/var/spool/slurm/d/job1433927/slurm_script: line 32: fg: no job control
Begin flipping the strand of read 2
Wed Oct 30 09:58:09 2019

Input not indexed. Indexing...
Wed Oct 30 10:10:29 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 10:39:32 2019

Input not indexed. Indexing...
Wed Oct 30 10:49:33 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 11:13:04 2019

Input not indexed. Indexing...
Wed Oct 30 11:20:52 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 11:40:37 2019

Input not indexed. Indexing...
Wed Oct 30 11:49:52 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 12:14:09 2019

Input not indexed. Indexing...
Wed Oct 30 12:24:17 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 12:47:40 2019

Input not indexed. Indexing...
Wed Oct 30 12:57:29 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 13:22:58 2019

Input not indexed. Indexing...
Wed Oct 30 13:31:50 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 13:51:11 2019

Input not indexed. Indexing...
Wed Oct 30 14:00:22 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 14:26:13 2019

Input not indexed. Indexing...
Wed Oct 30 14:37:04 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 15:03:22 2019

Input not indexed. Indexing...
Wed Oct 30 15:13:39 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 15:39:36 2019

Input not indexed. Indexing...
Wed Oct 30 15:52:04 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 16:12:49 2019

Input not indexed. Indexing...
Wed Oct 30 16:20:56 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 16:37:44 2019

Input not indexed. Indexing...
Wed Oct 30 16:44:47 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 17:00:50 2019

Input not indexed. Indexing...
Wed Oct 30 17:08:02 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 17:28:22 2019

Input not indexed. Indexing...
Wed Oct 30 17:35:56 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 17:54:55 2019

Input not indexed. Indexing...
Wed Oct 30 18:03:25 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 18:24:23 2019

Input not indexed. Indexing...
Wed Oct 30 18:33:42 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 18:55:13 2019

Input not indexed. Indexing...
Wed Oct 30 19:03:58 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 19:18:22 2019

Input not indexed. Indexing...
Wed Oct 30 19:26:13 2019

[mpileup] 1 samples in 1 input files
Begin flipping the strand of read 2
Wed Oct 30 19:48:03 2019

Input not indexed. Indexing...
Wed Oct 30 19:56:01 2019

[mpileup] 1 samples in 1 input files
/var/spool/slurm/d/job1433927/slurm_script: line 50: fg: no job control
usage: methylpy DMRfind [-h] --allc-files ALLC_FILES [ALLC_FILES ...]
                        --output-prefix OUTPUT_PREFIX
                        [--samples SAMPLES [SAMPLES ...]]
                        [--chroms CHROMS [CHROMS ...]]
                        [--mc-type MC_TYPE [MC_TYPE ...]]
                        [--num-procs NUM_PROCS] [--min-cov MIN_COV]
                        [--dmr-max-dist DMR_MAX_DIST]
                        [--sig-cutoff SIG_CUTOFF] [--num-sims NUM_SIMS]
                        [--min-tests MIN_TESTS] [--min-num-dms MIN_NUM_DMS]
                        [--sample-category SAMPLE_CATEGORY [SAMPLE_CATEGORY ...]]
                        [--mc-max-dist MC_MAX_DIST]
                        [--resid-cutoff RESID_CUTOFF]
                        [--keep-temp-files KEEP_TEMP_FILES]
                        [--min-cluster MIN_CLUSTER] [--seed SEED]
methylpy DMRfind: error: the following arguments are required: --output-prefix
/var/spool/slurm/d/job1433927/slurm_script: line 74: --samples: command not found
/var/spool/slurm/d/job1433927/slurm_script: line 89: fg: no job control
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_1_S13.sorted.bam --output-file 16C_26psu_1_S13.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_2_S14.sorted.bam --output-file 16C_26psu_2_S14.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_3_S15.sorted.bam --output-file 16C_26psu_3_S15.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_26psu_4_S16.sorted.bam --output-file 16C_26psu_4_S16.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_1_S1.sorted.bam --output-file 16C_32psu_1_S1.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_2_S2.sorted.bam --output-file 16C_32psu_2_S2.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_3_S3.sorted.bam --output-file 16C_32psu_3_S3.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/16C_32psu_4_S4.sorted.bam --output-file 16C_32psu_4_S4.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_1_S9.sorted.bam --output-file 8C_26psu_1_S9.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_2_S10.sorted.bam --output-file 8C_26psu_2_S10.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_3_S11.sorted.bam --output-file 8C_26psu_3_S11.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_26psu_4_S12.sorted.bam --output-file 8C_26psu_4_S12.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_1_S5.sorted.bam --output-file 8C_32psu_1_S5.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_2_S6.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_2_S6.sorted.bam --output-file 8C_32psu_2_S6.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_3_S7.sorted.bam --output-file 8C_32psu_3_S7.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/8C_32psu_4_S8.sorted.bam --output-file 8C_32psu_4_S8.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_1_S19.sorted.bam --output-file CTRL_16C_26psu_1_S19.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_16C_26psu_2_S21.sorted.bam --output-file CTRL_16C_26psu_2_S21.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_1_S17.sorted.bam --output-file CTRL_8C_26psu_1_S17.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
Processing /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18.sorted.bam file methylpy bam-quality-filter --input-file /gscratch/scrubbed/strigg/analyses/20190828_Salmo/CTRL_8C_26psu_2_S18.sorted.bam --output-file CTRL_8C_26psu_2_S18.sorted.bam.sorted.bam.MQ20.filtered.bam --ref-fasta /gscratch/srlab/strigg/data/Ssalar/GENOMES/chr1-29MT/GCF_000233375.1_ICSASG_v2_genomic.fa --min-mapq 20 --min-num-ch 3 --max-mch-level 0.7 --buffer-line-number 100
mv: cannot stat ‘/gscratch/scrubbed/strigg/analyses/20190828_Salmo/*.MQ20.filtered.bam’: No such file or directory
[E::hts_open_format] Failed to open file *.MQ20.filtered.bam
samtools index: failed to open "*.MQ20.filtered.bam": No such file or directory