.gz finished INFO(124173937481536)2025-04-24 09:33:43,428:************************* INFO(124173937481536)2025-04-24 09:33:43,428:deblurring started WARNING(124173937481536)2025-04-24 09:33:43,429:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1z_27_L001_R1_001.fastq.gz WARNING(124173937481536)2025-04-24 09:33:43,429:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1z_27_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124173937481536)2025-04-24 09:33:43,429:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124173937481536)2025-04-24 09:33:43,429:deblur worker thread started INFO(124173937481536)2025-04-24 09:33:43,429:processing per sample fasta files INFO(124173937481536)2025-04-24 09:33:43,429:-------------------------------------------------------- INFO(124173937481536)2025-04-24 09:33:43,429:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1z_27_L001_R1_001.fastq.gz INFO(136066510059328)2025-04-24 09:33:53,935:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim INFO(136066510059328)2025-04-24 09:33:54,366:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim.derep INFO(136066510059328)2025-04-24 09:33:55,221:total sequences 13856, passing sequences 13856, failing sequences 0 INFO(136066510059328)2025-04-24 09:33:55,222:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(138704924739392)2025-04-24 09:33:57,674:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim INFO(138704924739392)2025-04-24 09:33:57,729:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim.derep INFO(138704924739392)2025-04-24 09:33:58,248:total sequences 2487, passing sequences 2487, failing sequences 0 INFO(138704924739392)2025-04-24 09:33:58,249:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(138704924739392)2025-04-24 09:34:05,503:deblurring 2487 sequences INFO(125818049382208)2025-04-24 09:34:08,640:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim INFO(138704924739392)2025-04-24 09:34:08,707:939 unique sequences left following deblurring INFO(125818049382208)2025-04-24 09:34:08,714:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim.derep INFO(138704924739392)2025-04-24 09:34:08,716:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5o_45_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(138704924739392)2025-04-24 09:34:08,967:finished processing file INFO(138704924739392)2025-04-24 09:34:08,968:finished processing per sample fasta files INFO(138704924739392)2025-04-24 09:34:08,968:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5o_45_L001_R1_001.fastq.gz finished INFO(125818049382208)2025-04-24 09:34:09,345:total sequences 3526, passing sequences 3526, failing sequences 0 INFO(125818049382208)2025-04-24 09:34:09,346:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(128778296297280)2025-04-24 09:34:10,112:************************* INFO(128778296297280)2025-04-24 09:34:10,113:deblurring started WARNING(128778296297280)2025-04-24 09:34:10,113:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1o_18_L001_R1_001.fastq.gz WARNING(128778296297280)2025-04-24 09:34:10,113:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1o_18_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(128778296297280)2025-04-24 09:34:10,113:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(128778296297280)2025-04-24 09:34:10,113:deblur worker thread started INFO(128778296297280)2025-04-24 09:34:10,114:processing per sample fasta files INFO(128778296297280)2025-04-24 09:34:10,114:-------------------------------------------------------- INFO(128778296297280)2025-04-24 09:34:10,114:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1o_18_L001_R1_001.fastq.gz INFO(124173937481536)2025-04-24 09:34:11,241:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim INFO(124173937481536)2025-04-24 09:34:11,299:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim.derep INFO(124173937481536)2025-04-24 09:34:11,837:total sequences 2092, passing sequences 2092, failing sequences 0 INFO(124173937481536)2025-04-24 09:34:11,837:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124173937481536)2025-04-24 09:34:17,126:deblurring 2092 sequences INFO(124173937481536)2025-04-24 09:34:19,655:881 unique sequences left following deblurring INFO(124173937481536)2025-04-24 09:34:19,662:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1z_27_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(124173937481536)2025-04-24 09:34:19,903:finished processing file INFO(124173937481536)2025-04-24 09:34:19,904:finished processing per sample fasta files INFO(124173937481536)2025-04-24 09:34:19,904:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1z_27_L001_R1_001.fastq.gz finished INFO(125818049382208)2025-04-24 09:34:21,020:deblurring 3526 sequences INFO(137663957849920)2025-04-24 09:34:21,041:************************* INFO(137663957849920)2025-04-24 09:34:21,042:deblurring started WARNING(137663957849920)2025-04-24 09:34:21,042:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1s_22_L001_R1_001.fastq.gz WARNING(137663957849920)2025-04-24 09:34:21,042:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1s_22_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(137663957849920)2025-04-24 09:34:21,042:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(137663957849920)2025-04-24 09:34:21,043:deblur worker thread started INFO(137663957849920)2025-04-24 09:34:21,043:processing per sample fasta files INFO(137663957849920)2025-04-24 09:34:21,043:-------------------------------------------------------- INFO(137663957849920)2025-04-24 09:34:21,043:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1s_22_L001_R1_001.fastq.gz INFO(125818049382208)2025-04-24 09:34:30,296:1814 unique sequences left following deblurring INFO(125818049382208)2025-04-24 09:34:30,309:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1d_8_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(125818049382208)2025-04-24 09:34:30,809:finished processing file INFO(125818049382208)2025-04-24 09:34:30,810:finished processing per sample fasta files INFO(125818049382208)2025-04-24 09:34:30,811:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1d_8_L001_R1_001.fastq.gz finished INFO(124936141166400)2025-04-24 09:34:31,897:************************* INFO(124936141166400)2025-04-24 09:34:31,897:deblurring started WARNING(124936141166400)2025-04-24 09:34:31,898:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5m_43_L001_R1_001.fastq.gz WARNING(124936141166400)2025-04-24 09:34:31,898:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5m_43_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124936141166400)2025-04-24 09:34:31,899:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124936141166400)2025-04-24 09:34:31,899:deblur worker thread started INFO(124936141166400)2025-04-24 09:34:31,899:processing per sample fasta files INFO(124936141166400)2025-04-24 09:34:31,899:-------------------------------------------------------- INFO(124936141166400)2025-04-24 09:34:31,899:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5m_43_L001_R1_001.fastq.gz INFO(128778296297280)2025-04-24 09:34:48,402:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim INFO(128778296297280)2025-04-24 09:34:48,491:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim.derep INFO(128778296297280)2025-04-24 09:34:49,058:total sequences 4492, passing sequences 4492, failing sequences 0 INFO(128778296297280)2025-04-24 09:34:49,058:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124936141166400)2025-04-24 09:34:53,342:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim INFO(124936141166400)2025-04-24 09:34:53,386:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim.derep INFO(124936141166400)2025-04-24 09:34:53,935:total sequences 2330, passing sequences 2330, failing sequences 0 INFO(124936141166400)2025-04-24 09:34:53,935:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(137663957849920)2025-04-24 09:34:58,631:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim INFO(137663957849920)2025-04-24 09:34:58,735:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim.derep INFO(137663957849920)2025-04-24 09:34:59,351:total sequences 4269, passing sequences 4269, failing sequences 0 INFO(137663957849920)2025-04-24 09:34:59,352:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124936141166400)2025-04-24 09:34:59,960:deblurring 2330 sequences INFO(124936141166400)2025-04-24 09:35:04,659:1445 unique sequences left following deblurring INFO(124936141166400)2025-04-24 09:35:04,671:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5m_43_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(124936141166400)2025-04-24 09:35:05,064:finished processing file INFO(124936141166400)2025-04-24 09:35:05,065:finished processing per sample fasta files INFO(124936141166400)2025-04-24 09:35:05,065:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5m_43_L001_R1_001.fastq.gz finished INFO(137709812188992)2025-04-24 09:35:06,248:************************* INFO(137709812188992)2025-04-24 09:35:06,248:deblurring started WARNING(137709812188992)2025-04-24 09:35:06,249:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5ff_39_L001_R1_001.fastq.gz WARNING(137709812188992)2025-04-24 09:35:06,249:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5ff_39_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(137709812188992)2025-04-24 09:35:06,249:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(137709812188992)2025-04-24 09:35:06,249:deblur worker thread started INFO(137709812188992)2025-04-24 09:35:06,249:processing per sample fasta files INFO(137709812188992)2025-04-24 09:35:06,249:-------------------------------------------------------- INFO(137709812188992)2025-04-24 09:35:06,249:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5ff_39_L001_R1_001.fastq.gz