Multicore support not enabled. Proceeding with single-core trimming. Path to Cutadapt set as: '/usr/lusers/yaaminiv/.local/bin/cutadapt' (user defined) Cutadapt seems to be working fine (tested command '/usr/lusers/yaaminiv/.local/bin/cutadapt --version') Cutadapt version: 3.1 single-core operation. No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) Output will be written into the directory: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/ Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_1_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_1_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j 1 Writing final adapter and quality trimmed output to zr3616_1_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_1_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_1_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3834.05 s (24 µs/read; 2.52 M reads/minute). === Summary === Total reads processed: 161,236,355 Reads with adapters: 69,191,738 (42.9%) Reads written (passing filters): 161,236,355 (100.0%) Total basepairs processed: 16,097,674,230 bp Quality-trimmed: 12,874,747 bp (0.1%) Total written (filtered): 16,006,234,206 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 69191738 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.1% C: 10.9% G: 7.2% T: 36.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 62763288 40309088.8 0 62763288 2 4229388 10077272.2 0 4229388 3 1479655 2519318.0 0 1479655 4 709665 629829.5 0 709665 5 4423 157457.4 0 4423 6 1782 39364.3 0 1782 7 615 9841.1 0 615 8 147 2460.3 0 147 9 864 615.1 0 65 799 10 1561 153.8 1 10 1551 11 290 38.4 1 6 284 12 56 9.6 1 0 56 13 4 2.4 1 0 4 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_1_R1_val_1.fq.gz ============================================= 161236355 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_1_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_1_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_1_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_1_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_1_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3847.02 s (24 µs/read; 2.51 M reads/minute). === Summary === Total reads processed: 161,236,355 Reads with adapters: 69,092,736 (42.9%) Reads written (passing filters): 161,236,355 (100.0%) Total basepairs processed: 16,097,114,176 bp Quality-trimmed: 16,560,046 bp (0.1%) Total written (filtered): 16,002,140,047 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 69092736 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.2% C: 10.7% G: 7.2% T: 36.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 62721636 40309088.8 0 62721636 2 4174107 10077272.2 0 4174107 3 1471919 2519318.0 0 1471919 4 713701 629829.5 0 713701 5 6120 157457.4 0 6120 6 1724 39364.3 0 1724 7 626 9841.1 0 626 8 133 2460.3 0 133 9 843 615.1 0 76 767 10 1555 153.8 1 12 1543 11 325 38.4 1 1 324 12 42 9.6 1 0 42 13 4 2.4 1 0 4 14 1 2.4 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_1_R2_val_2.fq.gz ============================================= 161236355 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_1_R1_val_1_trimmed.fq.gz and zr3616_1_R2_val_2_trimmed.fq.gz file_1: zr3616_1_R1_val_1_trimmed.fq.gz, file_2: zr3616_1_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_1_R1_val_1_trimmed.fq.gz and zr3616_1_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_1_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_1_R2_val_2_val_2.fq.gz Total number of sequences analysed: 161236355 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 131647 (0.08%) >>> Now running FastQC on the validated data zr3616_1_R1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 644945420. >>> Now running FastQC on the validated data zr3616_1_R2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 644945420. Deleting both intermediate output files zr3616_1_R1_val_1_trimmed.fq.gz and zr3616_1_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_2_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_2_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_2_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_2_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_2_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3936.54 s (24 µs/read; 2.54 M reads/minute). === Summary === Total reads processed: 166,968,754 Reads with adapters: 72,050,260 (43.2%) Reads written (passing filters): 166,968,754 (100.0%) Total basepairs processed: 16,649,016,827 bp Quality-trimmed: 13,348,721 bp (0.1%) Total written (filtered): 16,553,811,294 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 72050260 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.1% C: 10.8% G: 7.2% T: 36.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 65331373 41742188.5 0 65331373 2 4414117 10435547.1 0 4414117 3 1549631 2608886.8 0 1549631 4 745094 652221.7 0 745094 5 4608 163055.4 0 4608 6 1733 40763.9 0 1733 7 578 10191.0 0 578 8 145 2547.7 0 145 9 919 636.9 0 60 859 10 1711 159.2 1 19 1692 11 302 39.8 1 2 300 12 48 10.0 1 0 48 13 1 2.5 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_2_R1_val_1.fq.gz ============================================= 166968754 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_2_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_2_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_2_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_2_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_2_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4025.76 s (24 µs/read; 2.49 M reads/minute). === Summary === Total reads processed: 166,968,754 Reads with adapters: 72,030,649 (43.1%) Reads written (passing filters): 166,968,754 (100.0%) Total basepairs processed: 16,652,184,280 bp Quality-trimmed: 18,025,036 bp (0.1%) Total written (filtered): 16,552,510,285 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 72030649 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.3% C: 10.7% G: 7.1% T: 36.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 65474090 41742188.5 0 65474090 2 4278730 10435547.1 0 4278730 3 1522141 2608886.8 0 1522141 4 744071 652221.7 0 744071 5 6464 163055.4 0 6464 6 1663 40763.9 0 1663 7 592 10191.0 0 592 8 148 2547.7 0 148 9 908 636.9 0 87 821 10 1470 159.2 1 13 1457 11 311 39.8 1 6 305 12 52 10.0 1 0 52 13 7 2.5 1 0 7 33 1 2.5 1 0 1 35 1 2.5 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_2_R2_val_2.fq.gz ============================================= 166968754 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_2_R1_val_1_trimmed.fq.gz and zr3616_2_R2_val_2_trimmed.fq.gz file_1: zr3616_2_R1_val_1_trimmed.fq.gz, file_2: zr3616_2_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_2_R1_val_1_trimmed.fq.gz and zr3616_2_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_2_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_2_R2_val_2_val_2.fq.gz Total number of sequences analysed: 166968754 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 136735 (0.08%) >>> Now running FastQC on the validated data zr3616_2_R1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 1312820436. >>> Now running FastQC on the validated data zr3616_2_R2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 1312820436. Deleting both intermediate output files zr3616_2_R1_val_1_trimmed.fq.gz and zr3616_2_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_3_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_3_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_3_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_3_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_3_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4163.00 s (22 µs/read; 2.72 M reads/minute). === Summary === Total reads processed: 188,570,462 Reads with adapters: 80,733,395 (42.8%) Reads written (passing filters): 188,570,462 (100.0%) Total basepairs processed: 17,936,139,623 bp Quality-trimmed: 13,556,549 bp (0.1%) Total written (filtered): 17,830,717,001 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 80733395 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.9% C: 10.8% G: 7.3% T: 37.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 73137967 47142615.5 0 73137967 2 4966325 11785653.9 0 4966325 3 1752381 2946413.5 0 1752381 4 865292 736603.4 0 865292 5 5112 184150.8 0 5112 6 2087 46037.7 0 2087 7 791 11509.4 0 791 8 123 2877.4 0 123 9 1079 719.3 0 66 1013 10 1861 179.8 1 25 1836 11 308 45.0 1 1 307 12 64 11.2 1 0 64 13 5 2.8 1 0 5 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_3_R1_val_1.fq.gz ============================================= 188570462 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_3_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_3_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_3_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_3_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_3_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4261.97 s (23 µs/read; 2.65 M reads/minute). === Summary === Total reads processed: 188,570,462 Reads with adapters: 80,665,127 (42.8%) Reads written (passing filters): 188,570,462 (100.0%) Total basepairs processed: 17,936,143,783 bp Quality-trimmed: 19,692,763 bp (0.1%) Total written (filtered): 17,824,830,257 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 80665127 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 10.8% G: 7.3% T: 37.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 73217738 47142615.5 0 73217738 2 4849872 11785653.9 0 4849872 3 1721795 2946413.5 0 1721795 4 861358 736603.4 0 861358 5 7989 184150.8 0 7989 6 2062 46037.7 0 2062 7 713 11509.4 0 713 8 175 2877.4 0 175 9 1044 719.3 0 85 959 10 1897 179.8 1 14 1883 11 424 45.0 1 1 423 12 54 11.2 1 0 54 13 6 2.8 1 0 6 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_3_R2_val_2.fq.gz ============================================= 188570462 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_3_R1_val_1_trimmed.fq.gz and zr3616_3_R2_val_2_trimmed.fq.gz file_1: zr3616_3_R1_val_1_trimmed.fq.gz, file_2: zr3616_3_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_3_R1_val_1_trimmed.fq.gz and zr3616_3_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_3_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_3_R2_val_2_val_2.fq.gz Total number of sequences analysed: 188570462 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 194796 (0.10%) >>> Now running FastQC on the validated data zr3616_3_R1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 2067102284. >>> Now running FastQC on the validated data zr3616_3_R2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 2067102284. Deleting both intermediate output files zr3616_3_R1_val_1_trimmed.fq.gz and zr3616_3_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_4_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_4_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_4_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_4_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_4_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4471.78 s (23 µs/read; 2.66 M reads/minute). === Summary === Total reads processed: 197,994,215 Reads with adapters: 85,382,636 (43.1%) Reads written (passing filters): 197,994,215 (100.0%) Total basepairs processed: 19,327,202,283 bp Quality-trimmed: 14,840,406 bp (0.1%) Total written (filtered): 19,215,160,741 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 85382636 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.9% C: 10.8% G: 7.4% T: 37.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 77293926 49498553.8 0 77293926 2 5309316 12374638.4 0 5309316 3 1862901 3093659.6 0 1862901 4 904500 773414.9 0 904500 5 5358 193353.7 0 5358 6 2008 48338.4 0 2008 7 782 12084.6 0 782 8 157 3021.2 0 157 9 1122 755.3 0 57 1065 10 2103 188.8 1 15 2088 11 393 47.2 1 5 388 12 66 11.8 1 0 66 13 2 3.0 1 0 2 19 2 3.0 1 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_4_R1_val_1.fq.gz ============================================= 197994215 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_4_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_4_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_4_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_4_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_4_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4583.87 s (23 µs/read; 2.59 M reads/minute). === Summary === Total reads processed: 197,994,215 Reads with adapters: 85,518,274 (43.2%) Reads written (passing filters): 197,994,215 (100.0%) Total basepairs processed: 19,331,276,134 bp Quality-trimmed: 21,095,559 bp (0.1%) Total written (filtered): 19,213,114,882 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 85518274 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 10.8% G: 7.2% T: 37.