INFO(128778296297280)2025-04-24 09:35:08,155:deblurring 4492 sequences INFO(137663957849920)2025-04-24 09:35:16,043:deblurring 4269 sequences INFO(128778296297280)2025-04-24 09:35:24,251:2458 unique sequences left following deblurring INFO(128778296297280)2025-04-24 09:35:24,269:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1o_18_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(128778296297280)2025-04-24 09:35:25,062:finished processing file INFO(128778296297280)2025-04-24 09:35:25,063:finished processing per sample fasta files INFO(128778296297280)2025-04-24 09:35:25,063:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1o_18_L001_R1_001.fastq.gz finished INFO(137283082520384)2025-04-24 09:35:27,022:************************* INFO(137283082520384)2025-04-24 09:35:27,022:deblurring started WARNING(137283082520384)2025-04-24 09:35:27,022:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5u_50_L001_R1_001.fastq.gz WARNING(137283082520384)2025-04-24 09:35:27,022:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5u_50_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(137283082520384)2025-04-24 09:35:27,022:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(137283082520384)2025-04-24 09:35:27,023:deblur worker thread started INFO(137283082520384)2025-04-24 09:35:27,023:processing per sample fasta files INFO(137283082520384)2025-04-24 09:35:27,023:-------------------------------------------------------- INFO(137283082520384)2025-04-24 09:35:27,023:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5u_50_L001_R1_001.fastq.gz INFO(137663957849920)2025-04-24 09:35:29,112:1982 unique sequences left following deblurring INFO(137663957849920)2025-04-24 09:35:29,131:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1s_22_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(137663957849920)2025-04-24 09:35:31,091:finished processing file INFO(137663957849920)2025-04-24 09:35:31,092:finished processing per sample fasta files INFO(137663957849920)2025-04-24 09:35:31,092:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1s_22_L001_R1_001.fastq.gz finished INFO(130083190830912)2025-04-24 09:35:32,675:************************* INFO(130083190830912)2025-04-24 09:35:32,675:deblurring started WARNING(130083190830912)2025-04-24 09:35:32,676:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5f_38_L001_R1_001.fastq.gz WARNING(130083190830912)2025-04-24 09:35:32,676:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5f_38_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(130083190830912)2025-04-24 09:35:32,676:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(130083190830912)2025-04-24 09:35:32,676:deblur worker thread started INFO(130083190830912)2025-04-24 09:35:32,676:processing per sample fasta files INFO(130083190830912)2025-04-24 09:35:32,676:-------------------------------------------------------- INFO(130083190830912)2025-04-24 09:35:32,676:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5f_38_L001_R1_001.fastq.gz INFO(130083190830912)2025-04-24 09:35:34,733:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim INFO(130083190830912)2025-04-24 09:35:34,743:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim.derep INFO(130083190830912)2025-04-24 09:35:35,237:total sequences 292, passing sequences 292, failing sequences 0 INFO(130083190830912)2025-04-24 09:35:35,238:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(130083190830912)2025-04-24 09:35:39,352:deblurring 292 sequences INFO(130083190830912)2025-04-24 09:35:39,426:152 unique sequences left following deblurring INFO(130083190830912)2025-04-24 09:35:39,427:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5f_38_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(130083190830912)2025-04-24 09:35:39,471:finished processing file INFO(130083190830912)2025-04-24 09:35:39,471:finished processing per sample fasta files INFO(130083190830912)2025-04-24 09:35:39,471:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5f_38_L001_R1_001.fastq.gz finished INFO(134847526795072)2025-04-24 09:35:40,940:************************* INFO(134847526795072)2025-04-24 09:35:40,940:deblurring started WARNING(134847526795072)2025-04-24 09:35:40,940:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1J_0_L001_R1_001.fastq.gz WARNING(134847526795072)2025-04-24 09:35:40,940:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1J_0_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134847526795072)2025-04-24 09:35:40,941:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134847526795072)2025-04-24 09:35:40,941:deblur worker thread started INFO(134847526795072)2025-04-24 09:35:40,941:processing per sample fasta files INFO(134847526795072)2025-04-24 09:35:40,941:-------------------------------------------------------- INFO(134847526795072)2025-04-24 09:35:40,941:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1J_0_L001_R1_001.fastq.gz INFO(134847526795072)2025-04-24 09:35:42,561:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim INFO(134847526795072)2025-04-24 09:35:42,574:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim.derep INFO(134847526795072)2025-04-24 09:35:43,113:total sequences 364, passing sequences 364, failing sequences 0 INFO(134847526795072)2025-04-24 09:35:43,113:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(137283082520384)2025-04-24 09:35:45,211:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim INFO(137283082520384)2025-04-24 09:35:45,253:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim.derep INFO(137283082520384)2025-04-24 09:35:45,790:total sequences 1726, passing sequences 1726, failing sequences 0 INFO(137283082520384)2025-04-24 09:35:45,791:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134847526795072)2025-04-24 09:35:48,171:deblurring 364 sequences INFO(134847526795072)2025-04-24 09:35:48,494:293 unique sequences left following deblurring INFO(134847526795072)2025-04-24 09:35:48,495:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1J_0_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(134847526795072)2025-04-24 09:35:48,604:finished processing file INFO(134847526795072)2025-04-24 09:35:48,604:finished processing per sample fasta files INFO(134847526795072)2025-04-24 09:35:48,605:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1J_0_L001_R1_001.fastq.gz finished INFO(139312442038080)2025-04-24 09:35:49,687:************************* INFO(139312442038080)2025-04-24 09:35:49,688:deblurring started WARNING(139312442038080)2025-04-24 09:35:49,688:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1h_14_L001_R1_001.fastq.gz WARNING(139312442038080)2025-04-24 09:35:49,688:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1h_14_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(139312442038080)2025-04-24 09:35:49,688:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(139312442038080)2025-04-24 09:35:49,688:deblur worker thread started INFO(139312442038080)2025-04-24 09:35:49,689:processing per sample fasta files INFO(139312442038080)2025-04-24 09:35:49,689:-------------------------------------------------------- INFO(139312442038080)2025-04-24 09:35:49,689:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1h_14_L001_R1_001.fastq.gz INFO(137283082520384)2025-04-24 09:35:49,988:deblurring 1726 sequences INFO(137283082520384)2025-04-24 09:35:53,511:904 unique sequences left following deblurring INFO(137283082520384)2025-04-24 09:35:53,516:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5u_50_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(137283082520384)2025-04-24 09:35:53,814:finished processing file INFO(137283082520384)2025-04-24 09:35:53,815:finished processing per sample fasta files INFO(137283082520384)2025-04-24 09:35:53,815:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5u_50_L001_R1_001.fastq.gz finished INFO(134483917367104)2025-04-24 09:35:55,461:************************* INFO(134483917367104)2025-04-24 09:35:55,461:deblurring started WARNING(134483917367104)2025-04-24 09:35:55,462:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5q_47_L001_R1_001.fastq.gz WARNING(134483917367104)2025-04-24 09:35:55,462:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5q_47_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134483917367104)2025-04-24 09:35:55,462:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134483917367104)2025-04-24 09:35:55,463:deblur worker thread started INFO(134483917367104)2025-04-24 09:35:55,463:processing per sample fasta files INFO(134483917367104)2025-04-24 09:35:55,463:-------------------------------------------------------- INFO(134483917367104)2025-04-24 09:35:55,463:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5q_47_L001_R1_001.fastq.gz INFO(139312442038080)2025-04-24 09:36:07,348:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim INFO(139312442038080)2025-04-24 09:36:07,376:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim.derep INFO(139312442038080)2025-04-24 09:36:07,901:total sequences 1031, passing sequences 1031, failing sequences 0 INFO(139312442038080)2025-04-24 09:36:07,902:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(139312442038080)2025-04-24 09:36:09,803:deblurring 1031 sequences INFO(139312442038080)2025-04-24 09:36:10,524:532 unique sequences left following deblurring INFO(139312442038080)2025-04-24 09:36:10,530:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1h_14_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(139312442038080)2025-04-24 09:36:10,664:finished processing file INFO(139312442038080)2025-04-24 09:36:10,665:finished processing per sample fasta files INFO(139312442038080)2025-04-24 09:36:10,665:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1h_14_L001_R1_001.fastq.gz finished INFO(129012491872064)2025-04-24 09:36:11,765:************************* INFO(129012491872064)2025-04-24 09:36:11,765:deblurring started WARNING(129012491872064)2025-04-24 09:36:11,766:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1L_1_L001_R1_001.fastq.gz WARNING(129012491872064)2025-04-24 09:36:11,766:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1L_1_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(129012491872064)2025-04-24 09:36:11,766:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(129012491872064)2025-04-24 09:36:11,766:deblur worker thread started INFO(129012491872064)2025-04-24 09:36:11,766:processing per sample fasta files INFO(129012491872064)2025-04-24 09:36:11,766:-------------------------------------------------------- INFO(129012491872064)2025-04-24 09:36:11,766:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1L_1_L001_R1_001.fastq.gz INFO(129012491872064)2025-04-24 09:36:21,253:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim INFO(129012491872064)2025-04-24 09:36:21,279:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim.derep INFO(129012491872064)2025-04-24 09:36:22,018:total sequences 1053, passing sequences 1053, failing sequences 0 INFO(129012491872064)2025-04-24 09:36:22,018:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(129012491872064)2025-04-24 09:36:24,372:deblurring 1053 sequences INFO(129012491872064)2025-04-24 09:36:25,100:598 unique sequences left following deblurring INFO(129012491872064)2025-04-24 09:36:25,103:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1L_1_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(129012491872064)2025-04-24 09:36:25,308:finished processing file INFO(129012491872064)2025-04-24 09:36:25,309:finished processing per sample fasta files INFO(129012491872064)2025-04-24 09:36:25,309:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1L_1_L001_R1_001.fastq.gz finished INFO(135779960964928)2025-04-24 09:36:26,429:************************* INFO(135779960964928)2025-04-24 09:36:26,429:deblurring started WARNING(135779960964928)2025-04-24 09:36:26,430:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5k_42_L001_R1_001.fastq.gz WARNING(135779960964928)2025-04-24 09:36:26,430:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5k_42_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(135779960964928)2025-04-24 09:36:26,430:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(135779960964928)2025-04-24 09:36:26,430:deblur worker thread started INFO(135779960964928)2025-04-24 09:36:26,430:processing per sample fasta files INFO(135779960964928)2025-04-24 09:36:26,431:-------------------------------------------------------- INFO(135779960964928)2025-04-24 09:36:26,431:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5k_42_L001_R1_001.fastq.gz INFO(134483917367104)2025-04-24 09:36:27,959:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim INFO(134483917367104)2025-04-24 09:36:28,258:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim.derep INFO(134483917367104)2025-04-24 09:36:29,015:total sequences 6897, passing sequences 6897, failing sequences 0 INFO(134483917367104)2025-04-24 09:36:29,016:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(137709812188992)2025-04-24 09:36:33,291:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim INFO(137709812188992)2025-04-24 09:36:33,762:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim.derep INFO(137709812188992)2025-04-24 09:36:34,704:total sequences 8154, passing sequences 8154, failing sequences 0 INFO(137709812188992)2025-04-24 09:36:34,704:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(135779960964928)2025-04-24 09:36:42,555:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim INFO(135779960964928)2025-04-24 09:36:42,600:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim.derep INFO(135779960964928)2025-04-24 09:36:43,271:total sequences 1255, passing sequences 1255, failing sequences 0 INFO(135779960964928)2025-04-24 09:36:43,271:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(135779960964928)2025-04-24 09:36:46,301:deblurring 1255 sequences INFO(135779960964928)2025-04-24 09:36:48,110:783 unique sequences left following deblurring INFO(135779960964928)2025-04-24 09:36:48,115:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5k_42_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(135779960964928)2025-04-24 09:36:48,409:finished processing file INFO(135779960964928)2025-04-24 09:36:48,410:finished processing per sample fasta files INFO(135779960964928)2025-04-24 09:36:48,410:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5k_42_L001_R1_001.fastq.gz finished INFO(135958085859136)2025-04-24 09:36:49,671:************************* INFO(135958085859136)2025-04-24 09:36:49,671:deblurring started WARNING(135958085859136)2025-04-24 09:36:49,672:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1dd_9_L001_R1_001.fastq.gz WARNING(135958085859136)2025-04-24 09:36:49,672:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1dd_9_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(135958085859136)2025-04-24 09:36:49,672:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(135958085859136)2025-04-24 09:36:49,672:deblur worker thread started INFO(135958085859136)2025-04-24 09:36:49,672:processing per sample fasta files INFO(135958085859136)2025-04-24 09:36:49,672:-------------------------------------------------------- INFO(135958085859136)2025-04-24 09:36:49,672:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1dd_9_L001_R1_001.fastq.gz INFO(136066510059328)2025-04-24 09:37:15,839:deblurring 13856 sequences INFO(134483917367104)2025-04-24 09:37:18,163:deblurring 6897 sequences INFO(137709812188992)2025-04-24 09:37:39,657:deblurring 8154 sequences INFO(135958085859136)2025-04-24 09:37:48,301:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim INFO(135958085859136)2025-04-24 09:37:48,428:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim.derep INFO(135958085859136)2025-04-24 09:37:49,048:total sequences 5382, passing sequences 5382, failing sequences 0 INFO(135958085859136)2025-04-24 09:37:49,048:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134483917367104)2025-04-24 09:38:06,100:4786 unique sequences left following deblurring INFO(134483917367104)2025-04-24 09:38:06,147:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5q_47_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(134483917367104)2025-04-24 09:38:07,741:finished processing file INFO(134483917367104)2025-04-24 09:38:07,744:finished processing per sample fasta files INFO(134483917367104)2025-04-24 09:38:07,745:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5q_47_L001_R1_001.fastq.gz finished INFO(126112567641920)2025-04-24 09:38:08,858:************************* INFO(126112567641920)2025-04-24 09:38:08,858:deblurring started WARNING(126112567641920)2025-04-24 09:38:08,859:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5h_41_L001_R1_001.fastq.gz WARNING(126112567641920)2025-04-24 09:38:08,859:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5h_41_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(126112567641920)2025-04-24 09:38:08,859:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(126112567641920)2025-04-24 09:38:08,859:deblur worker thread started INFO(126112567641920)2025-04-24 09:38:08,859:processing per sample fasta files INFO(126112567641920)2025-04-24 09:38:08,859:-------------------------------------------------------- INFO(126112567641920)2025-04-24 09:38:08,860:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5h_41_L001_R1_001.fastq.gz INFO(135958085859136)2025-04-24 09:38:15,081:deblurring 5382 sequences INFO(137709812188992)2025-04-24 09:38:17,510:3328 unique sequences left following deblurring INFO(137709812188992)2025-04-24 09:38:17,538:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5ff_39_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(137709812188992)2025-04-24 09:38:18,581:finished processing file INFO(137709812188992)2025-04-24 09:38:18,583:finished processing per sample fasta files INFO(137709812188992)2025-04-24 09:38:18,584:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5ff_39_L001_R1_001.fastq.gz finished INFO(128371142149952)2025-04-24 09:38:19,661:************************* INFO(128371142149952)2025-04-24 09:38:19,661:deblurring started WARNING(128371142149952)2025-04-24 09:38:19,662:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1q_20_L001_R1_001.fastq.gz WARNING(128371142149952)2025-04-24 09:38:19,662:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1q_20_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(128371142149952)2025-04-24 09:38:19,662:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(128371142149952)2025-04-24 09:38:19,663:deblur worker thread started INFO(128371142149952)2025-04-24 09:38:19,663:processing per sample fasta files INFO(128371142149952)2025-04-24 09:38:19,663:-------------------------------------------------------- INFO(128371142149952)2025-04-24 09:38:19,663:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1q_20_L001_R1_001.fastq.gz INFO(135958085859136)2025-04-24 09:38:30,292:2050 unique sequences left following deblurring INFO(135958085859136)2025-04-24 09:38:30,310:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1dd_9_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(135958085859136)2025-04-24 09:38:30,909:finished processing file INFO(135958085859136)2025-04-24 09:38:30,912:finished processing per sample fasta files INFO(135958085859136)2025-04-24 09:38:30,912:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1dd_9_L001_R1_001.fastq.gz finished INFO(130471349077824)2025-04-24 09:38:31,916:************************* INFO(130471349077824)2025-04-24 09:38:31,916:deblurring started WARNING(130471349077824)2025-04-24 