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 77651535 49498553.8 0 77651535 2 5133623 12374638.4 0 5133623 3 1820996 3093659.6 0 1820996 4 898055 773414.9 0 898055 5 7474 193353.7 0 7474 6 2069 48338.4 0 2069 7 771 12084.6 0 771 8 194 3021.2 0 194 9 1156 755.3 0 78 1078 10 1930 188.8 1 14 1916 11 389 47.2 1 1 388 12 78 11.8 1 0 78 13 4 3.0 1 0 4 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_4_R2_val_2.fq.gz ============================================= 197994215 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_4_R1_val_1_trimmed.fq.gz and zr3616_4_R2_val_2_trimmed.fq.gz file_1: zr3616_4_R1_val_1_trimmed.fq.gz, file_2: zr3616_4_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_4_R1_val_1_trimmed.fq.gz and zr3616_4_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_4_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_4_R2_val_2_val_2.fq.gz Total number of sequences analysed: 197994215 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 172073 (0.09%) >>> Now running FastQC on the validated data zr3616_4_R1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 2859079144. >>> Now running FastQC on the validated data zr3616_4_R2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 2859079144. Deleting both intermediate output files zr3616_4_R1_val_1_trimmed.fq.gz and zr3616_4_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_5_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_5_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_5_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_5_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_5_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3406.19 s (23 µs/read; 2.62 M reads/minute). === Summary === Total reads processed: 148,703,891 Reads with adapters: 64,090,433 (43.1%) Reads written (passing filters): 148,703,891 (100.0%) Total basepairs processed: 14,312,976,515 bp Quality-trimmed: 12,726,746 bp (0.1%) Total written (filtered): 14,227,316,196 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64090433 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.9% C: 10.8% G: 7.4% T: 36.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 58036774 37175972.8 0 58036774 2 3974093 9293993.2 0 3974093 3 1393864 2323498.3 0 1393864 4 676909 580874.6 0 676909 5 3986 145218.6 0 3986 6 1509 36304.7 0 1509 7 647 9076.2 0 647 8 117 2269.0 0 117 9 801 567.3 0 51 750 10 1395 141.8 1 12 1383 11 286 35.5 1 3 283 12 45 8.9 1 0 45 13 7 2.2 1 0 7 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_5_R1_val_1.fq.gz ============================================= 148703891 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_5_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_5_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_5_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_5_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_5_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3400.83 s (23 µs/read; 2.62 M reads/minute). === Summary === Total reads processed: 148,703,891 Reads with adapters: 63,834,369 (42.9%) Reads written (passing filters): 148,703,891 (100.0%) Total basepairs processed: 14,313,656,899 bp Quality-trimmed: 15,779,438 bp (0.1%) Total written (filtered): 14,225,303,648 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 63834369 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 10.8% G: 7.3% T: 37.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 57873635 37175972.8 0 57873635 2 3899292 9293993.2 0 3899292 3 1371063 2323498.3 0 1371063 4 679337 580874.6 0 679337 5 6129 145218.6 0 6129 6 1562 36304.7 0 1562 7 607 9076.2 0 607 8 132 2269.0 0 132 9 850 567.3 0 53 797 10 1426 141.8 1 17 1409 11 269 35.5 1 0 269 12 59 8.9 1 0 59 13 6 2.2 1 0 6 17 1 2.2 1 0 1 63 1 2.2 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_5_R2_val_2.fq.gz ============================================= 148703891 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_5_R1_val_1_trimmed.fq.gz and zr3616_5_R2_val_2_trimmed.fq.gz file_1: zr3616_5_R1_val_1_trimmed.fq.gz, file_2: zr3616_5_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_5_R1_val_1_trimmed.fq.gz and zr3616_5_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_5_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_5_R2_val_2_val_2.fq.gz Total number of sequences analysed: 148703891 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 147339 (0.10%) >>> Now running FastQC on the validated data zr3616_5_R1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 3453894708. >>> Now running FastQC on the validated data zr3616_5_R2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 3453894708. Deleting both intermediate output files zr3616_5_R1_val_1_trimmed.fq.gz and zr3616_5_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_6_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_6_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_6_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_6_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_6_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4492.65 s (23 µs/read; 2.60 M reads/minute). === Summary === Total reads processed: 195,031,602 Reads with adapters: 83,929,651 (43.0%) Reads written (passing filters): 195,031,602 (100.0%) Total basepairs processed: 18,448,842,626 bp Quality-trimmed: 17,583,668 bp (0.1%) Total written (filtered): 18,335,636,313 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 83929651 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.7% C: 10.9% G: 7.5% T: 36.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 75945182 48757900.5 0 75945182 2 5221016 12189475.1 0 5221016 3 1854537 3047368.8 0 1854537 4 893411 761842.2 0 893411 5 9023 190460.5 0 9023 6 2110 47615.1 0 2110 7 805 11903.8 0 805 8 137 2975.9 0 137 9 1139 744.0 0 81 1058 10 1883 186.0 1 16 1867 11 336 46.5 1 4 332 12 64 11.6 1 0 64 13 5 2.9 1 0 5 20 3 2.9 1 0 3 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_6_R1_val_1.fq.gz ============================================= 195031602 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_6_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_6_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_6_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_6_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_6_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4368.39 s (22 µs/read; 2.68 M reads/minute). === Summary === Total reads processed: 195,031,602 Reads with adapters: 83,611,065 (42.9%) Reads written (passing filters): 195,031,602 (100.0%) Total basepairs processed: 18,453,430,191 bp Quality-trimmed: 20,059,174 bp (0.1%) Total written (filtered): 18,338,376,548 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 83611065 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 10.8% G: 7.3% T: 36.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 75861779 48757900.5 0 75861779 2 5056910 12189475.1 0 5056910 3 1784972 3047368.8 0 1784972 4 893213 761842.2 0 893213 5 8094 190460.5 0 8094 6 1813 47615.1 0 1813 7 750 11903.8 0 750 8 152 2975.9 0 152 9 1111 744.0 0 68 1043 10 1791 186.0 1 19 1772 11 398 46.5 1 3 395 12 79 11.6 1 0 79 13 1 2.9 1 0 1 20 2 2.9 1 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_6_R2_val_2.fq.gz ============================================= 195031602 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_6_R1_val_1_trimmed.fq.gz and zr3616_6_R2_val_2_trimmed.fq.gz file_1: zr3616_6_R1_val_1_trimmed.fq.gz, file_2: zr3616_6_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_6_R1_val_1_trimmed.fq.gz and zr3616_6_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_6_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_6_R2_val_2_val_2.fq.gz Total number of sequences analysed: 195031602 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 209939 (0.11%) >>> Now running FastQC on the validated data zr3616_6_R1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 4234021116. >>> Now running FastQC on the validated data zr3616_6_R2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 4234021116. Deleting both intermediate output files zr3616_6_R1_val_1_trimmed.fq.gz and zr3616_6_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_7_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_7_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_7_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_7_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_7_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3412.55 s (23 µs/read; 2.62 M reads/minute). === Summary === Total reads processed: 149,222,025 Reads with adapters: 64,446,811 (43.2%) Reads written (passing filters): 149,222,025 (100.0%) Total basepairs processed: 14,426,231,802 bp Quality-trimmed: 12,087,412 bp (0.1%) Total written (filtered): 14,340,775,620 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64446811 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.7% C: 10.7% G: 7.3% T: 37.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 58345741 37305506.2 0 58345741 2 4001019 9326376.6 0 4001019 3 1403784 2331594.1 0 1403784 4 686989 582898.5 0 686989 5 4511 145724.6 0 4511 6 1581 36431.2 0 1581 7 534 9107.8 0 534 8 109 2276.9 0 109 9 828 569.2 0 39 789 10 1365 142.3 1 16 1349 11 284 35.6 1 1 283 12 62 8.9 1 0 62 13 2 2.2 1 0 2 16 1 2.2 1 0 1 20 1 2.2 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_7_R1_val_1.fq.gz ============================================= 149222025 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_7_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_7_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_7_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_7_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_7_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3473.50 s (23 µs/read; 2.58 M reads/minute). === Summary === Total reads processed: 149,222,025 Reads with adapters: 64,464,629 (43.2%) Reads written (passing filters): 149,222,025 (100.0%) Total basepairs processed: 14,426,694,309 bp Quality-trimmed: 16,612,357 bp (0.1%) Total written (filtered): 14,336,913,165 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64464629 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.9% C: 10.8% G: 7.2% T: 37.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 58535083 37305506.2 0 58535083 2 3869783 9326376.6 0 3869783 3 1371391 2331594.1 0 1371391 4 676997 582898.5 0 676997 5 6639 145724.6 0 6639 6 1592 36431.2 0 1592 7 522 9107.8 0 522 8 113 2276.9 0 113 9 829 569.2 0 67 762 10 1366 142.3 1 8 1358 11 260 35.6 1 3 257 12 43 8.9 1 0 43 13 9 2.2 1 0 9 29 2 2.2 1 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_7_R2_val_2.fq.gz ============================================= 149222025 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_7_R1_val_1_trimmed.fq.gz and zr3616_7_R2_val_2_trimmed.fq.gz file_1: zr3616_7_R1_val_1_trimmed.fq.gz, file_2: zr3616_7_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_7_R1_val_1_trimmed.fq.gz and zr3616_7_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_7_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_7_R2_val_2_val_2.fq.gz Total number of sequences analysed: 149222025 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 141961 (0.10%) >>> Now running FastQC on the validated data zr3616_7_R1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 4830909216. >>> Now running FastQC on the validated data zr3616_7_R2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 4830909216. Deleting both intermediate output files zr3616_7_R1_val_1_trimmed.fq.gz and zr3616_7_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_8_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_8_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_8_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_8_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_8_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3652.09 s (23 µs/read; 2.65 M reads/minute). === Summary === Total reads processed: 161,458,218 Reads with adapters: 69,685,366 (43.2%) Reads written (passing filters): 161,458,218 (100.0%) Total basepairs processed: 15,674,571,216 bp Quality-trimmed: 12,487,517 bp (0.1%) Total written (filtered): 15,582,808,489 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 69685366 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.9% C: 10.8% G: 7.3% T: 37.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 63131255 40364554.5 0 63131255 2 4295409 10091138.6 0 4295409 3 1509558 2522784.7 0 1509558 4 739241 630696.2 0 739241 5 4412 157674.0 0 4412 6 1725 39418.5 0 1725 7 598 9854.6 0 598 8 143 2463.7 0 143 9 914 615.9 0 47 867 10 1758 154.0 1 10 1748 11 288 38.5 1 2 286 12 60 9.6 1 0 60 13 5 2.4 1 0 5 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_8_R1_val_1.fq.gz ============================================= 161458218 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_8_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_8_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_8_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_8_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_8_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3769.29 s (23 µs/read; 2.57 M reads/minute). === Summary === Total reads processed: 161,458,218 Reads with adapters: 69,620,122 (43.1%) Reads written (passing filters): 161,458,218 (100.0%) Total basepairs processed: 15,679,022,191 bp Quality-trimmed: 17,518,289 bp (0.1%) Total written (filtered): 15,582,472,384 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 69620122 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 10.8% G: 7.2% T: 37.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 63214029 40364554.5 0 63214029 2 4176619 10091138.6 0 4176619 3 1483295 2522784.7 0 1483295 4 734105 630696.2 0 734105 5 6633 157674.0 0 6633 6 1712 39418.5 0 1712 7 684 9854.6 0 684 8 128 2463.7 0 128 9 920 615.9 0 50 870 10 1628 154.0 1 10 1618 11 315 38.5 1 5 310 12 47 9.6 1 0 47 13 5 2.4 1 0 5 15 1 2.4 1 0 1 28 1 2.4 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_8_R2_val_2.fq.gz ============================================= 161458218 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_8_R1_val_1_trimmed.fq.gz and zr3616_8_R2_val_2_trimmed.fq.gz file_1: zr3616_8_R1_val_1_trimmed.fq.gz, file_2: zr3616_8_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_8_R1_val_1_trimmed.fq.gz and zr3616_8_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_8_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_8_R2_val_2_val_2.fq.gz Total number of sequences analysed: 161458218 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 148434 (0.09%) >>> Now running FastQC on the validated data zr3616_8_R1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 5476742088. >>> Now running FastQC on the validated data zr3616_8_R2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 5476742088. Deleting both intermediate output files zr3616_8_R1_val_1_trimmed.fq.gz and zr3616_8_R2_val_2_trimmed.fq.gz ==================================================================================================== TrimGalore 2 complete [INFO ] multiqc : This is MultiQC v1.8 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching : /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2 [INFO ] cutadapt : Found 16 reports [INFO ] multiqc : Compressing plot data [WARNING] multiqc : Previous MultiQC output found! Adjusting filenames.. [WARNING] multiqc : Use -f or --force to overwrite existing reports instead [INFO ] multiqc : Report : multiqc_report_1.html [INFO ] multiqc : Data : multiqc_data_1 [INFO ] multiqc : MultiQC complete MultiQC2 complete Multicore support not enabled. Proceeding with single-core trimming. Path to Cutadapt set as: '/usr/lusers/yaaminiv/.local/bin/cutadapt' (user defined) Cutadapt seems to be working fine (tested command '/usr/lusers/yaaminiv/.local/bin/cutadapt --version') Cutadapt version: 3.1 single-core operation. No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) Output will be written into the directory: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/ Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_1_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_1_R1_val_1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j 1 Writing final adapter and quality trimmed output to zr3616_1_R1_val_1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_1_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_1_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3900.62 s (24 µs/read; 2.48 M reads/minute). === Summary === Total reads processed: 161,104,708 Reads with adapters: 17,875,932 (11.1%) Reads written (passing filters): 161,104,708 (100.0%) Total basepairs processed: 16,001,858,566 bp Quality-trimmed: 3,273,494 bp (0.0%) Total written (filtered): 15,778,099,632 bp (98.6%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 17875932 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 24.7% C: 4.8% G: 0.0% T: 70.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10884348 40276177.0 0 10884348 2 3228008 10069044.2 0 3228008 3 699678 2517261.1 0 699678 4 201565 629315.3 0 201565 5 59981 157328.8 0 59981 6 17764 39332.2 0 17764 7 7890 9833.1 0 7890 8 5644 2458.3 0 5644 9 5575 614.6 0 5575 10 10369 153.6 1 5164 5205 11 9180 38.4 1 4650 4530 12 7582 9.6 1 4084 3498 13 6734 2.4 1 3626 3108 14 6106 0.6 1 3225 2881 15 5445 0.2 1 2998 2447 16 4828 0.0 1 2657 2171 17 3902 0.0 1 2218 1684 18 3293 0.0 1 2161 1132 19 3037 0.0 1 1996 1041 20 4549 0.0 2 2075 1029 1445 21 3975 0.0 2 1867 934 1174 22 3721 0.0 2 1824 874 1023 23 3568 0.0 2 1824 814 930 24 3385 0.0 2 1719 798 868 25 3082 0.0 2 1567 740 775 26 2909 0.0 2 1476 689 744 27 2779 0.0 2 1430 672 677 28 2467 0.0 2 1429 612 426 29 2296 0.0 2 1275 577 444 30 2887 0.0 3 1247 593 398 649 31 2829 0.0 3 1262 549 443 575 32 2694 0.0 3 1156 533 424 581 33 2602 0.0 3 1141 557 378 526 34 2661 0.0 3 1172 551 402 536 35 2562 0.0 3 1105 571 404 482 36 2512 0.0 3 1134 529 391 458 37 2287 0.0 3 1074 488 306 419 38 2236 0.0 3 1105 481 347 303 39 2145 0.0 3 1107 467 299 272 40 2597 0.0 4 1034 468 337 281 477 41 2508 0.0 4 1014 466 296 277 455 42 2489 0.0 4 980 480 299 289 441 43 2576 0.0 4 1009 505 353 312 397 44 2240 0.0 4 881 449 287 272 351 45 2247 0.0 4 891 428 305 266 357 46 2227 0.0 4 954 448 255 229 341 47 2241 0.0 4 979 449 297 237 279 48 2571 0.0 4 1192 560 360 237 222 49 4774 0.0 4 2065 1061 717 526 405 50 5067 0.0 5 2042 1083 692 491 413 346 51 3718 0.0 5 1932 700 437 294 190 165 52 3387 0.0 5 1884 637 361 232 156 117 53 3143 0.0 5 1872 541 301 200 129 100 54 3120 0.0 5 1950 518 274 161 123 94 55 2889 0.0 5 1892 474 254 125 86 58 56 2872 0.0 5 1933 438 231 132 98 40 57 3108 0.0 5 2256 414 203 113 68 54 58 3847 0.0 5 3034 408 198 102 60 45 59 3848 0.0 5 3123 391 174 73 57 30 60 2354 0.0 5 1683 353 145 81 47 45 61 2370 0.0 5 1803 306 127 77 40 17 62 2655 0.0 5 2052 318 148 73 36 28 63 3468 0.0 5 2908 277 140 74 47 22 64 5285 0.0 5 4725 299 134 59 44 24 65 2617 0.0 5 1988 307 186 74 37 25 66 3197 0.0 5 2612 316 142 69 38 20 67 2602 0.0 5 2108 269 106 62 38 19 68 2800 0.0 5 2300 287 102 49 40 22 69 3628 0.0 5 3094 290 118 62 37 27 70 7032 0.0 5 6545 303 91 50 29 14 71 16115 0.0 5 15578 332 100 55 32 18 72 104862 0.0 5 104244 402 107 68 26 15 73 183893 0.0 5 183291 398 106 45 32 21 74 1469317 0.0 5 1468746 372 99 48 36 16 75 48741 0.0 5 48314 250 96 42 28 11 76 46631 0.0 5 46236 224 79 44 30 18 77 287320 0.0 5 286940 209 73 55 25 18 78 22515 0.0 5 22193 185 67 28 19 23 79 184264 0.0 5 183942 157 72 48 24 21 80 44340 0.0 5 44052 155 63 30 20 20 81 22849 0.0 5 22564 142 58 42 21 22 82 67259 0.0 5 67016 118 57 35 21 12 83 6009 0.0 5 5730 129 71 43 18 18 84 28039 0.0 5 27769 141 55 38 23 13 85 5635 0.0 5 5415 124 46 27 14 9 86 834 0.0 5 633 100 43 28 14 16 87 733 0.0 5 525 114 39 25 19 11 88 723 0.0 5 538 87 48 21 15 14 89 604 0.0 5 436 81 42 20 16 9 90 660 0.0 5 452 91 46 35 21 15 91 602 0.0 5 427 77 36 33 18 11 92 523 0.0 5 365 75 38 20 16 9 93 491 0.0 5 343 65 39 25 11 8 94 482 0.0 5 328 79 31 25 10 9 95 451 0.0 5 317 57 32 21 11 13 96 383 0.0 5 259 60 20 26 11 7 97 388 0.0 5 260 66 24 16 14 8 98 338 0.0 5 253 49 9 14 9 4 99 313 0.0 5 231 28 21 13 14 6 100 287 0.0 5 186 39 22 21 12 7 101 270 0.0 5 189 40 16 4 13 8 102 222 0.0 5 155 19 16 11 7 14 103 186 0.0 5 127 24 11 5 11 8 104 177 0.0 5 126 16 10 11 8 6 105 130 0.0 5 90 10 15 9 5 1 106 130 0.0 5 88 15 6 10 4 7 107 92 0.0 5 65 6 8 8 2 3 108 78 0.0 5 60 9 2 1 3 3 109 78 0.0 5 58 4 8 3 3 2 110 78 0.0 5 59 4 4 2 6 3 111 68 0.0 5 52 6 0 3 5 2 112 46 0.0 5 33 3 3 2 2 3 113 34 0.0 5 23 4 3 2 1 1 114 52 0.0 5 39 6 4 1 1 1 115 138 0.0 5 125 5 4 2 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_1_R1_val_1_val_1.fq.gz ============================================= 161104708 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_1_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_1_R2_val_2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_1_R2_val_2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_1_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_1_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3956.98 s (25 µs/read; 2.44 M reads/minute). === Summary === Total reads processed: 161,104,708 Reads with adapters: 17,645,060 (11.0%) Reads written (passing filters): 161,104,708 (100.0%) Total basepairs processed: 15,998,741,118 bp Quality-trimmed: 3,705,302 bp (0.0%) Total written (filtered): 15,671,714,831 bp (98.0%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 17645060 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 13.9% C: 5.5% G: 0.0% T: 80.4% none/other: 0.2% WARNING: The adapter is preceded by "T" extremely often. The provided adapter sequence could be incomplete at its 5' end. Overview of removed sequences length count expect max.err error counts 1 10759713 40276177.0 0 10759713 2 3172985 10069044.2 0 3172985 3 686503 2517261.1 0 686503 4 196142 629315.3 0 196142 5 57428 157328.8 0 57428 6 14331 39332.2 0 14331 7 4632 9833.1 0 4632 8 2835 2458.3 0 2835 9 2641 614.6 0 2641 10 7444 153.6 1 2368 5076 11 6072 38.4 1 2170 3902 12 5019 9.6 1 2029 2990 13 4279 2.4 1 1807 2472 14 3713 0.6 1 1577 2136 15 3446 0.2 1 1461 1985 16 2994 0.0 1 1324 1670 17 2333 0.0 1 1048 1285 18 1902 0.0 1 1032 870 19 1773 0.0 1 1012 761 20 3542 0.0 2 1328 741 1473 21 3301 0.0 2 1151 711 1439 22 3011 0.0 2 1062 630 1319 23 2933 0.0 2 1069 649 1215 24 2630 0.0 2 1009 563 1058 25 2436 0.0 2 911 538 987 26 2231 0.0 2 854 526 851 27 1922 0.0 2 865 387 670 28 1539 0.0 2 733 364 442 29 1592 0.0 2 759 350 483 30 2502 0.0 3 730 359 458 955 31 2370 0.0 3 669 350 427 924 32 2304 0.0 3 691 322 438 853 33 2309 0.0 3 751 381 395 782 34 2118 0.0 3 667 329 364 758 35 2078 0.0 3 657 340 380 701 36 1846 0.0 3 646 281 350 569 37 1699 0.0 3 594 307 273 525 38 1609 0.0 3 647 281 305 376 39 1539 0.0 3 610 306 299 324 40 2210 0.0 4 602 282 272 323 731 41 2172 0.0 4 602 300 265 346 659 42 2003 0.0 4 540 262 262 334 605 43 2014 0.0 4 507 281 247 353 626 44 2028 0.0 4 549 268 278 337 596 45 1968 0.0 4 572 273 248 306 569 46 1873 0.0 4 615 289 234 290 445 47 1895 0.0 4 646 338 277 208 426 48 2105 0.0 4 737 424 354 330 260 49 4857 0.0 4 1505 1100 901 726 625 50 5173 0.0 5 1419 1045 850 669 608 582 51 4051 0.0 5 1512 858 563 448 372 298 52 3355 0.0 5 1364 669 454 384 269 215 53 3032 0.0 5 1332 629 376 303 221 171 54 2891 0.0 5 1390 554 375 243 187 142 55 2523 0.0 5 1221 495 315 207 177 108 56 2443 0.0 5 1374 424 245 184 120 96 57 2339 0.0 5 1323 388 243 164 117 104 58 2244 0.0 5 1323 380 198 163 110 70 59 1975 0.0 5 1154 341 197 121 88 74 60 1804 0.0 5 1058 314 163 114 93 62 61 1775 0.0 5 1063 316 152 102 80 62 62 1802 0.0 5 1138 303 146 98 60 57 63 1636 0.0 5 1036 259 153 86 57 45 64 1700 0.0 5 1106 284 117 93 61 39 65 1634 0.0 5 1107 253 133 64 40 37 66 1543 0.0 5 1076 229 109 68 38 23 67 1572 0.0 5 1122 210 104 66 45 25 68 1664 0.0 5 1249 185 103 54 43 30 69 1512 0.0 5 1139 183 90 47 36 17 70 1353 0.0 5 968 192 80 50 35 28 71 1233 0.0 5 907 155 77 38 35 21 72 1260 0.0 5 959 147 70 36 27 21 73 1208 0.0 5 911 129 77 36 25 30 74 1148 0.0 5 875 115 67 45 30 16 75 1050 0.0 5 773 122 73 40 21 21 76 1158 0.0 5 925 117 48 28 28 12 77 1156 0.0 5 916 112 53 37 17 21 78 937 0.0 5 733 107 42 25 16 14 79 893 0.0 5 684 109 42 27 13 18 80 951 0.0 5 706 119 60 21 23 22 81 892 0.0 5 710 80 43 27 17 15 82 847 0.0 5 654 88 41 25 25 14 83 788 0.0 5 619 75 42 23 18 11 84 761 0.0 5 587 80 39 19 16 20 85 829 0.0 5 658 69 37 28 19 18 86 735 0.0 5 593 65 32 25 9 11 87 695 0.0 5 547 72 35 15 12 14 88 701 0.0 5 567 67 27 10 20 10 89 669 0.0 5 526 65 33 20 17 8 90 575 0.0 5 440 56 36 17 15 11 91 560 0.0 5 443 57 25 14 13 8 92 566 0.0 5 442 43 36 21 14 10 93 529 0.0 5 415 40 26 17 20 11 94 587 0.0 5 471 48 29 22 10 7 95 542 0.0 5 416 58 29 14 15 10 96 473 0.0 5 377 43 16 15 13 9 97 504 0.0 5 387 52 28 11 12 14 98 415 0.0 5 306 48 19 16 17 9 99 457 0.0 5 347 44 18 21 16 11 100 430 0.0 5 335 32 26 18 11 8 101 427 0.0 5 328 32 26 16 14 11 102 410 0.0 5 313 40 18 16 12 11 103 389 0.0 5 298 30 27 13 11 10 104 350 0.0 5 256 37 25 15 7 10 105 379 0.0 5 295 32 16 10 13 13 106 382 0.0 5 300 28 19 14 10 11 107 385 0.0 5 311 21 21 15 11 6 108 400 0.0 5 303 33 26 12 13 13 109 449 0.0 5 344 42 25 15 11 12 110 543 0.0 5 434 33 20 19 25 12 111 580 0.0 5 463 38 27 19 21 12 112 947 0.0 5 785 50 32 27 21 32 113 1227 0.0 5 1042 51 44 33 32 25 114 3851 0.0 5 3483 141 82 64 36 45 115 2557950 0.0 5 2557183 374 205 80 57 51 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_1_R2_val_2_val_2.fq.gz ============================================= 161104708 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_1_R1_val_1_val_1_trimmed.fq.gz and zr3616_1_R2_val_2_val_2_trimmed.fq.gz file_1: zr3616_1_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3616_1_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_1_R1_val_1_val_1_trimmed.fq.gz and zr3616_1_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_1_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_1_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 161104708 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2648078 (1.64%) >>> Now running FastQC on the validated data zr3616_1_R1_val_1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 644418832. >>> Now running FastQC on the validated data zr3616_1_R2_val_2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 644418832. Deleting both intermediate output files zr3616_1_R1_val_1_val_1_trimmed.fq.gz and zr3616_1_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_2_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_2_R1_val_1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_2_R1_val_1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_2_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_2_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3936.08 s (24 µs/read; 2.54 M reads/minute). === Summary === Total reads processed: 166,832,019 Reads with adapters: 17,883,352 (10.7%) Reads written (passing filters): 166,832,019 (100.0%) Total basepairs processed: 16,549,204,997 bp Quality-trimmed: 3,301,519 bp (0.0%) Total written (filtered): 16,366,200,743 bp (98.9%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 17883352 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 21.8% C: 5.0% G: 0.0% T: 73.