09:38:31,917:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1y_26_L001_R1_001.fastq.gz WARNING(130471349077824)2025-04-24 09:38:31,917:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1y_26_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(130471349077824)2025-04-24 09:38:31,917:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(130471349077824)2025-04-24 09:38:31,917:deblur worker thread started INFO(130471349077824)2025-04-24 09:38:31,917:processing per sample fasta files INFO(130471349077824)2025-04-24 09:38:31,917:-------------------------------------------------------- INFO(130471349077824)2025-04-24 09:38:31,917:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1y_26_L001_R1_001.fastq.gz INFO(136066510059328)2025-04-24 09:38:32,606:3387 unique sequences left following deblurring INFO(136066510059328)2025-04-24 09:38:32,648:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1p_19_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(136066510059328)2025-04-24 09:38:33,651:finished processing file INFO(136066510059328)2025-04-24 09:38:33,655:finished processing per sample fasta files INFO(136066510059328)2025-04-24 09:38:33,655:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1p_19_L001_R1_001.fastq.gz finished INFO(139160704694080)2025-04-24 09:38:34,710:************************* INFO(139160704694080)2025-04-24 09:38:34,710:deblurring started WARNING(139160704694080)2025-04-24 09:38:34,711:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5J_28_L001_R1_001.fastq.gz WARNING(139160704694080)2025-04-24 09:38:34,711:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5J_28_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(139160704694080)2025-04-24 09:38:34,711:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(139160704694080)2025-04-24 09:38:34,711:deblur worker thread started INFO(139160704694080)2025-04-24 09:38:34,711:processing per sample fasta files INFO(139160704694080)2025-04-24 09:38:34,711:-------------------------------------------------------- INFO(139160704694080)2025-04-24 09:38:34,711:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5J_28_L001_R1_001.fastq.gz INFO(139160704694080)2025-04-24 09:38:34,726:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5J_28_L001_R1_001.fastq.gz.trim INFO(139160704694080)2025-04-24 09:38:34,730:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5J_28_L001_R1_001.fastq.gz.trim.derep WARNING(139160704694080)2025-04-24 09:38:34,730:file /tmp/tmpc40oidxs/deblur_working_dir/Site5J_28_L001_R1_001.fastq.gz.trim.derep has size 0, continuing WARNING(139160704694080)2025-04-24 09:38:34,730:remove artifacts failed, aborting WARNING(139160704694080)2025-04-24 09:38:34,731:deblurring failed for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5J_28_L001_R1_001.fastq.gz INFO(139160704694080)2025-04-24 09:38:34,731:finished processing per sample fasta files INFO(139160704694080)2025-04-24 09:38:34,731:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5J_28_L001_R1_001.fastq.gz finished INFO(124165256369984)2025-04-24 09:38:35,752:************************* INFO(124165256369984)2025-04-24 09:38:35,753:deblurring started WARNING(124165256369984)2025-04-24 09:38:35,753:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5L_29_L001_R1_001.fastq.gz WARNING(124165256369984)2025-04-24 09:38:35,753:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5L_29_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124165256369984)2025-04-24 09:38:35,753:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124165256369984)2025-04-24 09:38:35,754:deblur worker thread started INFO(124165256369984)2025-04-24 09:38:35,754:processing per sample fasta files INFO(124165256369984)2025-04-24 09:38:35,754:-------------------------------------------------------- INFO(124165256369984)2025-04-24 09:38:35,754:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5L_29_L001_R1_001.fastq.gz INFO(128371142149952)2025-04-24 09:38:46,587:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim INFO(128371142149952)2025-04-24 09:38:46,613:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim.derep INFO(128371142149952)2025-04-24 09:38:47,093:total sequences 965, passing sequences 965, failing sequences 0 INFO(128371142149952)2025-04-24 09:38:47,093:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(128371142149952)2025-04-24 09:38:48,903:deblurring 965 sequences INFO(128371142149952)2025-04-24 09:38:49,587:536 unique sequences left following deblurring INFO(128371142149952)2025-04-24 09:38:49,592:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1q_20_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(128371142149952)2025-04-24 09:38:49,724:finished processing file INFO(128371142149952)2025-04-24 09:38:49,724:finished processing per sample fasta files INFO(128371142149952)2025-04-24 09:38:49,725:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1q_20_L001_R1_001.fastq.gz finished INFO(126789219891008)2025-04-24 09:38:50,798:************************* INFO(126789219891008)2025-04-24 09:38:50,798:deblurring started WARNING(126789219891008)2025-04-24 09:38:50,799:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5b_32_L001_R1_001.fastq.gz WARNING(126789219891008)2025-04-24 09:38:50,799:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5b_32_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(126789219891008)2025-04-24 09:38:50,799:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(126789219891008)2025-04-24 09:38:50,799:deblur worker thread started INFO(126789219891008)2025-04-24 09:38:50,799:processing per sample fasta files INFO(126789219891008)2025-04-24 09:38:50,799:-------------------------------------------------------- INFO(126789219891008)2025-04-24 09:38:50,799:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5b_32_L001_R1_001.fastq.gz INFO(130471349077824)2025-04-24 09:38:58,673:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim INFO(130471349077824)2025-04-24 09:38:58,745:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim.derep INFO(130471349077824)2025-04-24 09:38:59,273:total sequences 3287, passing sequences 3287, failing sequences 0 INFO(130471349077824)2025-04-24 09:38:59,273:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124165256369984)2025-04-24 09:39:07,456:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim INFO(124165256369984)2025-04-24 09:39:07,531:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim.derep INFO(124165256369984)2025-04-24 09:39:08,095:total sequences 3817, passing sequences 3817, failing sequences 0 INFO(124165256369984)2025-04-24 09:39:08,095:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(130471349077824)2025-04-24 09:39:08,974:deblurring 3287 sequences INFO(126112567641920)2025-04-24 09:39:13,028:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim INFO(126112567641920)2025-04-24 09:39:13,099:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim.derep INFO(126112567641920)2025-04-24 09:39:13,631:total sequences 1546, passing sequences 1546, failing sequences 0 INFO(126112567641920)2025-04-24 09:39:13,632:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(130471349077824)2025-04-24 09:39:14,941:1392 unique sequences left following deblurring INFO(130471349077824)2025-04-24 09:39:14,952:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1y_26_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(130471349077824)2025-04-24 09:39:15,346:finished processing file INFO(130471349077824)2025-04-24 09:39:15,347:finished processing per sample fasta files INFO(130471349077824)2025-04-24 09:39:15,348:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1y_26_L001_R1_001.fastq.gz finished INFO(135812053362496)2025-04-24 09:39:16,429:************************* INFO(135812053362496)2025-04-24 09:39:16,430:deblurring started WARNING(135812053362496)2025-04-24 09:39:16,430:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5e_36_L001_R1_001.fastq.gz WARNING(135812053362496)2025-04-24 09:39:16,430:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5e_36_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(135812053362496)2025-04-24 09:39:16,430:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(135812053362496)2025-04-24 09:39:16,430:deblur worker thread started INFO(135812053362496)2025-04-24 09:39:16,430:processing per sample fasta files INFO(135812053362496)2025-04-24 09:39:16,430:-------------------------------------------------------- INFO(135812053362496)2025-04-24 09:39:16,430:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5e_36_L001_R1_001.fastq.gz INFO(126112567641920)2025-04-24 09:39:17,077:deblurring 1546 sequences INFO(126112567641920)2025-04-24 09:39:18,139:511 unique sequences left following deblurring INFO(126112567641920)2025-04-24 09:39:18,144:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5h_41_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(126112567641920)2025-04-24 09:39:18,312:finished processing file INFO(126112567641920)2025-04-24 09:39:18,312:finished processing per sample fasta files INFO(126112567641920)2025-04-24 09:39:18,313:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5h_41_L001_R1_001.fastq.gz finished INFO(126030248830784)2025-04-24 09:39:19,466:************************* INFO(126030248830784)2025-04-24 09:39:19,466:deblurring started WARNING(126030248830784)2025-04-24 09:39:19,466:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1g_13_L001_R1_001.fastq.gz WARNING(126030248830784)2025-04-24 09:39:19,466:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1g_13_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(126030248830784)2025-04-24 09:39:19,467:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(126030248830784)2025-04-24 09:39:19,467:deblur worker thread started INFO(126030248830784)2025-04-24 09:39:19,467:processing per sample fasta files