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11285978 41708004.8 0 11285978 2 3352840 10427001.2 0 3352840 3 722486 2606750.3 0 722486 4 206221 651687.6 0 206221 5 62359 162921.9 0 62359 6 17727 40730.5 0 17727 7 8073 10182.6 0 8073 8 5535 2545.7 0 5535 9 5745 636.4 0 5745 10 10634 159.1 1 5435 5199 11 9278 39.8 1 4850 4428 12 7801 9.9 1 4112 3689 13 6950 2.5 1 3672 3278 14 6400 0.6 1 3483 2917 15 5472 0.2 1 2978 2494 16 5001 0.0 1 2745 2256 17 3825 0.0 1 2162 1663 18 3311 0.0 1 2114 1197 19 3120 0.0 1 2073 1047 20 4630 0.0 2 2149 1006 1475 21 4080 0.0 2 1986 944 1150 22 3745 0.0 2 1863 823 1059 23 3551 0.0 2 1760 858 933 24 3579 0.0 2 1805 861 913 25 3174 0.0 2 1619 746 809 26 2994 0.0 2 1487 784 723 27 2874 0.0 2 1563 668 643 28 2729 0.0 2 1489 719 521 29 2423 0.0 2 1390 605 428 30 3066 0.0 3 1361 613 461 631 31 2886 0.0 3 1292 583 421 590 32 2869 0.0 3 1259 581 437 592 33 2719 0.0 3 1237 524 417 541 34 2706 0.0 3 1142 584 438 542 35 2620 0.0 3 1137 581 401 501 36 2605 0.0 3 1167 572 381 485 37 2527 0.0 3 1219 549 341 418 38 2360 0.0 3 1196 571 320 273 39 2267 0.0 3 1111 513 324 319 40 2617 0.0 4 1055 515 358 280 409 41 2581 0.0 4 1015 479 341 283 463 42 2537 0.0 4 1031 469 340 303 394 43 2455 0.0 4 949 483 340 307 376 44 2345 0.0 4 985 456 287 271 346 45 2326 0.0 4 967 439 314 265 341 46 2157 0.0 4 900 434 279 263 281 47 2314 0.0 4 1030 522 284 206 272 48 2529 0.0 4 1149 551 357 244 228 49 4582 0.0 4 1920 1047 685 547 383 50 4836 0.0 5 2029 1052 649 474 342 290 51 3641 0.0 5 1968 657 419 270 174 153 52 3165 0.0 5 1834 561 321 205 135 109 53 3091 0.0 5 1887 559 288 167 97 93 54 3064 0.0 5 1981 492 267 144 118 62 55 2875 0.0 5 1880 459 251 157 73 55 56 2987 0.0 5 2110 414 202 118 89 54 57 3463 0.0 5 2601 428 196 117 70 51 58 3356 0.0 5 2633 359 165 99 51 49 59 2894 0.0 5 2236 326 160 84 47 41 60 2354 0.0 5 1688 328 157 92 57 32 61 2416 0.0 5 1834 319 118 76 43 26 62 2930 0.0 5 2353 283 154 71 45 24 63 3818 0.0 5 3204 341 134 62 43 34 64 3488 0.0 5 2953 291 109 81 20 34 65 2414 0.0 5 1820 297 154 88 36 19 66 2758 0.0 5 2172 315 143 61 41 26 67 2491 0.0 5 1931 305 137 56 44 18 68 2778 0.0 5 2293 264 116 48 34 23 69 3854 0.0 5 3347 309 93 49 28 28 70 8046 0.0 5 7522 325 99 54 20 26 71 24602 0.0 5 24038 354 102 48 38 22 72 80938 0.0 5 80393 328 95 56 38 28 73 316767 0.0 5 316233 315 115 48 33 23 74 953499 0.0 5 952998 295 98 53 38 17 75 43254 0.0 5 42782 266 92 58 29 27 76 77338 0.0 5 76893 241 94 55 29 26 77 179877 0.0 5 179490 207 84 54 26 16 78 43978 0.0 5 43586 219 93 37 26 17 79 115275 0.0 5 114886 199 84 56 32 18 80 30555 0.0 5 30229 158 84 38 22 24 81 26012 0.0 5 25637 198 94 32 28 23 82 37525 0.0 5 37254 144 58 27 31 11 83 18735 0.0 5 18440 151 64 34 21 25 84 32421 0.0 5 32135 140 71 36 24 15 85 5987 0.0 5 5719 124 61 39 25 19 86 1179 0.0 5 946 116 48 30 24 15 87 818 0.0 5 583 108 50 35 28 14 88 715 0.0 5 493 106 56 23 14 23 89 690 0.0 5 500 86 43 19 25 17 90 680 0.0 5 472 87 54 28 22 17 91 637 0.0 5 450 92 46 24 13 12 92 570 0.0 5 376 82 46 32 20 14 93 521 0.0 5 375 59 43 17 19 8 94 475 0.0 5 320 74 43 14 10 14 95 411 0.0 5 271 51 36 24 15 14 96 459 0.0 5 300 65 36 22 20 16 97 379 0.0 5 253 54 23 27 12 10 98 328 0.0 5 223 50 24 10 15 6 99 305 0.0 5 210 44 26 10 9 6 100 308 0.0 5 199 41 27 17 15 9 101 303 0.0 5 210 29 22 18 16 8 102 227 0.0 5 158 20 22 12 12 3 103 198 0.0 5 146 17 11 8 7 9 104 155 0.0 5 113 13 10 11 4 4 105 139 0.0 5 101 14 9 11 1 3 106 105 0.0 5 70 10 7 8 6 4 107 100 0.0 5 72 9 6 5 2 6 108 94 0.0 5 65 8 4 3 8 6 109 70 0.0 5 53 6 3 1 2 5 110 70 0.0 5 55 3 2 5 0 5 111 62 0.0 5 50 3 2 2 1 4 112 43 0.0 5 28 2 4 4 1 4 113 31 0.0 5 22 2 0 2 2 3 114 35 0.0 5 28 2 3 2 115 160 0.0 5 144 5 5 2 2 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_2_R1_val_1_val_1.fq.gz ============================================= 166832019 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_2_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_2_R2_val_2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_2_R2_val_2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_2_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_2_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4017.41 s (24 µs/read; 2.49 M reads/minute). === Summary === Total reads processed: 166,832,019 Reads with adapters: 17,423,292 (10.4%) Reads written (passing filters): 166,832,019 (100.0%) Total basepairs processed: 16,548,960,510 bp Quality-trimmed: 4,272,473 bp (0.0%) Total written (filtered): 16,284,859,854 bp (98.4%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 17423292 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 14.0% C: 5.4% G: 0.0% T: 80.6% none/other: 0.1% WARNING: The adapter is preceded by "T" extremely often. The provided adapter sequence could be incomplete at its 5' end. Overview of removed sequences length count expect max.err error counts 1 11020761 41708004.8 0 11020761 2 3225765 10427001.2 0 3225765 3 700743 2606750.3 0 700743 4 199754 651687.6 0 199754 5 58835 162921.9 0 58835 6 14425 40730.5 0 14425 7 4917 10182.6 0 4917 8 2830 2545.7 0 2830 9 2613 636.4 0 2613 10 7299 159.1 1 2320 4979 11 6085 39.8 1 2148 3937 12 4966 9.9 1 2064 2902 13 4195 2.5 1 1746 2449 14 3940 0.6 1 1633 2307 15 3285 0.2 1 1471 1814 16 2784 0.0 1 1245 1539 17 2348 0.0 1 1094 1254 18 1916 0.0 1 1077 839 19 1798 0.0 1 995 803 20 3512 0.0 2 1289 726 1497 21 3212 0.0 2 1169 700 1343 22 3100 0.0 2 1115 695 1290 23 2982 0.0 2 1132 632 1218 24 2669 0.0 2 981 624 1064 25 2628 0.0 2 992 607 1029 26 2252 0.0 2 885 481 886 27 1964 0.0 2 854 409 701 28 1764 0.0 2 858 411 495 29 1682 0.0 2 804 413 465 30 2621 0.0 3 791 365 517 948 31 2450 0.0 3 708 384 426 932 32 2336 0.0 3 738 371 406 821 33 2274 0.0 3 725 375 397 777 34 2321 0.0 3 746 395 381 799 35 2150 0.0 3 678 385 388 699 36 1879 0.0 3 684 292 337 566 37 1783 0.0 3 631 322 294 536 38 1574 0.0 3 600 330 281 363 39 1542 0.0 3 564 318 281 379 40 2247 0.0 4 597 292 296 358 704 41 2171 0.0 4 524 341 275 329 702 42 2112 0.0 4 581 294 271 344 622 43 1987 0.0 4 495 284 267 346 595 44 2064 0.0 4 608 293 261 327 575 45 1972 0.0 4 610 241 252 317 552 46 1916 0.0 4 633 280 218 301 484 47 1874 0.0 4 635 331 279 229 400 48 2176 0.0 4 725 442 387 346 276 49 5033 0.0 4 1567 1109 872 823 662 50 5243 0.0 5 1414 1081 876 689 636 547 51 4068 0.0 5 1510 823 613 457 360 305 52 3448 0.0 5 1453 687 474 361 249 224 53 3045 0.0 5 1337 643 366 269 240 190 54 2912 0.0 5 1350 580 370 264 193 155 55 2651 0.0 5 1304 516 296 213 209 113 56 2488 0.0 5 1295 447 285 207 143 111 57 2257 0.0 5 1267 403 231 175 113 68 58 2249 0.0 5 1288 397 227 150 98 89 59 1962 0.0 5 1091 347 200 138 109 77 60 1844 0.0 5 1112 288 188 122 74 60 61 1802 0.0 5 1106 295 163 103 85 50 62 1731 0.0 5 1070 303 157 101 62 38 63 1680 0.0 5 1076 261 144 88 62 49 64 1678 0.0 5 1076 263 136 90 65 48 65 1661 0.0 5 1093 250 133 95 48 42 66 1503 0.0 5 1025 234 112 58 47 27 67 1650 0.0 5 1148 225 120 77 46 34 68 1664 0.0 5 1215 222 114 43 48 22 69 1460 0.0 5 1087 186 79 49 32 27 70 1305 0.0 5 952 190 72 38 26 27 71 1266 0.0 5 943 151 81 50 25 16 72 1259 0.0 5 926 159 78 48 30 18 73 1158 0.0 5 852 157 57 42 29 21 74 1088 0.0 5 823 120 55 40 22 28 75 1072 0.0 5 815 123 65 39 15 15 76 1108 0.0 5 868 113 62 31 19 15 77 1066 0.0 5 817 124 56 34 16 19 78 893 0.0 5 704 87 52 21 16 13 79 883 0.0 5 680 99 48 28 19 9 80 919 0.0 5 729 94 33 31 18 14 81 788 0.0 5 638 80 31 16 14 9 82 731 0.0 5 583 60 31 26 13 18 83 795 0.0 5 626 82 30 22 16 19 84 685 0.0 5 526 69 41 18 19 12 85 756 0.0 5 597 61 41 26 19 12 86 656 0.0 5 517 65 30 23 10 11 87 647 0.0 5 509 65 26 19 14 14 88 701 0.0 5 561 63 24 16 21 16 89 605 0.0 5 468 60 34 19 15 9 90 580 0.0 5 432 77 24 19 17 11 91 536 0.0 5 431 44 26 17 10 8 92 515 0.0 5 407 48 27 13 11 9 93 522 0.0 5 408 63 23 11 9 8 94 540 0.0 5 430 51 21 15 11 12 95 494 0.0 5 393 42 23 21 6 9 96 419 0.0 5 337 31 13 15 9 14 97 497 0.0 5 394 45 24 16 7 11 98 418 0.0 5 324 38 22 14 17 3 99 421 0.0 5 327 48 12 14 11 9 100 384 0.0 5 294 26 23 17 13 11 101 399 0.0 5 320 37 10 9 12 11 102 381 0.0 5 304 20 26 12 11 8 103 387 0.0 5 311 31 15 9 6 15 104 339 0.0 5 275 18 19 13 7 7 105 394 0.0 5 326 31 6 12 11 8 106 410 0.0 5 327 32 12 16 11 12 107 400 0.0 5 315 26 13 17 15 14 108 360 0.0 5 278 29 13 11 17 12 109 456 0.0 5 367 32 14 17 13 13 110 549 0.0 5 460 22 19 16 19 13 111 580 0.0 5 463 38 26 23 12 18 112 921 0.0 5 750 49 33 30 29 30 113 1304 0.0 5 1108 62 43 24 33 34 114 3982 0.0 5 3628 140 67 61 46 40 115 2002221 0.0 5 2001464 342 181 103 81 50 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_2_R2_val_2_val_2.fq.gz ============================================= 166832019 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_2_R1_val_1_val_1_trimmed.fq.gz and zr3616_2_R2_val_2_val_2_trimmed.fq.gz file_1: zr3616_2_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3616_2_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_2_R1_val_1_val_1_trimmed.fq.gz and zr3616_2_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_2_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_2_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 166832019 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2094853 (1.26%) >>> Now running FastQC on the validated data zr3616_2_R1_val_1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 1311746908. >>> Now running FastQC on the validated data zr3616_2_R2_val_2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 1311746908. Deleting both intermediate output files zr3616_2_R1_val_1_val_1_trimmed.fq.gz and zr3616_2_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_3_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_3_R1_val_1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_3_R1_val_1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_3_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_3_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4187.98 s (22 µs/read; 2.70 M reads/minute). === Summary === Total reads processed: 188,375,666 Reads with adapters: 21,487,316 (11.4%) Reads written (passing filters): 188,375,666 (100.0%) Total basepairs processed: 17,824,771,638 bp Quality-trimmed: 3,215,006 bp (0.0%) Total written (filtered): 17,516,630,527 bp (98.3%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 21487316 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 26.4% C: 4.8% G: 0.0% T: 68.