INFO(126030248830784)2025-04-24 09:39:19,467:-------------------------------------------------------- INFO(126030248830784)2025-04-24 09:39:19,467:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1g_13_L001_R1_001.fastq.gz INFO(124165256369984)2025-04-24 09:39:21,093:deblurring 3817 sequences INFO(126789219891008)2025-04-24 09:39:25,488:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim INFO(126789219891008)2025-04-24 09:39:25,542:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim.derep INFO(126789219891008)2025-04-24 09:39:26,091:total sequences 2458, passing sequences 2458, failing sequences 0 INFO(126789219891008)2025-04-24 09:39:26,092:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124165256369984)2025-04-24 09:39:31,453:2318 unique sequences left following deblurring INFO(124165256369984)2025-04-24 09:39:31,466:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5L_29_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(126789219891008)2025-04-24 09:39:32,014:deblurring 2458 sequences INFO(124165256369984)2025-04-24 09:39:32,151:finished processing file INFO(124165256369984)2025-04-24 09:39:32,152:finished processing per sample fasta files INFO(124165256369984)2025-04-24 09:39:32,152:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5L_29_L001_R1_001.fastq.gz finished INFO(131688908080960)2025-04-24 09:39:33,188:************************* INFO(131688908080960)2025-04-24 09:39:33,188:deblurring started WARNING(131688908080960)2025-04-24 09:39:33,188:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5bb_33_L001_R1_001.fastq.gz WARNING(131688908080960)2025-04-24 09:39:33,188:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5bb_33_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(131688908080960)2025-04-24 09:39:33,189:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(131688908080960)2025-04-24 09:39:33,189:deblur worker thread started INFO(131688908080960)2025-04-24 09:39:33,189:processing per sample fasta files INFO(131688908080960)2025-04-24 09:39:33,189:-------------------------------------------------------- INFO(131688908080960)2025-04-24 09:39:33,189:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5bb_33_L001_R1_001.fastq.gz INFO(126789219891008)2025-04-24 09:39:35,293:1022 unique sequences left following deblurring INFO(126789219891008)2025-04-24 09:39:35,300:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5b_32_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(126789219891008)2025-04-24 09:39:35,571:finished processing file INFO(126789219891008)2025-04-24 09:39:35,572:finished processing per sample fasta files INFO(126789219891008)2025-04-24 09:39:35,572:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5b_32_L001_R1_001.fastq.gz finished INFO(139898426345280)2025-04-24 09:39:36,617:************************* INFO(139898426345280)2025-04-24 09:39:36,618:deblurring started WARNING(139898426345280)2025-04-24 09:39:36,618:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1U_2_L001_R1_001.fastq.gz WARNING(139898426345280)2025-04-24 09:39:36,619:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1U_2_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(139898426345280)2025-04-24 09:39:36,619:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(139898426345280)2025-04-24 09:39:36,619:deblur worker thread started INFO(139898426345280)2025-04-24 09:39:36,619:processing per sample fasta files INFO(139898426345280)2025-04-24 09:39:36,619:-------------------------------------------------------- INFO(139898426345280)2025-04-24 09:39:36,619:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1U_2_L001_R1_001.fastq.gz INFO(139898426345280)2025-04-24 09:39:44,422:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim INFO(139898426345280)2025-04-24 09:39:44,453:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim.derep INFO(139898426345280)2025-04-24 09:39:44,920:total sequences 1527, passing sequences 1527, failing sequences 0 INFO(139898426345280)2025-04-24 09:39:44,920:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(139898426345280)2025-04-24 09:39:47,922:deblurring 1527 sequences INFO(139898426345280)2025-04-24 09:39:50,023:1111 unique sequences left following deblurring INFO(139898426345280)2025-04-24 09:39:50,031:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1U_2_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(139898426345280)2025-04-24 09:39:50,296:finished processing file INFO(139898426345280)2025-04-24 09:39:50,296:finished processing per sample fasta files INFO(139898426345280)2025-04-24 09:39:50,297:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1U_2_L001_R1_001.fastq.gz finished INFO(130667858646848)2025-04-24 09:39:51,334:************************* INFO(130667858646848)2025-04-24 09:39:51,334:deblurring started WARNING(130667858646848)2025-04-24 09:39:51,335:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1n_17_L001_R1_001.fastq.gz WARNING(130667858646848)2025-04-24 09:39:51,335:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1n_17_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(130667858646848)2025-04-24 09:39:51,335:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(130667858646848)2025-04-24 09:39:51,335:deblur worker thread started INFO(130667858646848)2025-04-24 09:39:51,335:processing per sample fasta files INFO(130667858646848)2025-04-24 09:39:51,335:-------------------------------------------------------- INFO(130667858646848)2025-04-24 09:39:51,335:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1n_17_L001_R1_001.fastq.gz INFO(126030248830784)2025-04-24 09:39:55,976:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim INFO(126030248830784)2025-04-24 09:39:56,054:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim.derep INFO(126030248830784)2025-04-24 09:39:56,557:total sequences 3187, passing sequences 3187, failing sequences 0 INFO(126030248830784)2025-04-24 09:39:56,557:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(126030248830784)2025-04-24 09:40:06,215:deblurring 3187 sequences INFO(126030248830784)2025-04-24 09:40:11,109:1183 unique sequences left following deblurring INFO(126030248830784)2025-04-24 09:40:11,117:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1g_13_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(126030248830784)2025-04-24 09:40:11,422:finished processing file INFO(126030248830784)2025-04-24 09:40:11,423:finished processing per sample fasta files INFO(126030248830784)2025-04-24 09:40:11,423:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1g_13_L001_R1_001.fastq.gz finished INFO(125110877538112)2025-04-24 09:40:12,468:************************* INFO(125110877538112)2025-04-24 09:40:12,468:deblurring started WARNING(125110877538112)2025-04-24 09:40:12,469:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1k_15_L001_R1_001.fastq.gz WARNING(125110877538112)2025-04-24 09:40:12,469:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1k_15_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(125110877538112)2025-04-24 09:40:12,469:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(125110877538112)2025-04-24 09:40:12,469:deblur worker thread started INFO(125110877538112)2025-04-24 09:40:12,469:processing per sample fasta files INFO(125110877538112)2025-04-24 09:40:12,469:-------------------------------------------------------- INFO(125110877538112)2025-04-24 09:40:12,470:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1k_15_L001_R1_001.fastq.gz INFO(135812053362496)2025-04-24 09:40:15,433:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim INFO(135812053362496)2025-04-24 09:40:15,575:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim.derep INFO(135812053362496)2025-04-24 09:40:16,117:total sequences 3017, passing sequences 3017, failing sequences 0 INFO(135812053362496)2025-04-24 09:40:16,117:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(135812053362496)2025-04-24 09:40:25,399:deblurring 3017 sequences INFO(135812053362496)2025-04-24 09:40:29,034:999 unique sequences left following deblurring INFO(135812053362496)2025-04-24 09:40:29,042:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5e_36_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(135812053362496)2025-04-24 09:40:29,317:finished processing file INFO(135812053362496)2025-04-24 09:40:29,318:finished processing per sample fasta files INFO(135812053362496)2025-04-24 09:40:29,318:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5e_36_L001_R1_001.fastq.gz finished INFO(134218361722688)2025-04-24 09:40:30,369:************************* INFO(134218361722688)2025-04-24 09:40:30,369:deblurring started WARNING(134218361722688)2025-04-24 09:40:30,369:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5a_30_L001_R1_001.fastq.gz WARNING(134218361722688)2025-04-24 09:40:30,370:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5a_30_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134218361722688)2025-04-24 09:40:30,370:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134218361722688)2025-04-24 09:40:30,370:deblur worker thread started INFO(134218361722688)2025-04-24 09:40:30,370:processing per sample fasta files INFO(134218361722688)2025-04-24 09:40:30,370:-------------------------------------------------------- INFO(134218361722688)2025-04-24 09:40:30,370:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5a_30_L001_R1_001.fastq.gz INFO(130667858646848)2025-04-24 09:40:31,867:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim INFO(130667858646848)2025-04-24 09:40:31,966:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim.derep INFO(125110877538112)2025-04-24 09:40:32,191:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim INFO(125110877538112)2025-04-24 09:40:32,252:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim.derep INFO(130667858646848)2025-04-24 09:40:32,591:total sequences 4681, passing sequences 4681, failing sequences 0 INFO(130667858646848)2025-04-24 09:40:32,591:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(125110877538112)2025-04-24 09:40:32,809:total sequences 2521, passing sequences 2521, failing sequences 0 INFO(125110877538112)2025-04-24 09:40:32,809:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131688908080960)2025-04-24 09:40:37,310:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim INFO(131688908080960)2025-04-24 09:40:37,528:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim.derep INFO(131688908080960)2025-04-24 09:40:38,207:total sequences 7234, passing sequences 7234, failing sequences 0 INFO(131688908080960)2025-04-24 09:40:38,208:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(125110877538112)2025-04-24 09:40:39,373:deblurring 2521 sequences INFO(125110877538112)2025-04-24 09:40:43,349:1140 unique sequences left following deblurring INFO(125110877538112)2025-04-24 09:40:43,356:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1k_15_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(125110877538112)2025-04-24 09:40:43,678:finished processing file INFO(125110877538112)2025-04-24 09:40:43,679:finished processing per sample fasta files INFO(125110877538112)2025-04-24 09:40:43,679:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1k_15_L001_R1_001.fastq.gz finished INFO(139802580404032)2025-04-24 09:40:44,780:************************* INFO(139802580404032)2025-04-24 09:40:44,781:deblurring started WARNING(139802580404032)2025-04-24 09:40:44,781:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5z_53_L001_R1_001.fastq.gz WARNING(139802580404032)2025-04-24 09:40:44,781:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5z_53_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(139802580404032)2025-04-24 09:40:44,781:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(139802580404032)2025-04-24 09:40:44,781:deblur worker thread started INFO(139802580404032)2025-04-24 09:40:44,781:processing per sample fasta files INFO(139802580404032)2025-04-24 09:40:44,781:-------------------------------------------------------- INFO(139802580404032)2025-04-24 09:40:44,781:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5z_53_L001_R1_001.fastq.gz INFO(130667858646848)2025-04-24 09:40:52,852:deblurring 4681 sequences INFO(134218361722688)2025-04-24 09:40:58,975:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim INFO(134218361722688)2025-04-24 09:40:58,996:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim.derep INFO(134218361722688)2025-04-24 09:40:59,442:total sequences 902, passing sequences 902, failing sequences 0 INFO(134218361722688)2025-04-24 09:40:59,442:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134218361722688)2025-04-24 09:41:01,061:deblurring 902 sequences INFO(134218361722688)2025-04-24 09:41:01,629:495 unique sequences left following deblurring INFO(134218361722688)2025-04-24 09:41:01,632:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5a_30_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(134218361722688)2025-04-24 09:41:01,754:finished processing file INFO(134218361722688)2025-04-24 09:41:01,755:finished processing per sample fasta files INFO(134218361722688)2025-04-24 09:41:01,755:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5a_30_L001_R1_001.fastq.gz finished INFO(127014216513344)2025-04-24 09:41:02,827:************************* INFO(127014216513344)2025-04-24 09:41:02,827:deblurring started WARNING(127014216513344)2025-04-24 09:41:02,828:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1t_23_L001_R1_001.fastq.gz WARNING(127014216513344)2025-04-24 09:41:02,828:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1t_23_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(127014216513344)2025-04-24 09:41:02,828:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(127014216513344)2025-04-24 09:41:02,828:deblur worker thread started INFO(127014216513344)2025-04-24 09:41:02,828:processing per sample fasta files INFO(127014216513344)2025-04-24 09:41:02,828:-------------------------------------------------------- INFO(127014216513344)2025-04-24 09:41:02,828:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1t_23_L001_R1_001.fastq.gz INFO(130667858646848)2025-04-24 09:41:07,830:2322 unique sequences left following deblurring INFO(130667858646848)2025-04-24 09:41:07,846:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1n_17_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(130667858646848)2025-04-24 09:41:08,471:finished processing file INFO(130667858646848)2025-04-24 09:41:08,473:finished processing per sample fasta files INFO(130667858646848)2025-04-24 09:41:08,473:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1n_17_L001_R1_001.fastq.gz finished INFO(137325370251072)2025-04-24 09:41:09,558:************************* INFO(137325370251072)2025-04-24 09:41:09,558:deblurring started WARNING(137325370251072)2025-04-24 09:41:09,559:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1ee_11_L001_R1_001.fastq.gz WARNING(137325370251072)2025-04-24 09:41:09,559:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1ee_11_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(137325370251072)2025-04-24 09:41:09,559:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(137325370251072)2025-04-24 09:41:09,559:deblur worker thread started INFO(137325370251072)2025-04-24 09:41:09,559:processing per sample fasta files INFO(137325370251072)2025-04-24 09:41:09,559:-------------------------------------------------------- INFO(137325370251072)2025-04-24 09:41:09,559:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1ee_11_L001_R1_001.fastq.gz INFO(131688908080960)2025-04-24 09:41:24,278:deblurring 7234 sequences INFO(127014216513344)2025-04-24 09:41:36,939:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim INFO(127014216513344)2025-04-24 09:41:37,031:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim.derep INFO(127014216513344)2025-04-24 09:41:37,623:total sequences 4668, passing sequences 4668, failing sequences 0 INFO(127014216513344)2025-04-24 09:41:37,624:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(137325370251072)2025-04-24 09:41:47,660:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim INFO(137325370251072)2025-04-24 09:41:47,739:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim.derep INFO(137325370251072)2025-04-24 09:41:48,326:total sequences 3407, passing sequences 3407, failing sequences 0 INFO(137325370251072)2025-04-24 09:41:48,326:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131688908080960)2025-04-24 09:41:55,474:2772 unique sequences left following deblurring INFO(131688908080960)2025-04-24 09:41:55,500:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5bb_33_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(131688908080960)2025-04-24 09:41:56,353:finished processing file INFO(131688908080960)2025-04-24 09:41:56,356:finished processing per sample fasta files INFO(131688908080960)2025-04-24 09:41:56,356:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5bb_33_L001_R1_001.fastq.gz finished INFO(134789583140672)2025-04-24 09:41:57,500:************************* INFO(134789583140672)2025-04-24 09:41:57,500:deblurring started WARNING(134789583140672)2025-04-24 09:41:57,501:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5g_40_L001_R1_001.fastq.gz WARNING(134789583140672)2025-04-24 09:41:57,501:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5g_40_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134789583140672)2025-04-24 09:41:57,501:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134789583140672)2025-04-24 09:41:57,501:deblur worker thread started INFO(134789583140672)2025-04-24 09:41:57,501:processing per sample fasta files INFO(134789583140672)2025-04-24 09:41:57,501:-------------------------------------------------------- INFO(134789583140672)2025-04-24 09:41:57,501:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5g_40_L001_R1_001.fastq.gz INFO(127014216513344)2025-04-24 09:41:57,519:deblurring 4668 sequences INFO(137325370251072)2025-04-24 09:41:58,787:deblurring 3407 sequences INFO(137325370251072)2025-04-24 09:42:06,316:1904 unique sequences left following deblurring INFO(137325370251072)2025-04-24 09:42:06,327:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1ee_11_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(137325370251072)2025-04-24 09:42:06,858:finished processing file INFO(137325370251072)2025-04-24 09:42:06,859:finished processing per sample fasta files INFO(137325370251072)2025-04-24 09:42:06,859:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1ee_11_L001_R1_001.fastq.gz finished INFO(133546518677312)2025-04-24 09:42:07,948:************************* INFO(133546518677312)2025-04-24 09:42:07,948:deblurring started WARNING(133546518677312)2025-04-24 09:42:07,949:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5n_44_L001_R1_001.fastq.gz WARNING(133546518677312)2025-04-24 09:42:07,949:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5n_44_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133546518677312)2025-04-24 09:42:07,949:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133546518677312)2025-04-24 09:42:07,949:deblur worker thread started INFO(133546518677312)2025-04-24 09:42:07,949:processing per sample fasta files INFO(133546518677312)2025-04-24 09:42:07,949:-------------------------------------------------------- INFO(133546518677312)2025-04-24 09:42:07,949:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5n_44_L001_R1_001.fastq.gz INFO(127014216513344)2025-04-24 09:42:11,508:2324 unique sequences left following deblurring INFO(127014216513344)2025-04-24 