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12641085 47093916.5 0 12641085 2 3819940 11773479.1 0 3819940 3 818216 2943369.8 0 818216 4 234891 735842.4 0 234891 5 70824 183960.6 0 70824 6 20278 45990.2 0 20278 7 9122 11497.5 0 9122 8 6477 2874.4 0 6477 9 6440 718.6 0 6440 10 11606 179.6 1 5859 5747 11 10276 44.9 1 5251 5025 12 8714 11.2 1 4548 4166 13 7477 2.8 1 3942 3535 14 6748 0.7 1 3522 3226 15 5893 0.2 1 3045 2848 16 5158 0.0 1 2800 2358 17 4001 0.0 1 2221 1780 18 3396 0.0 1 2200 1196 19 3084 0.0 1 1996 1088 20 4649 0.0 2 2053 1006 1590 21 4154 0.0 2 1972 921 1261 22 3873 0.0 2 1864 897 1112 23 3765 0.0 2 1909 847 1009 24 3677 0.0 2 1753 895 1029 25 3324 0.0 2 1662 843 819 26 2905 0.0 2 1452 687 766 27 2911 0.0 2 1528 671 712 28 2553 0.0 2 1450 601 502 29 2473 0.0 2 1370 623 480 30 3100 0.0 3 1282 612 489 717 31 2966 0.0 3 1305 575 443 643 32 2839 0.0 3 1181 588 424 646 33 2909 0.0 3 1277 570 422 640 34 2776 0.0 3 1161 573 428 614 35 2830 0.0 3 1144 599 476 611 36 2520 0.0 3 1088 506 388 538 37 2546 0.0 3 1152 542 375 477 38 2348 0.0 3 1146 547 339 316 39 2384 0.0 3 1130 525 376 353 40 2945 0.0 4 1108 556 390 352 539 41 2746 0.0 4 1008 477 391 352 518 42 2694 0.0 4 1020 504 369 331 470 43 2722 0.0 4 1001 515 380 378 448 44 2565 0.0 4 906 504 334 326 495 45 2553 0.0 4 1037 464 352 300 400 46 2479 0.0 4 1013 500 315 289 362 47 2509 0.0 4 1076 503 329 253 348 48 2846 0.0 4 1222 632 431 283 278 49 5862 0.0 4 2461 1342 887 653 519 50 6105 0.0 5 2396 1308 868 617 515 401 51 4688 0.0 5 2494 876 527 355 246 190 52 3964 0.0 5 2252 729 399 270 180 134 53 3763 0.0 5 2275 687 319 209 153 120 54 3657 0.0 5 2311 619 333 180 118 96 55 3390 0.0 5 2176 557 308 169 105 75 56 3641 0.0 5 2560 487 271 151 111 61 57 4177 0.0 5 3173 476 248 114 101 65 58 4958 0.0 5 4010 468 238 130 74 38 59 4573 0.0 5 3708 422 200 105 86 52 60 2904 0.0 5 2106 408 188 94 66 42 61 2926 0.0 5 2181 385 163 99 61 37 62 3283 0.0 5 2613 352 142 81 61 34 63 4465 0.0 5 3818 361 139 60 46 41 64 6007 0.0 5 5330 376 142 79 45 35 65 3203 0.0 5 2450 344 227 102 50 30 66 3882 0.0 5 3172 389 189 58 50 24 67 3282 0.0 5 2631 366 131 79 53 22 68 3709 0.0 5 3107 348 127 69 37 21 69 4833 0.0 5 4191 410 109 62 41 20 70 10036 0.0 5 9436 376 120 57 30 17 71 26300 0.0 5 25603 441 137 62 28 29 72 161602 0.0 5 160850 514 125 66 32 15 73 313026 0.0 5 312367 439 121 57 22 20 74 2036504 0.0 5 2035846 442 108 52 41 15 75 90984 0.0 5 90513 287 94 48 22 20 76 81294 0.0 5 80829 273 92 52 28 20 77 406407 0.0 5 405997 246 75 37 32 20 78 39317 0.0 5 38952 213 68 47 21 16 79 241697 0.0 5 241343 184 91 39 23 17 80 52913 0.0 5 52567 180 68 56 25 17 81 32905 0.0 5 32580 185 61 36 28 15 82 83320 0.0 5 83028 157 50 43 27 15 83 7092 0.0 5 6801 149 60 36 25 21 84 22662 0.0 5 22392 152 64 28 17 9 85 3825 0.0 5 3581 126 60 20 26 12 86 977 0.0 5 709 117 69 43 23 16 87 912 0.0 5 698 118 44 24 18 10 88 858 0.0 5 650 94 62 29 14 9 89 743 0.0 5 548 94 44 22 16 19 90 683 0.0 5 496 92 40 24 14 17 91 725 0.0 5 515 107 51 27 18 7 92 614 0.0 5 431 92 48 22 12 9 93 612 0.0 5 451 64 42 30 16 9 94 509 0.0 5 365 62 30 20 22 10 95 507 0.0 5 361 67 29 18 15 17 96 435 0.0 5 288 55 38 27 13 14 97 392 0.0 5 283 46 27 17 12 7 98 356 0.0 5 241 44 30 16 13 12 99 346 0.0 5 239 36 30 26 12 3 100 301 0.0 5 218 37 21 7 14 4 101 271 0.0 5 180 34 23 17 12 5 102 243 0.0 5 168 32 14 13 10 6 103 225 0.0 5 164 22 12 8 8 11 104 196 0.0 5 145 18 14 7 4 8 105 155 0.0 5 117 16 9 5 2 6 106 126 0.0 5 88 15 11 5 2 5 107 120 0.0 5 86 11 8 5 3 7 108 102 0.0 5 72 5 7 9 4 5 109 82 0.0 5 57 7 7 5 3 3 110 77 0.0 5 58 4 4 4 4 3 111 81 0.0 5 70 2 2 5 1 1 112 49 0.0 5 39 1 2 3 3 1 113 50 0.0 5 41 2 2 0 2 3 114 48 0.0 5 40 2 1 2 2 1 115 178 0.0 5 170 4 2 1 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_3_R1_val_1_val_1.fq.gz ============================================= 188375666 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_3_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_3_R2_val_2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_3_R2_val_2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_3_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_3_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4254.60 s (23 µs/read; 2.66 M reads/minute). === Summary === Total reads processed: 188,375,666 Reads with adapters: 21,144,092 (11.2%) Reads written (passing filters): 188,375,666 (100.0%) Total basepairs processed: 17,820,129,803 bp Quality-trimmed: 4,295,767 bp (0.0%) Total written (filtered): 17,363,855,972 bp (97.4%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 21144092 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 14.1% C: 5.6% G: 0.0% T: 80.4% none/other: 0.0% WARNING: The adapter is preceded by "T" extremely often. The provided adapter sequence could be incomplete at its 5' end. Overview of removed sequences length count expect max.err error counts 1 12434198 47093916.5 0 12434198 2 3725377 11773479.1 0 3725377 3 801023 2943369.8 0 801023 4 228671 735842.4 0 228671 5 68703 183960.6 0 68703 6 16655 45990.2 0 16655 7 5597 11497.5 0 5597 8 3566 2874.4 0 3566 9 3133 718.6 0 3133 10 8168 179.6 1 2810 5358 11 6672 44.9 1 2548 4124 12 5286 11.2 1 2312 2974 13 4543 2.8 1 2061 2482 14 4203 0.7 1 1847 2356 15 3670 0.2 1 1657 2013 16 3121 0.0 1 1466 1655 17 2758 0.0 1 1309 1449 18 2222 0.0 1 1290 932 19 1977 0.0 1 1121 856 20 3735 0.0 2 1540 796 1399 21 3562 0.0 2 1363 751 1448 22 3244 0.0 2 1362 680 1202 23 3257 0.0 2 1370 665 1222 24 3032 0.0 2 1296 666 1070 25 2929 0.0 2 1213 691 1025 26 2456 0.0 2 1075 561 820 27 2370 0.0 2 1083 538 749 28 2050 0.0 2 1091 469 490 29 1881 0.0 2 960 476 445 30 2815 0.0 3 949 426 486 954 31 2651 0.0 3 873 433 451 894 32 2637 0.0 3 902 460 432 843 33 2545 0.0 3 932 412 390 811 34 2538 0.0 3 914 426 422 776 35 2261 0.0 3 765 433 381 682 36 2259 0.0 3 902 370 393 594 37 2016 0.0 3 826 371 300 519 38 1944 0.0 3 860 391 321 372 39 1790 0.0 3 721 385 308 376 40 2669 0.0 4 866 393 340 357 713 41 2476 0.0 4 748 353 341 385 649 42 2489 0.0 4 808 341 343 368 629 43 2390 0.0 4 652 370 340 379 649 44 2341 0.0 4 742 378 305 326 590 45 2277 0.0 4 789 337 311 322 518 46 2242 0.0 4 836 379 269 294 464 47 2189 0.0 4 858 412 248 251 420 48 2677 0.0 4 1016 532 411 364 354 49 5724 0.0 4 1966 1306 981 797 674 50 5877 0.0 5 1794 1218 942 745 626 552 51 4634 0.0 5 1897 886 668 487 375 321 52 4049 0.0 5 1856 798 508 379 294 214 53 3661 0.0 5 1783 654 471 322 258 173 54 3510 0.0 5 1793 689 429 250 209 140 55 3232 0.0 5 1770 573 341 224 193 131 56 3073 0.0 5 1728 549 317 168 177 134 57 2966 0.0 5 1796 504 288 154 121 103 58 2925 0.0 5 1809 485 263 152 129 87 59 2455 0.0 5 1494 405 229 133 109 85 60 2349 0.0 5 1457 364 215 142 102 69 61 2415 0.0 5 1515 421 209 115 94 61 62 2338 0.0 5 1544 351 186 120 71 66 63 2278 0.0 5 1547 339 173 91 69 59 64 2302 0.0 5 1565 339 164 100 80 54 65 2150 0.0 5 1518 289 146 83 73 41 66 2107 0.0 5 1481 300 135 89 55 47 67 2135 0.0 5 1554 278 119 75 59 50 68 2183 0.0 5 1665 246 96 90 46 40 69 2150 0.0 5 1590 281 126 59 49 45 70 1914 0.0 5 1402 259 113 72 47 21 71 1747 0.0 5 1321 205 96 62 36 27 72 1822 0.0 5 1378 226 84 52 54 28 73 1675 0.0 5 1281 205 78 50 37 24 74 1587 0.0 5 1216 183 90 40 38 20 75 1582 0.0 5 1263 152 71 47 32 17 76 1592 0.0 5 1259 154 75 42 38 24 77 1563 0.0 5 1273 135 69 40 26 20 78 1366 0.0 5 1070 152 52 50 25 17 79 1251 0.0 5 1004 125 57 32 15 18 80 1382 0.0 5 1113 149 41 38 25 16 81 1266 0.0 5 1028 119 58 27 17 17 82 1153 0.0 5 931 110 47 26 21 18 83 1100 0.0 5 905 105 46 16 20 8 84 1055 0.0 5 860 83 41 36 20 15 85 1161 0.0 5 950 103 49 28 19 12 86 1030 0.0 5 831 103 44 21 18 13 87 991 0.0 5 798 85 37 30 26 15 88 959 0.0 5 772 80 48 24 22 13 89 905 0.0 5 727 84 37 25 13 19 90 876 0.0 5 689 88 55 19 14 11 91 783 0.0 5 615 81 31 21 18 17 92 862 0.0 5 697 74 41 24 16 10 93 787 0.0 5 624 65 41 18 20 19 94 743 0.0 5 597 72 25 23 17 9 95 724 0.0 5 592 58 31 15 13 15 96 726 0.0 5 598 64 25 19 9 11 97 690 0.0 5 580 48 31 10 10 11 98 633 0.0 5 503 55 35 13 16 11 99 598 0.0 5 472 55 32 15 10 14 100 570 0.0 5 458 48 18 19 17 10 101 548 0.0 5 441 50 21 16 11 9 102 583 0.0 5 463 49 27 26 8 10 103 510 0.0 5 415 39 21 14 8 13 104 477 0.0 5 387 29 20 16 13 12 105 514 0.0 5 428 31 21 13 10 11 106 480 0.0 5 392 32 14 19 8 15 107 488 0.0 5 384 36 26 17 13 12 108 441 0.0 5 346 39 19 14 8 15 109 575 0.0 5 461 35 23 18 19 19 110 735 0.0 5 601 41 27 20 21 25 111 731 0.0 5 605 48 26 21 13 18 112 1160 0.0 5 984 51 31 35 30 29 113 1555 0.0 5 1312 88 47 43 26 39 114 4928 0.0 5 4567 157 89 43 39 33 115 3627496 0.0 5 3626617 451 198 98 81 51 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_3_R2_val_2_val_2.fq.gz ============================================= 188375666 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_3_R1_val_1_val_1_trimmed.fq.gz and zr3616_3_R2_val_2_val_2_trimmed.fq.gz file_1: zr3616_3_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3616_3_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_3_R1_val_1_val_1_trimmed.fq.gz and zr3616_3_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_3_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_3_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 188375666 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 3749793 (1.99%) >>> Now running FastQC on the validated data zr3616_3_R1_val_1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 2065249572. >>> Now running FastQC on the validated data zr3616_3_R2_val_2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 2065249572. Deleting both intermediate output files zr3616_3_R1_val_1_val_1_trimmed.fq.gz and zr3616_3_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_4_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_4_R1_val_1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_4_R1_val_1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_4_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_4_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4467.36 s (23 µs/read; 2.66 M reads/minute). === Summary === Total reads processed: 197,822,142 Reads with adapters: 21,373,406 (10.8%) Reads written (passing filters): 197,822,142 (100.0%) Total basepairs processed: 19,209,489,295 bp Quality-trimmed: 3,593,209 bp (0.0%) Total written (filtered): 18,997,290,406 bp (98.9%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 21373406 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 22.0% C: 5.0% G: 0.0% T: 73.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13485831 49455535.5 0 13485831 2 4067387 12363883.9 0 4067387 3 882409 3090971.0 0 882409 4 254872 772742.7 0 254872 5 75779 193185.7 0 75779 6 22085 48296.4 0 22085 7 9677 12074.1 0 9677 8 6853 3018.5 0 6853 9 6827 754.6 0 6827 10 12720 188.7 1 6450 6270 11 10888 47.2 1 5671 5217 12 9323 11.8 1 4929 4394 13 8458 2.9 1 4556 3902 14 7529 0.7 1 4004 3525 15 6746 0.2 1 3631 3115 16 5766 0.0 1 3241 2525 17 4821 0.0 1 2682 2139 18 3902 0.0 1 2520 1382 19 3556 0.0 1 2302 1254 20 5372 0.0 2 2427 1194 1751 21 4669 0.0 2 2220 1057 1392 22 4499 0.0 2 2227 991 1281 23 4267 0.0 2 2123 993 1151 24 4214 0.0 2 2090 1033 1091 25 3743 0.0 2 1875 930 938 26 3303 0.0 2 1666 855 782 27 3257 0.0 2 1753 740 764 28 2989 0.0 2 1680 760 549 29 2825 0.0 2 1611 708 506 30 3334 0.0 3 1430 679 520 705 31 3407 0.0 3 1494 697 506 710 32 3435 0.0 3 1492 689 552 702 33 3310 0.0 3 1423 675 552 660 34 3155 0.0 3 1370 667 528 590 35 3028 0.0 3 1323 638 498 569 36 2910 0.0 3 1303 647 463 497 37 2833 0.0 3 1250 647 419 517 38 2746 0.0 3 1352 657 418 319 39 2696 0.0 3 1315 626 399 356 40 3077 0.0 4 1187 613 391 362 524 41 3176 0.0 4 1271 628 426 367 484 42 3037 0.0 4 1179 582 382 357 537 43 3063 0.0 4 1216 630 384 327 506 44 2911 0.0 4 1180 564 380 337 450 45 2820 0.0 4 1175 548 401 321 375 46 2771 0.0 4 1201 564 338 286 382 47 2786 0.0 4 1200 647 377 269 293 48 3099 0.0 4 1396 651 456 345 251 49 5860 0.0 4 2520 1306 889 662 483 50 6145 0.0 5 2495 1308 835 640 478 389 51 4637 0.0 5 2526 851 516 343 226 175 52 4015 0.0 5 2360 697 416 249 173 120 53 3730 0.0 5 2301 638 341 204 144 102 54 3634 0.0 5 2355 630 288 173 104 84 55 3463 0.0 5 2325 529 278 160 107 64 56 3460 0.0 5 2443 489 228 157 88 55 57 3797 0.0 5 2800 463 245 141 86 62 58 4018 0.0 5 3150 410 211 118 72 57 59 3950 0.0 5 3147 402 171 99 86 45 60 2713 0.0 5 1972 376 172 78 68 47 61 2824 0.0 5 2134 362 148 87 54 39 62 3006 0.0 5 2381 332 148 71 51 23 63 3731 0.0 5 3126 328 120 86 48 23 64 4553 0.0 5 3934 333 116 83 59 28 65 2834 0.0 5 2186 319 174 84 39 32 66 3268 0.0 5 2630 353 147 80 33 25 67 2811 0.0 5 2183 343 150 68 41 26 68 3220 0.0 5 2627 329 132 66 45 21 69 3876 0.0 5 3306 343 111 56 41 19 70 7126 0.0 5 6537 371 107 59 32 20 71 17595 0.0 5 17045 333 109 48 41 19 72 97387 0.0 5 96737 428 103 59 34 26 73 201695 0.0 5 201076 384 120 70 27 18 74 1277550 0.0 5 1276974 365 105 55 31 20 75 59639 0.0 5 59128 274 110 63 33 31 76 53289 0.0 5 52818 263 112 46 32 18 77 259250 0.0 5 258872 195 80 54 27 22 78 26245 0.0 5 25834 217 91 50 37 16 79 147142 0.0 5 146785 166 90 44 35 22 80 33506 0.0 5 33118 195 86 63 18 26 81 20536 0.0 5 20146 189 87 59 35 20 82 52938 0.0 5 52648 150 62 47 19 12 83 8773 0.0 5 8430 167 84 49 23 20 84 28873 0.0 5 28554 180 62 37 27 13 85 7709 0.0 5 7426 133 58 54 25 13 86 1268 0.0 5 1014 113 75 27 19 20 87 999 0.0 5 745 123 59 35 17 20 88 836 0.0 5 604 102 58 26 21 25 89 833 0.0 5 614 107 50 28 16 18 90 842 0.0 5 598 118 53 31 23 19 91 791 0.0 5 560 98 53 40 26 14 92 674 0.0 5 500 80 43 26 16 9 93 663 0.0 5 490 74 47 25 13 14 94 610 0.0 5 446 74 39 21 17 13 95 568 0.0 5 411 64 34 22 18 19 96 495 0.0 5 349 63 30 21 20 12 97 461 0.0 5 328 50 27 28 13 15 98 452 0.0 5 329 50 32 14 13 14 99 375 0.0 5 265 48 19 24 10 9 100 399 0.0 5 280 51 30 8 22 8 101 274 0.0 5 195 32 19 15 6 7 102 290 0.0 5 210 31 17 12 4 16 103 233 0.0 5 160 21 18 13 11 10 104 188 0.0 5 120 30 12 9 10 7 105 182 0.0 5 126 27 7 8 5 9 106 146 0.0 5 103 11 12 12 3 5 107 123 0.0 5 83 15 6 5 7 7 108 117 0.0 5 82 12 7 4 7 5 109 88 0.0 5 67 7 7 4 3 110 76 0.0 5 56 4 6 4 3 3 111 88 0.0 5 72 7 2 3 1 3 112 70 0.0 5 55 6 1 2 5 1 113 49 0.0 5 32 5 3 4 2 3 114 46 0.0 5 37 2 3 0 1 3 115 211 0.0 5 202 5 1 3 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_4_R1_val_1_val_1.fq.gz ============================================= 197822142 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_4_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_4_R2_val_2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_4_R2_val_2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_4_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_4_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4577.21 s (23 µs/read; 2.59 M reads/minute). === Summary === Total reads processed: 197,822,142 Reads with adapters: 20,805,963 (10.5%) Reads written (passing filters): 197,822,142 (100.0%) Total basepairs processed: 19,208,738,542 bp Quality-trimmed: 4,664,617 bp (0.0%) Total written (filtered): 18,903,811,337 bp (98.4%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 20805963 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 14.1% C: 5.6% G: 0.0% T: 80.1% none/other: 0.2% WARNING: The adapter is preceded by "T" extremely often. The provided adapter sequence could be incomplete at its 5' end. Overview of removed sequences length count expect max.err error counts 1 13162651 49455535.5 0 13162651 2 3910753 12363883.9 0 3910753 3 855916 3090971.0 0 855916 4 246767 772742.7 0 246767 5 71050 193185.7 0 71050 6 17757 48296.4 0 17757 7 5666 12074.1 0 5666 8 3491 3018.5 0 3491 9 3088 754.6 0 3088 10 8720 188.7 1 2774 5946 11 7347 47.2 1 2617 4730 12 5863 11.8 1 2380 3483 13 5091 2.9 1 2163 2928 14 4505 0.7 1 1889 2616 15 3910 0.2 1 1702 2208 16 3312 0.0 1 1496 1816 17 2864 0.0 1 1321 1543 18 2335 0.0 1 1321 1014 19 2009 0.0 1 1109 900 20 4241 0.0 2 1683 870 1688 21 3929 0.0 2 1424 896 1609 22 3611 0.0 2 1362 751 1498 23 3424 0.0 2 1307 747 1370 24 3207 0.0 2 1307 697 1203 25 3021 0.0 2 1140 670 1211 26 2602 0.0 2 1079 550 973 27 2296 0.0 2 1017 493 786 28 2073 0.0 2 1048 471 554 29 1937 0.0 2 932 482 523 30 3088 0.0 3 952 471 532 1133 31 2889 0.0 3 843 454 536 1056 32 2788 0.0 3 938 425 489 936 33 2774 0.0 3 880 488 474 932 34 2632 0.0 3 841 434 472 885 35 2485 0.0 3 841 396 458 790 36 2294 0.0 3 843 374 382 695 37 2095 0.0 3 784 391 337 583 38 1848 0.0 3 780 354 320 394 39 1835 0.0 3 718 394 331 392 40 2723 0.0 4 828 349 311 434 801 41 2610 0.0 4 702 355 341 406 806 42 2498 0.0 4 746 345 313 362 732 43 2451 0.0 4 632 375 321 393 730 44 2552 0.0 4 744 384 361 393 670 45 2394 0.0 4 745 306 328 388 627 46 2310 0.0 4 793 347 303 335 532 47 2333 0.0 4 793 416 338 305 481 48 2661 0.0 4 885 551 470 396 359 49 6078 0.0 4 1973 1384 1078 891 752 50 6135 0.0 5 1767 1251 977 787 746 607 51 4724 0.0 5 1772 991 683 528 427 323 52 4122 0.0 5 1772 836 545 409 310 250 53 3642 0.0 5 1600 751 473 355 226 237 54 3455 0.0 5 1655 711 397 306 215 171 55 3031 0.0 5 1581 574 310 235 195 136 56 2955 0.0 5 1609 534 297 222 168 125 57 2873 0.0 5 1641 515 289 199 125 104 58 2682 0.0 5 1606 430 268 143 124 111 59 2363 0.0 5 1381 404 248 148 101 81 60 2161 0.0 5 1330 334 202 138 91 66 61 2085 0.0 5 1318 355 176 100 82 54 62 2073 0.0 5 1327 343 181 97 74 51 63 1960 0.0 5 1291 310 158 87 69 45 64 1913 0.0 5 1306 302 137 70 64 34 65 1841 0.0 5 1238 274 129 92 62 46 66 1885 0.0 5 1329 275 124 77 51 29 67 1828 0.0 5 1293 279 104 67 50 35 68 1991 0.0 5 1477 255 119 62 43 35 69 1818 0.0 5 1375 235 89 63 34 22 70 1542 0.0 5 1181 183 81 47 25 25 71 1614 0.0 5 1152 223 96 75 35 33 72 1529 0.0 5 1163 179 97 42 29 19 73 1379 0.0 5 1088 142 70 33 30 16 74 1312 0.0 5 1040 143 60 28 23 18 75 1298 0.0 5 1021 127 55 44 30 21 76 1275 0.0 5 1005 132 60 28 25 25 77 1214 0.0 5 959 134 61 27 21 12 78 1091 0.0 5 867 106 61 32 10 15 79 1057 0.0 5 858 105 38 20 22 14 80 1079 0.0 5 850 111 54 31 25 8 81 1043 0.0 5 829 101 48 26 19 20 82 966 0.0 5 785 93 44 21 12 11 83 935 0.0 5 751 97 39 25 13 10 84 870 0.0 5 688 82 45 21 19 15 85 880 0.0 5 702 70 54 22 17 15 86 784 0.0 5 651 56 34 21 11 11 87 830 0.0 5 675 68 24 30 16 17 88 799 0.0 5 655 51 46 22 13 12 89 716 0.0 5 581 57 28 24 14 12 90 701 0.0 5 572 59 30 17 11 12 91 637 0.0 5 520 52 28 19 9 9 92 660 0.0 5 533 55 21 20 17 14 93 626 0.0 5 518 46 25 15 11 11 94 590 0.0 5 453 68 22 19 16 12 95 611 0.0 5 508 46 24 11 12 10 96 506 0.0 5 413 39 21 11 13 9 97 564 0.0 5 457 53 16 15 12 11 98 457 0.0 5 369 37 20 14 9 8 99 501 0.0 5 411 33 25 16 10 6 100 462 0.0 5 362 36 17 16 17 14 101 446 0.0 5 377 20 17 14 8 10 102 401 0.0 5 323 30 15 11 11 11 103 456 0.0 5 379 28 23 10 5 11 104 428 0.0 5 353 26 17 8 14 10 105 433 0.0 5 363 24 12 13 10 11 106 423 0.0 5 356 26 9 20 4 8 107 439 0.0 5 367 29 15 9 8 11 108 413 0.0 5 330 30 16 14 12 11 109 533 0.0 5 420 34 20 23 21 15 110 631 0.0 5 524 30 16 21 20 20 111 696 0.0 5 578 35 25 19 24 15 112 1153 0.0 5 915 74 34 50 37 43 113 1534 0.0 5 1286 60 53 45 52 38 114 4480 0.0 5 4129 150 73 42 40 46 115 2302658 0.0 5 2301919 354 150 100 77 58 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_4_R2_val_2_val_2.fq.gz ============================================= 197822142 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_4_R1_val_1_val_1_trimmed.fq.gz and zr3616_4_R2_val_2_val_2_trimmed.fq.gz file_1: zr3616_4_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3616_4_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_4_R1_val_1_val_1_trimmed.fq.gz and zr3616_4_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_4_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_4_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 197822142 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2417618 (1.22%) >>> Now running FastQC on the validated data zr3616_4_R1_val_1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 2856538140. >>> Now running FastQC on the validated data zr3616_4_R2_val_2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 2856538140. Deleting both intermediate output files zr3616_4_R1_val_1_val_1_trimmed.fq.gz and zr3616_4_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_5_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_5_R1_val_1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_5_R1_val_1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_5_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_5_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3403.76 s (23 µs/read; 2.62 M reads/minute). === Summary === Total reads processed: 148,556,552 Reads with adapters: 16,348,719 (11.0%) Reads written (passing filters): 148,556,552 (100.0%) Total basepairs processed: 14,222,653,957 bp Quality-trimmed: 3,116,855 bp (0.0%) Total written (filtered): 14,037,493,557 bp (98.7%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 16348719 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 23.8% C: 4.8% G: 0.0% T: 71.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10087226 37139138.0 0 10087226 2 3044735 9284784.5 0 3044735 3 662617 2321196.1 0 662617 4 193189 580299.0 0 193189 5 59703 145074.8 0 59703 6 16899 36268.7 0 16899 7 7655 9067.2 0 7655 8 5339 2266.8 0 5339 9 5357 566.7 0 5357 10 9717 141.7 1 4825 4892 11 8684 35.4 1 4481 4203 12 7228 8.9 1 3838 3390 13 6672 2.2 1 3545 3127 14 5739 0.6 1 3098 2641 15 5182 0.1 1 2835 2347 16 4430 0.0 1 2445 1985 17 3681 0.0 1 2096 1585 18 2991 0.0 1 1941 1050 19 2765 0.0 1 1802 963 20 4178 0.0 2 1889 923 1366 21 3608 0.0 2 1769 845 994 22 3426 0.0 2 1681 752 993 23 3245 0.0 2 1611 752 882 24 3168 0.0 2 1546 795 827 25 2860 0.0 2 1462 703 695 26 2590 0.0 2 1282 661 647 27 2606 0.0 2 1370 660 576 28 2305 0.0 2 1243 625 437 29 2214 0.0 2 1274 548 392 30 2746 0.0 3 1225 535 395 591 31 2617 0.0 3 1100 536 411 570 32 2592 0.0 3 1102 541 347 602 33 2496 0.0 3 1071 520 377 528 34 2387 0.0 3 1060 520 346 461 35 2489 0.0 3 1060 538 407 484 36 2277 0.0 3 1007 500 335 435 37 2253 0.0 3 1091 474 310 378 38 2174 0.0 3 1085 464 330 295 39 2071 0.0 3 973 527 272 299 40 2461 0.0 4 976 435 323 287 440 41 2440 0.0 4 997 462 310 261 410 42 2312 0.0 4 918 404 312 280 398 43 2466 0.0 4 961 494 315 298 398 44 2329 0.0 4 894 446 305 248 436 45 2111 0.0 4 877 400 265 250 319 46 2173 0.0 4 947 408 255 240 323 47 2079 0.0 4 926 443 243 198 269 48 2346 0.0 4 1014 523 320 264 225 49 4688 0.0 4 1911 1077 728 544 428 50 5022 0.0 5 1938 1083 746 542 418 295 51 3927 0.0 5 1952 786 435 328 252 174 52 3420 0.0 5 1796 654 384 265 189 132 53 3205 0.0 5 1750 617 354 233 165 86 54 3066 0.0 5 1824 554 298 184 106 100 55 2851 0.0 5 1732 525 281 160 84 69 56 2911 0.0 5 1917 496 227 132 81 58 57 3141 0.0 5 2209 466 199 132 79 56 58 3509 0.0 5 2662 403 191 124 77 52 59 3416 0.0 5 2617 414 185 96 63 41 60 2295 0.0 5 1592 364 152 96 51 40 61 2258 0.0 5 1608 332 163 70 48 37 62 2452 0.0 5 1837 296 164 70 53 32 63 3119 0.0 5 2469 364 132 80 49 25 64 4389 0.0 5 3792 323 128 73 53 20 65 2328 0.0 5 1731 296 147 83 40 31 66 2647 0.0 5 2068 307 143 64 35 30 67 2261 0.0 5 1697 303 143 58 38 22 68 2493 0.0 5 1955 295 108 76 42 17 69 2990 0.0 5 2445 282 135 74 40 14 70 5283 0.0 5 4796 284 108 42 32 21 71 11806 0.0 5 11259 346 91 57 33 20 72 82817 0.0 5 82198 393 108 54 39 25 73 124837 0.0 5 124239 362 112 57 35 32 74 1207358 0.0 5 1206776 348 115 59 36 24 75 55484 0.0 5 55039 247 82 53 43 20 76 36184 0.0 5 35783 219 90 54 18 20 77 245197 0.0 5 244795 227 80 50 23 22 78 16995 0.0 5 16622 196 76 44 33 24 79 144664 0.0 5 144307 196 83 40 22 16 80 32559 0.0 5 32271 162 44 44 24 14 81 17777 0.0 5 17437 156 85 57 21 21 82 50121 0.0 5 49830 133 76 44 25 13 83 4753 0.0 5 4469 147 68 25 25 19 84 18019 0.0 5 17720 132 84 45 26 12 85 4428 0.0 5 4200 113 47 28 25 15 86 791 0.0 5 552 117 58 36 18 10 87 775 0.0 5 534 115 67 28 18 13 88 657 0.0 5 469 80 42 32 24 10 89 642 0.0 5 453 85 43 27 17 17 90 627 0.0 5 424 91 51 24 12 25 91 566 0.0 5 392 81 32 32 9 20 92 500 0.0 5 350 63 36 24 15 12 93 513 0.0 5 338 74 33 30 22 16 94 431 0.0 5 282 59 38 20 19 13 95 392 0.0 5 268 42 43 15 18 6 96 376 0.0 5 244 59 30 24 9 10 97 352 0.0 5 233 56 34 13 7 9 98 321 0.0 5 209 47 25 22 13 5 99 278 0.0 5 176 38 32 15 11 6 100 285 0.0 5 194 41 18 13 10 9 101 233 0.0 5 156 32 17 14 10 4 102 229 0.0 5 158 34 11 13 9 4 103 160 0.0 5 105 18 12 9 8 8 104 148 0.0 5 100 17 9 6 10 6 105 132 0.0 5 83 21 11 7 7 3 106 115 0.0 5 78 11 10 9 4 3 107 116 0.0 5 82 8 7 7 6 6 108 106 0.0 5 69 13 13 5 1 5 109 76 0.0 5 54 5 4 5 4 4 110 60 0.0 5 42 3 5 3 5 2 111 41 0.0 5 32 2 2 1 0 4 112 52 0.0 5 36 7 2 6 0 1 113 31 0.0 5 21 3 3 1 2 1 114 47 0.0 5 39 5 0 3 115 169 0.0 5 161 5 0 1 1 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_5_R1_val_1_val_1.fq.gz ============================================= 148556552 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_5_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_5_R2_val_2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_5_R2_val_2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_5_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_5_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3388.77 s (23 µs/read; 2.63 M reads/minute). === Summary === Total reads processed: 148,556,552 Reads with adapters: 16,112,459 (10.8%) Reads written (passing filters): 148,556,552 (100.0%) Total basepairs processed: 14,221,637,036 bp Quality-trimmed: 3,330,879 bp (0.0%) Total written (filtered): 13,952,076,286 bp (98.1%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 16112459 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 14.2% C: 5.5% G: 0.0% T: 80.1% none/other: 0.2% WARNING: The adapter is preceded by "T" extremely often. The provided adapter sequence could be incomplete at its 5' end. Overview of removed sequences length count expect max.err error counts 1 9950820 37139138.0 0 9950820 2 2984814 9284784.5 0 2984814 3 647858 2321196.1 0 647858 4 187678 580299.0 0 187678 5 55129 145074.8 0 55129 6 13530 36268.7 0 13530 7 4375 9067.2 0 4375 8 2680 2266.8 0 2680 9 2366 566.7 0 2366 10 6997 141.7 1 2195 4802 11 5387 35.4 1 2012 3375 12 4607 8.9 1 1880 2727 13 3936 2.2 1 1647 2289 14 3478 0.6 1 1550 1928 15 3181 0.1 1 1415 1766 16 2711 0.0 1 1239 1472 17 2220 0.0 1 1025 1195 18 1768 0.0 1 1023 745 19 1737 0.0 1 997 740 20 3353 0.0 2 1293 716 1344 21 3164 0.0 2 1139 688 1337 22 2949 0.0 2 1046 696 1207 23 2822 0.0 2 1072 605 1145 24 2630 0.0 2 1048 567 1015 25 2510 0.0 2 961 595 954 26 2183 0.0 2 904 483 796 27 1976 0.0 2 870 407 699 28 1660 0.0 2 817 405 438 29 1616 0.0 2 808 383 425 30 2500 0.0 3 793 393 429 885 31 2429 0.0 3 762 371 431 865 32 2269 0.0 3 739 402 354 774 33 2248 0.0 3 754 320 410 764 34 2248 0.0 3 725 381 378 764 35 2015 0.0 3 652 348 370 645 36 1900 0.0 3 703 295 323 579 37 1754 