09:42:11,526:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1t_23_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(127014216513344)2025-04-24 09:42:12,212:finished processing file INFO(127014216513344)2025-04-24 09:42:12,213:finished processing per sample fasta files INFO(127014216513344)2025-04-24 09:42:12,214:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1t_23_L001_R1_001.fastq.gz finished INFO(128288287651648)2025-04-24 09:42:13,232:************************* INFO(128288287651648)2025-04-24 09:42:13,232:deblurring started WARNING(128288287651648)2025-04-24 09:42:13,232:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1c_6_L001_R1_001.fastq.gz WARNING(128288287651648)2025-04-24 09:42:13,233:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1c_6_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(128288287651648)2025-04-24 09:42:13,233:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(128288287651648)2025-04-24 09:42:13,233:deblur worker thread started INFO(128288287651648)2025-04-24 09:42:13,233:processing per sample fasta files INFO(128288287651648)2025-04-24 09:42:13,233:-------------------------------------------------------- INFO(128288287651648)2025-04-24 09:42:13,233:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1c_6_L001_R1_001.fastq.gz INFO(139802580404032)2025-04-24 09:42:13,701:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim INFO(139802580404032)2025-04-24 09:42:14,061:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim.derep INFO(139802580404032)2025-04-24 09:42:14,868:total sequences 12415, passing sequences 12415, failing sequences 0 INFO(139802580404032)2025-04-24 09:42:14,869:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134789583140672)2025-04-24 09:42:16,522:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim INFO(134789583140672)2025-04-24 09:42:16,629:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim.derep INFO(134789583140672)2025-04-24 09:42:17,225:total sequences 5221, passing sequences 5221, failing sequences 0 INFO(134789583140672)2025-04-24 09:42:17,225:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(133546518677312)2025-04-24 09:42:26,990:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim INFO(133546518677312)2025-04-24 09:42:27,040:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim.derep INFO(133546518677312)2025-04-24 09:42:27,552:total sequences 2366, passing sequences 2366, failing sequences 0 INFO(133546518677312)2025-04-24 09:42:27,553:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(133546518677312)2025-04-24 09:42:33,735:deblurring 2366 sequences INFO(128288287651648)2025-04-24 09:42:35,568:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim INFO(128288287651648)2025-04-24 09:42:35,616:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim.derep INFO(128288287651648)2025-04-24 09:42:36,125:total sequences 2341, passing sequences 2341, failing sequences 0 INFO(128288287651648)2025-04-24 09:42:36,125:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(133546518677312)2025-04-24 09:42:38,055:1270 unique sequences left following deblurring INFO(133546518677312)2025-04-24 09:42:38,065:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5n_44_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(133546518677312)2025-04-24 09:42:38,413:finished processing file INFO(133546518677312)2025-04-24 09:42:38,414:finished processing per sample fasta files INFO(133546518677312)2025-04-24 09:42:38,414:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5n_44_L001_R1_001.fastq.gz finished INFO(134325032511296)2025-04-24 09:42:39,505:************************* INFO(134325032511296)2025-04-24 09:42:39,506:deblurring started WARNING(134325032511296)2025-04-24 09:42:39,506:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1f_12_L001_R1_001.fastq.gz WARNING(134325032511296)2025-04-24 09:42:39,507:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1f_12_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(134325032511296)2025-04-24 09:42:39,507:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(134325032511296)2025-04-24 09:42:39,507:deblur worker thread started INFO(134325032511296)2025-04-24 09:42:39,507:processing per sample fasta files INFO(134325032511296)2025-04-24 09:42:39,507:-------------------------------------------------------- INFO(134325032511296)2025-04-24 09:42:39,507:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1f_12_L001_R1_001.fastq.gz INFO(134789583140672)2025-04-24 09:42:40,121:deblurring 5221 sequences INFO(128288287651648)2025-04-24 09:42:42,060:deblurring 2341 sequences INFO(128288287651648)2025-04-24 09:42:45,931:1258 unique sequences left following deblurring INFO(128288287651648)2025-04-24 09:42:45,939:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1c_6_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(128288287651648)2025-04-24 09:42:46,294:finished processing file INFO(128288287651648)2025-04-24 09:42:46,295:finished processing per sample fasta files INFO(128288287651648)2025-04-24 09:42:46,295:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1c_6_L001_R1_001.fastq.gz finished INFO(136418259023680)2025-04-24 09:42:47,440:************************* INFO(136418259023680)2025-04-24 09:42:47,440:deblurring started WARNING(136418259023680)2025-04-24 09:42:47,441:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5ee_37_L001_R1_001.fastq.gz WARNING(136418259023680)2025-04-24 09:42:47,441:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5ee_37_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(136418259023680)2025-04-24 09:42:47,441:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(136418259023680)2025-04-24 09:42:47,441:deblur worker thread started INFO(136418259023680)2025-04-24 09:42:47,442:processing per sample fasta files INFO(136418259023680)2025-04-24 09:42:47,442:-------------------------------------------------------- INFO(136418259023680)2025-04-24 09:42:47,442:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5ee_37_L001_R1_001.fastq.gz INFO(134789583140672)2025-04-24 09:42:58,392:2509 unique sequences left following deblurring INFO(134789583140672)2025-04-24 09:42:58,409:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5g_40_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(134789583140672)2025-04-24 09:42:59,186:finished processing file INFO(134789583140672)2025-04-24 09:42:59,188:finished processing per sample fasta files INFO(134789583140672)2025-04-24 09:42:59,188:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5g_40_L001_R1_001.fastq.gz finished INFO(124419504039744)2025-04-24 09:43:00,252:************************* INFO(124419504039744)2025-04-24 09:43:00,252:deblurring started WARNING(124419504039744)2025-04-24 09:43:00,253:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5r_48_L001_R1_001.fastq.gz WARNING(124419504039744)2025-04-24 09:43:00,253:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5r_48_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(124419504039744)2025-04-24 09:43:00,253:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(124419504039744)2025-04-24 09:43:00,253:deblur worker thread started INFO(124419504039744)2025-04-24 09:43:00,253:processing per sample fasta files INFO(124419504039744)2025-04-24 09:43:00,253:-------------------------------------------------------- INFO(124419504039744)2025-04-24 09:43:00,254:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5r_48_L001_R1_001.fastq.gz INFO(134325032511296)2025-04-24 09:43:29,863:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim INFO(134325032511296)2025-04-24 09:43:29,919:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim.derep INFO(134325032511296)2025-04-24 09:43:30,418:total sequences 1867, passing sequences 1867, failing sequences 0 INFO(134325032511296)2025-04-24 09:43:30,418:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124419504039744)2025-04-24 09:43:33,677:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim INFO(124419504039744)2025-04-24 09:43:33,749:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim.derep INFO(124419504039744)2025-04-24 09:43:34,277:total sequences 2928, passing sequences 2928, failing sequences 0 INFO(124419504039744)2025-04-24 09:43:34,277:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(134325032511296)2025-04-24 09:43:34,867:deblurring 1867 sequences INFO(134325032511296)2025-04-24 09:43:36,111:526 unique sequences left following deblurring INFO(134325032511296)2025-04-24 09:43:36,116:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1f_12_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(134325032511296)2025-04-24 09:43:36,282:finished processing file INFO(134325032511296)2025-04-24 09:43:36,283:finished processing per sample fasta files INFO(134325032511296)2025-04-24 09:43:36,283:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1f_12_L001_R1_001.fastq.gz finished INFO(124419504039744)2025-04-24 09:43:42,482:deblurring 2928 sequences INFO(136418259023680)2025-04-24 09:43:42,598:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim INFO(136418259023680)2025-04-24 09:43:42,671:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim.derep INFO(136418259023680)2025-04-24 09:43:43,217:total sequences 3216, passing sequences 3216, failing sequences 0 INFO(136418259023680)2025-04-24 09:43:43,217:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(124419504039744)2025-04-24 09:43:48,730:1667 unique sequences left following deblurring INFO(124419504039744)2025-04-24 09:43:48,743:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5r_48_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(124419504039744)2025-04-24 09:43:49,175:finished processing file INFO(124419504039744)2025-04-24 09:43:49,177:finished processing per sample fasta files INFO(124419504039744)2025-04-24 