0.0 3 645 311 281 517 38 1607 0.0 3 648 337 288 334 39 1537 0.0 3 600 319 265 353 40 2416 0.0 4 726 318 264 361 747 41 2263 0.0 4 641 323 285 349 665 42 2140 0.0 4 635 305 260 327 613 43 2064 0.0 4 535 306 301 339 583 44 2107 0.0 4 627 329 289 313 549 45 2039 0.0 4 646 297 291 309 496 46 1921 0.0 4 681 287 238 259 456 47 2000 0.0 4 722 331 270 256 421 48 2195 0.0 4 790 445 396 300 264 49 5025 0.0 4 1669 1087 885 777 607 50 5294 0.0 5 1552 1082 842 755 575 488 51 4060 0.0 5 1662 767 591 397 338 305 52 3554 0.0 5 1619 665 472 325 237 236 53 3217 0.0 5 1544 607 388 281 216 181 54 2841 0.0 5 1429 550 345 234 149 134 55 2733 0.0 5 1422 496 300 217 180 118 56 2576 0.0 5 1430 470 260 192 125 99 57 2471 0.0 5 1451 416 243 168 107 86 58 2244 0.0 5 1374 361 178 123 123 85 59 2056 0.0 5 1265 348 184 118 93 48 60 1979 0.0 5 1197 345 201 109 74 53 61 1869 0.0 5 1209 287 165 98 60 50 62 1871 0.0 5 1231 297 156 92 49 46 63 1837 0.0 5 1214 281 145 82 61 54 64 1843 0.0 5 1260 271 139 90 49 34 65 1784 0.0 5 1252 262 124 63 50 33 66 1771 0.0 5 1285 247 111 55 41 32 67 1687 0.0 5 1257 232 88 51 35 24 68 1798 0.0 5 1325 237 91 72 35 38 69 1667 0.0 5 1259 186 110 53 32 27 70 1540 0.0 5 1107 209 96 65 38 25 71 1468 0.0 5 1106 184 74 51 33 20 72 1405 0.0 5 1055 178 75 46 27 24 73 1333 0.0 5 1034 161 55 33 32 18 74 1332 0.0 5 1011 159 68 41 35 18 75 1204 0.0 5 936 146 53 37 22 10 76 1328 0.0 5 1033 136 65 42 30 22 77 1250 0.0 5 957 129 62 52 34 16 78 1111 0.0 5 881 115 44 26 28 17 79 1051 0.0 5 813 122 56 28 22 10 80 1088 0.0 5 881 109 49 19 14 16 81 1017 0.0 5 834 81 35 27 22 18 82 922 0.0 5 734 90 38 26 19 15 83 922 0.0 5 723 88 51 26 22 12 84 885 0.0 5 719 73 43 21 15 14 85 860 0.0 5 680 87 45 18 15 15 86 831 0.0 5 676 64 43 22 13 13 87 772 0.0 5 619 53 40 28 18 14 88 813 0.0 5 646 79 36 20 17 15 89 731 0.0 5 569 69 37 30 18 8 90 695 0.0 5 545 69 30 22 14 15 91 614 0.0 5 502 39 28 23 14 8 92 601 0.0 5 487 55 26 16 10 7 93 572 0.0 5 464 46 21 18 13 10 94 591 0.0 5 460 61 28 17 11 14 95 618 0.0 5 499 49 24 24 9 13 96 498 0.0 5 393 52 21 15 7 10 97 551 0.0 5 426 51 23 24 13 14 98 480 0.0 5 376 41 22 20 15 6 99 505 0.0 5 402 41 27 16 10 9 100 454 0.0 5 363 36 24 9 13 9 101 482 0.0 5 379 36 17 23 10 17 102 445 0.0 5 358 33 21 16 12 5 103 415 0.0 5 321 30 23 16 14 11 104 392 0.0 5 302 34 21 15 13 7 105 391 0.0 5 314 30 16 11 11 9 106 344 0.0 5 271 29 19 9 8 8 107 387 0.0 5 299 34 19 17 11 7 108 339 0.0 5 264 25 15 14 10 11 109 425 0.0 5 339 26 20 15 13 12 110 554 0.0 5 472 28 18 12 13 11 111 582 0.0 5 481 31 19 16 16 19 112 931 0.0 5 801 41 26 17 27 19 113 1206 0.0 5 1016 68 35 22 38 27 114 3723 0.0 5 3403 148 60 53 30 29 115 2069837 0.0 5 2069167 326 160 77 58 49 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_5_R2_val_2_val_2.fq.gz ============================================= 148556552 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_5_R1_val_1_val_1_trimmed.fq.gz and zr3616_5_R2_val_2_val_2_trimmed.fq.gz file_1: zr3616_5_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3616_5_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_5_R1_val_1_val_1_trimmed.fq.gz and zr3616_5_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_5_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_5_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 148556552 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2163491 (1.46%) >>> Now running FastQC on the validated data zr3616_5_R1_val_1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 3450764348. >>> Now running FastQC on the validated data zr3616_5_R2_val_2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 3450764348. Deleting both intermediate output files zr3616_5_R1_val_1_val_1_trimmed.fq.gz and zr3616_5_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_6_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_6_R1_val_1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_6_R1_val_1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_6_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_6_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4479.26 s (23 µs/read; 2.61 M reads/minute). === Summary === Total reads processed: 194,821,663 Reads with adapters: 22,011,384 (11.3%) Reads written (passing filters): 194,821,663 (100.0%) Total basepairs processed: 18,329,414,001 bp Quality-trimmed: 4,444,384 bp (0.0%) Total written (filtered): 18,054,741,769 bp (98.5%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 22011384 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 24.7% C: 4.8% G: 0.0% T: 70.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13318172 48705415.8 0 13318172 2 4043535 12176353.9 0 4043535 3 883652 3044088.5 0 883652 4 256064 761022.1 0 256064 5 79698 190255.5 0 79698 6 22627 47563.9 0 22627 7 9771 11891.0 0 9771 8 7035 2972.7 0 7035 9 6780 743.2 0 6780 10 12942 185.8 1 6323 6619 11 11367 46.4 1 5535 5832 12 9608 11.6 1 4990 4618 13 8292 2.9 1 4292 4000 14 7434 0.7 1 3838 3596 15 6674 0.2 1 3440 3234 16 5606 0.0 1 2939 2667 17 4419 0.0 1 2376 2043 18 3617 0.0 1 2252 1365 19 3270 0.0 1 2091 1179 20 5224 0.0 2 2184 1120 1920 21 4782 0.0 2 2091 1075 1616 22 4380 0.0 2 1935 981 1464 23 3975 0.0 2 1710 987 1278 24 3912 0.0 2 1787 933 1192 25 3468 0.0 2 1677 818 973 26 3118 0.0 2 1475 758 885 27 3044 0.0 2 1452 734 858 28 2688 0.0 2 1442 722 524 29 2499 0.0 2 1364 630 505 30 3310 0.0 3 1244 713 463 890 31 3167 0.0 3 1221 629 516 801 32 3157 0.0 3 1225 664 480 788 33 3156 0.0 3 1235 636 507 778 34 2940 0.0 3 1102 658 475 705 35 2887 0.0 3 1085 620 480 702 36 2838 0.0 3 1179 607 473 579 37 2680 0.0 3 1166 559 404 551 38 2465 0.0 3 1123 553 391 398 39 2444 0.0 3 1129 573 372 370 40 2990 0.0 4 1075 536 357 350 672 41 3019 0.0 4 1049 594 421 374 581 42 2935 0.0 4 1067 563 375 321 609 43 2936 0.0 4 1016 585 386 359 590 44 2807 0.0 4 988 551 373 341 554 45 2712 0.0 4 1012 480 350 337 533 46 2655 0.0 4 1016 539 367 308 425 47 2678 0.0 4 1026 605 345 271 431 48 2863 0.0 4 1119 645 446 336 317 49 6170 0.0 4 2262 1348 1061 870 629 50 6669 0.0 5 2308 1425 1040 779 627 490 51 5168 0.0 5 2320 1024 687 499 340 298 52 4526 0.0 5 2077 934 569 427 292 227 53 4229 0.0 5 2113 894 497 329 219 177 54 3995 0.0 5 2164 769 452 289 170 151 55 3770 0.0 5 2149 717 393 246 147 118 56 3725 0.0 5 2209 682 341 215 152 126 57 4213 0.0 5 2806 677 312 186 143 89 58 4897 0.0 5 3642 573 296 184 114 88 59 4668 0.0 5 3542 532 253 163 101 77 60 3031 0.0 5 2007 467 260 143 94 60 61 3046 0.0 5 2056 495 227 145 71 52 62 3366 0.0 5 2458 448 212 105 88 55 63 4356 0.0 5 3505 424 188 125 71 43 64 6120 0.0 5 5247 449 186 104 86 48 65 3134 0.0 5 2163 433 284 137 74 43 66 3736 0.0 5 2868 448 214 104 59 43 67 3038 0.0 5 2298 412 159 87 49 33 68 3472 0.0 5 2706 398 188 90 53 37 69 4241 0.0 5 3480 413 171 78 57 42 70 8174 0.0 5 7442 411 145 91 50 35 71 19775 0.0 5 19014 467 140 71 53 30 72 121068 0.0 5 120214 553 143 74 44 40 73 238161 0.0 5 237330 502 150 80 51 48 74 1778702 0.0 5 1777903 465 151 100 52 31 75 82657 0.0 5 82020 346 142 70 51 28 76 63529 0.0 5 62968 319 111 69 37 25 77 374472 0.0 5 373944 292 110 69 31 26 78 29760 0.0 5 29287 248 118 56 35 16 79 212697 0.0 5 212210 244 106 68 38 31 80 46691 0.0 5 46277 212 103 52 26 21 81 26170 0.0 5 25753 206 85 66 37 23 82 73137 0.0 5 72770 172 84 53 27 31 83 7384 0.0 5 7000 163 99 57 44 21 84 29497 0.0 5 29086 213 87 55 31 25 85 6586 0.0 5 6262 162 62 39 38 23 86 963 0.0 5 637 144 85 40 32 25 87 932 0.0 5 626 140 69 49 34 14 88 803 0.0 5 521 117 64 42 30 29 89 739 0.0 5 484 112 57 42 23 21 90 676 0.0 5 442 100 56 31 22 25 91 701 0.0 5 472 96 51 43 24 15 92 552 0.0 5 350 83 43 36 26 14 93 571 0.0 5 361 85 46 34 27 18 94 551 0.0 5 332 90 57 24 30 18 95 510 0.0 5 329 65 41 40 23 12 96 414 0.0 5 254 59 39 27 19 16 97 442 0.0 5 270 66 43 33 18 12 98 413 0.0 5 253 55 36 24 29 16 99 344 0.0 5 205 45 43 18 18 15 100 292 0.0 5 194 31 26 20 9 12 101 297 0.0 5 193 48 22 17 11 6 102 259 0.0 5 184 29 16 13 9 8 103 232 0.0 5 155 28 16 12 15 6 104 195 0.0 5 123 22 18 17 9 6 105 154 0.0 5 107 16 15 3 5 8 106 159 0.0 5 102 19 10 10 6 12 107 131 0.0 5 84 13 10 5 11 8 108 125 0.0 5 87 8 7 6 4 13 109 109 0.0 5 84 9 6 1 1 8 110 82 0.0 5 56 11 5 5 2 3 111 63 0.0 5 41 5 4 6 5 2 112 55 0.0 5 41 4 5 1 1 3 113 43 0.0 5 30 6 0 3 0 4 114 62 0.0 5 42 7 2 3 2 6 115 193 0.0 5 179 9 1 2 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_6_R1_val_1_val_1.fq.gz ============================================= 194821663 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_6_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_6_R2_val_2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_6_R2_val_2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_6_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_6_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4370.36 s (22 µs/read; 2.67 M reads/minute). === Summary === Total reads processed: 194,821,663 Reads with adapters: 21,438,386 (11.0%) Reads written (passing filters): 194,821,663 (100.0%) Total basepairs processed: 18,333,205,768 bp Quality-trimmed: 4,157,915 bp (0.0%) Total written (filtered): 17,933,262,213 bp (97.8%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 21438386 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 14.1% C: 5.7% G: 0.0% T: 80.0% none/other: 0.2% WARNING: The adapter is preceded by "T" extremely often. The provided adapter sequence could be incomplete at its 5' end. Overview of removed sequences length count expect max.err error counts 1 12949866 48705415.8 0 12949866 2 3934592 12176353.9 0 3934592 3 848769 3044088.5 0 848769 4 242850 761022.1 0 242850 5 72591 190255.5 0 72591 6 17494 47563.9 0 17494 7 5410 11891.0 0 5410 8 3228 2972.7 0 3228 9 2796 743.2 0 2796 10 8042 185.8 1 2625 5417 11 7096 46.4 1 2641 4455 12 5250 11.6 1 2195 3055 13 4457 2.9 1 1894 2563 14 4279 0.7 1 1816 2463 15 3797 0.2 1 1683 2114 16 3184 0.0 1 1455 1729 17 2658 0.0 1 1251 1407 18 2215 0.0 1 1277 938 19 1996 0.0 1 1120 876 20 3967 0.0 2 1547 839 1581 21 3827 0.0 2 1336 856 1635 22 3536 0.0 2 1355 747 1434 23 3344 0.0 2 1275 736 1333 24 3100 0.0 2 1205 672 1223 25 3030 0.0 2 1113 714 1203 26 2663 0.0 2 1095 564 1004 27 2481 0.0 2 1121 482 878 28 2086 0.0 2 1053 457 576 29 1941 0.0 2 993 446 502 30 2965 0.0 3 950 459 550 1006 31 2974 0.0 3 916 439 514 1105 32 2739 0.0 3 853 440 458 988 33 2697 0.0 3 899 427 465 906 34 2774 0.0 3 906 446 471 951 35 2466 0.0 3 832 409 436 789 36 2338 0.0 3 835 332 410 761 37 2074 0.0 3 703 388 353 630 38 1944 0.0 3 806 377 335 426 39 1943 0.0 3 767 369 368 439 40 2729 0.0 4 795 373 353 408 800 41 2670 0.0 4 694 349 366 459 802 42 2651 0.0 4 794 369 361 397 730 43 2546 0.0 4 630 389 352 422 753 44 2547 0.0 4 794 369 351 364 669 45 2442 0.0 4 755 331 332 382 642 46 2411 0.0 4 872 352 275 323 589 47 2458 0.0 4 847 384 351 333 543 48 2689 0.0 4 951 508 478 397 355 49 6237 0.0 4 2005 1356 1182 903 791 50 6357 0.0 5 1783 1330 980 883 770 611 51 4871 0.0 5 1839 1017 704 560 388 363 52 4332 0.0 5 1906 866 543 416 312 289 53 3637 0.0 5 1584 780 474 356 238 205 54 3622 0.0 5 1761 701 445 316 213 186 55 3139 0.0 5 1581 620 334 249 218 137 56 3022 0.0 5 1610 535 322 241 182 132 57 2967 0.0 5 1764 506 274 185 131 107 58 2875 0.0 5 1726 497 256 182 127 87 59 2370 0.0 5 1417 379 232 156 106 80 60 2177 0.0 5 1299 367 216 126 93 76 61 2200 0.0 5 1360 357 191 128 110 54 62 2185 0.0 5 1457 336 162 103 75 52 63 2044 0.0 5 1336 329 162 98 64 55 64 2079 0.0 5 1390 325 147 99 74 44 65 1986 0.0 5 1342 312 135 87 55 55 66 1851 0.0 5 1319 240 121 83 46 42 67 1930 0.0 5 1401 273 112 78 36 30 68 1895 0.0 5 1406 244 121 56 41 27 69 1928 0.0 5 1470 239 97 57 38 27 70 1666 0.0 5 1235 216 88 57 41 29 71 1621 0.0 5 1250 181 77 57 33 23 72 1584 0.0 5 1236 167 81 49 28 23 73 1532 0.0 5 1165 187 80 48 31 21 74 1397 0.0 5 1122 136 66 40 18 15 75 1439 0.0 5 1135 168 61 40 25 10 76 1474 0.0 5 1189 157 62 25 29 12 77 1396 0.0 5 1134 139 50 39 19 15 78 1279 0.0 5 1014 139 53 33 21 19 79 1197 0.0 5 935 131 52 30 26 23 80 1289 0.0 5 1011 124 63 41 27 23 81 1185 0.0 5 983 90 47 28 21 16 82 1072 0.0 5 858 110 41 27 20 16 83 974 0.0 5 786 93 40 21 19 15 84 1007 0.0 5 820 96 37 24 20 10 85 1059 0.0 5 890 85 31 17 22 14 86 980 0.0 5 808 82 35 22 18 15 87 898 0.0 5 728 81 40 27 13 9 88 924 0.0 5 756 75 34 23 22 14 89 861 0.0 5 707 69 28 22 16 19 90 853 0.0 5 688 71 36 22 24 12 91 713 0.0 5 591 57 29 12 16 8 92 733 0.0 5 591 65 39 16 14 8 93 677 0.0 5 561 53 20 19 15 9 94 694 0.0 5 557 58 33 14 21 11 95 682 0.0 5 571 58 18 14 12 9 96 575 0.0 5 445 55 34 24 10 7 97 627 0.0 5 513 51 20 20 15 8 98 564 0.0 5 443 56 27 19 9 10 99 515 0.0 5 417 38 15 14 17 14 100 490 0.0 5 388 43 27 16 9 7 101 552 0.0 5 453 34 19 19 10 17 102 511 0.0 5 399 49 20 12 16 15 103 450 0.0 5 367 37 15 11 10 10 104 422 0.0 5 342 40 15 10 8 7 105 425 0.0 5 330 36 11 24 15 9 106 422 0.0 5 345 28 15 14 13 7 107 449 0.0 5 372 29 13 