09:43:49,177:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5r_48_L001_R1_001.fastq.gz finished INFO(131194571511616)2025-04-24 09:43:50,188:************************* INFO(131194571511616)2025-04-24 09:43:50,188:deblurring started WARNING(131194571511616)2025-04-24 09:43:50,188:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1v_24_L001_R1_001.fastq.gz WARNING(131194571511616)2025-04-24 09:43:50,188:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1v_24_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(131194571511616)2025-04-24 09:43:50,189:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(131194571511616)2025-04-24 09:43:50,189:deblur worker thread started INFO(131194571511616)2025-04-24 09:43:50,189:processing per sample fasta files INFO(131194571511616)2025-04-24 09:43:50,189:-------------------------------------------------------- INFO(131194571511616)2025-04-24 09:43:50,189:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1v_24_L001_R1_001.fastq.gz INFO(136418259023680)2025-04-24 09:43:52,920:deblurring 3216 sequences INFO(136418259023680)2025-04-24 09:43:58,619:1427 unique sequences left following deblurring INFO(136418259023680)2025-04-24 09:43:58,630:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5ee_37_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(136418259023680)2025-04-24 09:43:59,014:finished processing file INFO(136418259023680)2025-04-24 09:43:59,015:finished processing per sample fasta files INFO(136418259023680)2025-04-24 09:43:59,015:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5ee_37_L001_R1_001.fastq.gz finished INFO(133061256075072)2025-04-24 09:44:00,044:************************* INFO(133061256075072)2025-04-24 09:44:00,044:deblurring started WARNING(133061256075072)2025-04-24 09:44:00,045:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5p_46_L001_R1_001.fastq.gz WARNING(133061256075072)2025-04-24 09:44:00,045:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5p_46_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(133061256075072)2025-04-24 09:44:00,045:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(133061256075072)2025-04-24 09:44:00,045:deblur worker thread started INFO(133061256075072)2025-04-24 09:44:00,045:processing per sample fasta files INFO(133061256075072)2025-04-24 09:44:00,045:-------------------------------------------------------- INFO(133061256075072)2025-04-24 09:44:00,045:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5p_46_L001_R1_001.fastq.gz INFO(131194571511616)2025-04-24 09:44:19,956:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim INFO(131194571511616)2025-04-24 09:44:20,003:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim.derep INFO(131194571511616)2025-04-24 09:44:20,474:total sequences 2467, passing sequences 2467, failing sequences 0 INFO(131194571511616)2025-04-24 09:44:20,474:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(139802580404032)2025-04-24 09:44:20,968:deblurring 12415 sequences INFO(133061256075072)2025-04-24 09:44:22,781:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim INFO(133061256075072)2025-04-24 09:44:22,831:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim.derep INFO(133061256075072)2025-04-24 09:44:23,328:total sequences 3193, passing sequences 3193, failing sequences 0 INFO(133061256075072)2025-04-24 09:44:23,328:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(131194571511616)2025-04-24 09:44:26,344:deblurring 2467 sequences INFO(131194571511616)2025-04-24 09:44:30,050:1239 unique sequences left following deblurring INFO(131194571511616)2025-04-24 09:44:30,058:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1v_24_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(131194571511616)2025-04-24 09:44:30,378:finished processing file INFO(131194571511616)2025-04-24 09:44:30,379:finished processing per sample fasta files INFO(131194571511616)2025-04-24 09:44:30,380:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1v_24_L001_R1_001.fastq.gz finished INFO(133061256075072)2025-04-24 09:44:32,122:deblurring 3193 sequences INFO(133061256075072)2025-04-24 09:44:39,024:2027 unique sequences left following deblurring INFO(133061256075072)2025-04-24 09:44:39,036:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5p_46_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(133061256075072)2025-04-24 09:44:39,513:finished processing file INFO(133061256075072)2025-04-24 09:44:39,514:finished processing per sample fasta files INFO(133061256075072)2025-04-24 09:44:39,514:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5p_46_L001_R1_001.fastq.gz finished INFO(139802580404032)2025-04-24 09:46:17,897:7155 unique sequences left following deblurring INFO(139802580404032)2025-04-24 09:46:17,956:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site5z_53_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(139802580404032)2025-04-24 09:46:19,972:finished processing file INFO(139802580404032)2025-04-24 09:46:19,976:finished processing per sample fasta files INFO(139802580404032)2025-04-24 09:46:19,977:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site5z_53_L001_R1_001.fastq.gz finished INFO(123248336131904)2025-04-24 09:46:20,767:************************* INFO(123248336131904)2025-04-24 09:46:20,768:deblurring started WARNING(123248336131904)2025-04-24 09:46:20,768:deblur version 1.1.1 workflow started on /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1bb_5_L001_R1_001.fastq.gz WARNING(123248336131904)2025-04-24 09:46:20,768:parameters: {'seqs_fp': '/tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1bb_5_L001_R1_001.fastq.gz', 'output_dir': '/tmp/tmpc40oidxs', 'pos_ref_fp': ('/tmp/qiime2/sam/data/a7432d0f-b5f7-409f-9daf-cd33db5de53f/data/dna-sequences.fasta',), 'pos_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/dna-sequences',), 'neg_ref_fp': (), 'neg_ref_db_fp': ('/tmp/tmpc40oidxs/deblur_working_dir/artifacts',), 'overwrite': True, 'mean_error': 0.005, 'error_dist': [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005], 'indel_prob': 0.01, 'indel_max': 3, 'trim_length': 150, 'left_trim_length': 0, 'min_reads': 10, 'min_size': 2, 'threads_per_sample': 1, 'keep_tmp_files': True, 'log_level': 2, 'log_file': '/home/sam/gitrepos/RobertsLab/project-eDNA-yellow/code/deblur.log', 'jobs_to_start': 1, 'is_worker_thread': True, 'logger': } INFO(123248336131904)2025-04-24 09:46:20,768:error_dist is : [1.0, 0.06, 0.02, 0.02, 0.01, 0.005, 0.005, 0.005, 0.001, 0.001, 0.001, 0.0005] INFO(123248336131904)2025-04-24 09:46:20,768:deblur worker thread started INFO(123248336131904)2025-04-24 09:46:20,768:processing per sample fasta files INFO(123248336131904)2025-04-24 09:46:20,768:-------------------------------------------------------- INFO(123248336131904)2025-04-24 09:46:20,768:launch_workflow for file /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1bb_5_L001_R1_001.fastq.gz INFO(123248336131904)2025-04-24 09:46:42,477:dereplicate seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim INFO(123248336131904)2025-04-24 09:46:42,501:remove_artifacts_seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim.derep INFO(123248336131904)2025-04-24 09:46:42,894:total sequences 1030, passing sequences 1030, failing sequences 0 INFO(123248336131904)2025-04-24 09:46:42,894:multiple_sequence_alignment seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim.derep.no_artifacts INFO(123248336131904)2025-04-24 09:46:44,396:deblurring 1030 sequences INFO(123248336131904)2025-04-24 09:46:44,867:506 unique sequences left following deblurring INFO(123248336131904)2025-04-24 09:46:44,869:remove_chimeras_denovo_from_seqs seqs file /tmp/tmpc40oidxs/deblur_working_dir/Site1bb_5_L001_R1_001.fastq.gz.trim.derep.no_artifacts.msa.deblurto working dir /tmp/tmpc40oidxs/deblur_working_dir INFO(123248336131904)2025-04-24 09:46:44,979:finished processing file INFO(123248336131904)2025-04-24 09:46:44,979:finished processing per sample fasta files INFO(123248336131904)2025-04-24 09:46:44,979:worker thread for /tmp/qiime2/sam/data/de09150f-6cca-41e4-8755-16795f8a2df1/data/Site1bb_5_L001_R1_001.fastq.gz finished INFO(124786264745792)2025-04-24 09:46:45,129:create_otu_table for 52 samples, into output table /tmp/tmpc40oidxs/all.biom INFO(124786264745792)2025-04-24 09:46:47,575:for output biom table loaded 52 samples, 20785 unique sequences INFO(124786264745792)2025-04-24 09:46:47,602:keeping 5670 (out of 20785 sequences) with >=10 reads INFO(124786264745792)2025-04-24 09:46:47,776:saved to biom file /tmp/tmpc40oidxs/all.biom INFO(124786264745792)2025-04-24 09:46:47,781:saved sequence fasta file to /tmp/tmpc40oidxs/all.seqs.fa INFO(124786264745792)2025-04-24 09:46:47,786:getting 16s sequences from the biom table INFO(124786264745792)2025-04-24 09:46:47,787:remove_artifacts_seqs file /tmp/tmpc40oidxs/all.seqs.fa INFO(124786264745792)2025-04-24 09:47:28,364:total sequences 5670, passing sequences 706, failing sequences 4964 INFO(124786264745792)2025-04-24 09:47:28,434:wrote artifact only filtered biom table to /tmp/tmpc40oidxs/reference-non-hit.biom INFO(124786264745792)2025-04-24 09:47:28,441:saved biom table sequences to fasta file /tmp/tmpc40oidxs/reference-non-hit.seqs.fa WARNING(124786264745792)2025-04-24 09:47:28,445:removed 2 samples with reads per sample<1 INFO(124786264745792)2025-04-24 09:47:28,455:wrote 16s filtered biom table to /tmp/tmpc40oidxs/reference-hit.biom INFO(124786264745792)2025-04-24 09:47:28,457:saved biom table sequences to fasta file /tmp/tmpc40oidxs/reference-hit.seqs.fa INFO(124786264745792)2025-04-24 09:47:28,457:Keeping temp files INFO(124786264745792)2025-04-24 09:47:28,457:deblur workflow finished INFO(124786264745792)2025-04-24 09:47:28,457:output saved to /tmp/tmpc40oidxs/all.biom INFO(124786264745792)2025-04-24 09:47:28,457:------------------