10 15 10 108 458 0.0 5 352 29 22 18 16 21 109 528 0.0 5 428 35 18 16 16 15 110 670 0.0 5 560 40 24 12 13 21 111 692 0.0 5 574 38 19 23 19 19 112 1212 0.0 5 972 64 44 51 44 37 113 1610 0.0 5 1333 87 57 57 34 42 114 4750 0.0 5 4352 150 68 70 65 45 115 3130972 0.0 5 3130192 358 182 107 77 56 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_6_R2_val_2_val_2.fq.gz ============================================= 194821663 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_6_R1_val_1_val_1_trimmed.fq.gz and zr3616_6_R2_val_2_val_2_trimmed.fq.gz file_1: zr3616_6_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3616_6_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_6_R1_val_1_val_1_trimmed.fq.gz and zr3616_6_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_6_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_6_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 194821663 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 3261624 (1.67%) >>> Now running FastQC on the validated data zr3616_6_R1_val_1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 4230051000. >>> Now running FastQC on the validated data zr3616_6_R2_val_2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 4230051000. Deleting both intermediate output files zr3616_6_R1_val_1_val_1_trimmed.fq.gz and zr3616_6_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_7_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_7_R1_val_1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_7_R1_val_1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_7_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_7_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3396.86 s (23 µs/read; 2.63 M reads/minute). === Summary === Total reads processed: 149,080,064 Reads with adapters: 15,781,866 (10.6%) Reads written (passing filters): 149,080,064 (100.0%) Total basepairs processed: 14,336,134,965 bp Quality-trimmed: 2,861,987 bp (0.0%) Total written (filtered): 14,195,752,064 bp (99.0%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 15781866 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 21.1% C: 5.3% G: 0.0% T: 73.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10148986 37270016.0 0 10148986 2 3024060 9317504.0 0 3024060 3 654853 2329376.0 0 654853 4 189120 582344.0 0 189120 5 57921 145586.0 0 57921 6 16863 36396.5 0 16863 7 7524 9099.1 0 7524 8 5391 2274.8 0 5391 9 5431 568.7 0 5431 10 9900 142.2 1 4991 4909 11 8910 35.5 1 4458 4452 12 7357 8.9 1 3843 3514 13 6758 2.2 1 3671 3087 14 5865 0.6 1 3204 2661 15 5223 0.1 1 2736 2487 16 4717 0.0 1 2565 2152 17 3787 0.0 1 2115 1672 18 3054 0.0 1 1982 1072 19 2871 0.0 1 1906 965 20 4159 0.0 2 1832 990 1337 21 3872 0.0 2 1829 882 1161 22 3590 0.0 2 1755 812 1023 23 3308 0.0 2 1616 812 880 24 3352 0.0 2 1685 800 867 25 2930 0.0 2 1474 733 723 26 2616 0.0 2 1318 662 636 27 2631 0.0 2 1400 632 599 28 2370 0.0 2 1282 598 490 29 2287 0.0 2 1279 563 445 30 2721 0.0 3 1116 555 413 637 31 2675 0.0 3 1191 558 391 535 32 2616 0.0 3 1140 521 391 564 33 2534 0.0 3 1144 498 359 533 34 2533 0.0 3 1094 548 407 484 35 2438 0.0 3 1076 541 369 452 36 2389 0.0 3 1094 483 387 425 37 2289 0.0 3 1111 515 316 347 38 2171 0.0 3 1054 487 341 289 39 2230 0.0 3 1077 529 321 303 40 2583 0.0 4 994 487 353 297 452 41 2463 0.0 4 961 467 323 279 433 42 2470 0.0 4 980 462 316 289 423 43 2405 0.0 4 931 485 316 295 378 44 2297 0.0 4 914 445 305 290 343 45 2255 0.0 4 911 410 332 257 345 46 2198 0.0 4 912 424 322 225 315 47 2255 0.0 4 956 454 304 248 293 48 2488 0.0 4 1107 516 366 298 201 49 4775 0.0 4 2066 1090 701 532 386 50 4939 0.0 5 1930 1053 703 528 400 325 51 3782 0.0 5 2046 691 424 268 216 137 52 3324 0.0 5 1907 610 337 209 147 114 53 3177 0.0 5 1950 553 292 169 126 87 54 2921 0.0 5 1840 515 227 157 105 77 55 2911 0.0 5 1888 476 250 148 91 58 56 2813 0.0 5 1963 423 181 109 66 71 57 2979 0.0 5 2156 379 210 107 76 51 58 3233 0.0 5 2459 383 178 102 60 51 59 3317 0.0 5 2597 359 159 94 59 49 60 2324 0.0 5 1666 325 164 79 59 31 61 2311 0.0 5 1700 302 140 89 50 30 62 2443 0.0 5 1858 292 159 57 49 28 63 2817 0.0 5 2297 296 106 70 25 23 64 3865 0.0 5 3312 301 113 66 47 26 65 2261 0.0 5 1716 288 139 61 43 14 66 2584 0.0 5 2062 268 127 62 44 21 67 2241 0.0 5 1741 275 111 53 39 22 68 2337 0.0 5 1876 263 104 55 26 13 69 2667 0.0 5 2220 268 90 41 25 23 70 4097 0.0 5 3648 251 99 43 35 21 71 8474 0.0 5 8011 264 102 44 26 27 72 50693 0.0 5 50202 292 108 36 34 21 73 94651 0.0 5 94131 310 111 52 27 20 74 827845 0.0 5 827358 304 94 49 27 13 75 39636 0.0 5 39209 257 83 45 25 17 76 30938 0.0 5 30538 228 79 40 29 24 77 172160 0.0 5 171816 205 59 33 25 22 78 15591 0.0 5 15248 201 67 37 25 13 79 104325 0.0 5 103986 172 91 39 19 18 80 23980 0.0 5 23662 172 70 34 27 15 81 13119 0.0 5 12812 157 69 39 21 21 82 34953 0.0 5 34688 139 49 37 22 18 83 6948 0.0 5 6693 131 60 28 21 15 84 27291 0.0 5 27015 143 59 41 17 16 85 6396 0.0 5 6161 127 50 27 18 13 86 1170 0.0 5 945 114 55 25 16 15 87 905 0.0 5 642 135 64 40 10 14 88 779 0.0 5 575 85 46 27 21 25 89 687 0.0 5 495 100 38 22 19 13 90 755 0.0 5 521 120 45 37 18 14 91 673 0.0 5 485 86 40 24 21 17 92 601 0.0 5 416 92 31 26 22 14 93 528 0.0 5 383 61 37 23 13 11 94 548 0.0 5 393 67 40 10 27 11 95 451 0.0 5 325 57 29 20 14 6 96 435 0.0 5 317 51 29 13 15 10 97 455 0.0 5 317 59 32 22 13 12 98 409 0.0 5 272 57 30 17 16 17 99 360 0.0 5 250 40 25 25 11 9 100 307 0.0 5 224 29 22 17 5 10 101 275 0.0 5 189 41 17 17 8 3 102 279 0.0 5 202 29 21 7 8 12 103 213 0.0 5 151 24 13 15 5 5 104 171 0.0 5 119 20 9 8 6 9 105 136 0.0 5 94 16 9 6 7 4 106 125 0.0 5 86 18 9 5 6 1 107 126 0.0 5 94 9 4 7 4 8 108 106 0.0 5 75 10 10 8 1 2 109 82 0.0 5 64 3 2 1 6 6 110 80 0.0 5 61 5 7 5 1 1 111 68 0.0 5 51 8 1 4 1 3 112 47 0.0 5 35 4 0 1 5 2 113 52 0.0 5 38 3 3 2 2 4 114 41 0.0 5 37 1 0 1 1 1 115 168 0.0 5 159 4 2 1 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_7_R1_val_1_val_1.fq.gz ============================================= 149080064 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_7_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_7_R2_val_2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_7_R2_val_2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_7_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_7_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3468.66 s (23 µs/read; 2.58 M reads/minute). === Summary === Total reads processed: 149,080,064 Reads with adapters: 15,309,340 (10.3%) Reads written (passing filters): 149,080,064 (100.0%) Total basepairs processed: 14,333,353,408 bp Quality-trimmed: 3,668,034 bp (0.0%) Total written (filtered): 14,133,103,122 bp (98.6%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 15309340 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 14.2% C: 5.7% G: 0.0% T: 80.0% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 9852792 37270016.0 0 9852792 2 2903952 9317504.0 0 2903952 3 633635 2329376.0 0 633635 4 181368 582344.0 0 181368 5 53687 145586.0 0 53687 6 13761 36396.5 0 13761 7 4483 9099.1 0 4483 8 2925 2274.8 0 2925 9 2551 568.7 0 2551 10 6976 142.2 1 2259 4717 11 5723 35.5 1 2131 3592 12 4665 8.9 1 1956 2709 13 4088 2.2 1 1740 2348 14 3606 0.6 1 1560 2046 15 3246 0.1 1 1413 1833 16 2789 0.0 1 1322 1467 17 2317 0.0 1 1085 1232 18 1825 0.0 1 1065 760 19 1673 0.0 1 961 712 20 3253 0.0 2 1274 682 1297 21 3157 0.0 2 1154 698 1305 22 2758 0.0 2 1031 603 1124 23 2841 0.0 2 1142 602 1097 24 2578 0.0 2 1060 533 985 25 2407 0.0 2 957 548 902 26 2300 0.0 2 914 537 849 27 1987 0.0 2 862 418 707 28 1674 0.0 2 840 394 440 29 1600 0.0 2 795 400 405 30 2432 0.0 3 806 377 423 826 31 2363 0.0 3 781 382 397 803 32 2345 0.0 3 821 339 383 802 33 2354 0.0 3 841 403 405 705 34 2174 0.0 3 798 331 374 671 35 1981 0.0 3 706 323 372 580 36 2007 0.0 3 778 346 330 553 37 1768 0.0 3 644 316 295 513 38 1662 0.0 3 677 345 285 355 39 1593 0.0 3 662 317 260 354 40 2257 0.0 4 703 328 266 323 637 41 2190 0.0 4 618 318 295 338 621 42 2159 0.0 4 728 322 230 291 588 43 2039 0.0 4 573 311 290 333 532 44 2072 0.0 4 666 310 285 299 512 45 1974 0.0 4 642 272 255 298 507 46 1900 0.0 4 717 289 231 245 418 47 1947 0.0 4 693 368 272 214 400 48 2295 0.0 4 817 487 363 319 309 49 4975 0.0 4 1646 1091 880 753 605 50 5255 0.0 5 1555 1086 801 713 598 502 51 3966 0.0 5 1564 803 555 424 350 270 52 3518 0.0 5 1548 715 461 338 243 213 53 3063 0.0 5 1391 601 402 305 209 155 54 2935 0.0 5 1502 566 314 232 171 150 55 2566 0.0 5 1355 465 286 192 158 110 56 2564 0.0 5 1426 443 286 164 140 105 57 2532 0.0 5 1483 454 233 159 109 94 58 2288 0.0 5 1337 386 215 157 112 81 59 2121 0.0 5 1280 354 209 122 80 76 60 1854 0.0 5 1136 308 155 114 82 59 61 1938 0.0 5 1218 315 169 89 90 57 62 1970 0.0 5 1305 303 154 91 80 37 63 1870 0.0 5 1247 292 132 91 63 45 64 1799 0.0 5 1213 285 121 81 69 30 65 1703 0.0 5 1184 237 109 81 49 43 66 1660 0.0 5 1153 261 122 53 44 27 67 1684 0.0 5 1245 209 108 66 35 21 68 1679 0.0 5 1251 199 122 51 26 30 69 1608 0.0 5 1199 201 87 58 43 20 70 1412 0.0 5 1029 178 86 54 41 24 71 1364 0.0 5 1024 174 68 45 30 23 72 1400 0.0 5 1095 145 71 34 25 30 73 1269 0.0 5 981 148 61 36 27 16 74 1303 0.0 5 987 160 75 48 18 15 75 1194 0.0 5 900 136 70 43 24 21 76 1226 0.0 5 979 123 53 37 21 13 77 1220 0.0 5 955 127 63 32 27 16 78 1030 0.0 5 806 104 36 36 26 22 79 997 0.0 5 787 109 47 24 20 10 80 982 0.0 5 793 85 43 23 24 14 81 973 0.0 5 774 97 39 20 24 19 82 934 0.0 5 747 92 42 25 14 14 83 854 0.0 5 666 93 37 24 15 19 84 828 0.0 5 664 96 25 21 13 9 85 865 0.0 5 694 91 40 15 15 10 86 828 0.0 5 664 82 37 23 12 10 87 748 0.0 5 610 64 25 18 19 12 88 781 0.0 5 625 68 46 11 20 11 89 672 0.0 5 528 67 30 22 16 9 90 659 0.0 5 525 60 28 22 13 11 91 602 0.0 5 453 59 39 28 15 8 92 575 0.0 5 435 62 31 21 12 14 93 572 0.0 5 451 47 27 12 24 11 94 549 0.0 5 434 53 23 21 7 11 95 521 0.0 5 422 44 22 8 11 14 96 488 0.0 5 383 44 28 15 11 7 97 514 0.0 5 415 43 21 12 13 10 98 424 0.0 5 335 29 12 21 15 12 99 495 0.0 5 393 39 19 23 11 10 100 444 0.0 5 366 35 16 10 10 7 101 428 0.0 5 339 42 21 11 2 13 102 433 0.0 5 331 38 29 16 11 8 103 382 0.0 5 305 30 12 16 10 9 104 365 0.0 5 291 28 17 14 6 9 105 400 0.0 5 317 32 19 12 15 5 106 357 0.0 5 272 36 15 18 11 5 107 391 0.0 5 309 29 21 9 11 12 108 359 0.0 5 279 33 9 19 10 9 109 411 0.0 5 332 25 22 15 7 10 110 520 0.0 5 416 42 17 20 11 14 111 606 0.0 5 472 48 28 17 33 8 112 887 0.0 5 750 43 31 21 23 19 113 1208 0.0 5 1034 64 41 24 28 17 114 3647 0.0 5 3348 110 65 45 37 42 115 1468546 0.0 5 1467891 325 148 75 61 46 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_7_R2_val_2_val_2.fq.gz ============================================= 149080064 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_7_R1_val_1_val_1_trimmed.fq.gz and zr3616_7_R2_val_2_val_2_trimmed.fq.gz file_1: zr3616_7_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3616_7_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_7_R1_val_1_val_1_trimmed.fq.gz and zr3616_7_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_7_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_7_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 149080064 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1561649 (1.05%) >>> Now running FastQC on the validated data zr3616_7_R1_val_1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 4826371256. >>> Now running FastQC on the validated data zr3616_7_R2_val_2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 4826371256. Deleting both intermediate output files zr3616_7_R1_val_1_val_1_trimmed.fq.gz and zr3616_7_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_8_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_8_R1_val_1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_8_R1_val_1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_8_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_8_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3629.43 s (22 µs/read; 2.67 M reads/minute). === Summary === Total reads processed: 161,309,784 Reads with adapters: 17,262,120 (10.7%) Reads written (passing filters): 161,309,784 (100.0%) Total basepairs processed: 15,578,048,811 bp Quality-trimmed: 3,003,729 bp (0.0%) Total written (filtered): 15,408,768,753 bp (98.9%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 17262120 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 21.5% C: 5.0% G: 0.0% T: 73.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10929782 40327446.0 0 10929782 2 3286493 10081861.5 0 3286493 3 707881 2520465.4 0 707881 4 202931 630116.3 0 202931 5 60454 157529.1 0 60454 6 17546 39382.3 0 17546 7 7906 9845.6 0 7906 8 5715 2461.4 0 5715 9 5467 615.3 0 5467 10 10075 153.8 1 5095 4980 11 8735 38.5 1 4527 4208 12 7645 9.6 1 4103 3542 13 6792 2.4 1 3687 3105 14 6118 0.6 1 3335 2783 15 5278 0.2 1 2828 2450 16 4548 0.0 1 2549 1999 17 3790 0.0 1 2120 1670 18 3078 0.0 1 2013 1065 19 2834 0.0 1 1887 947 20 4180 0.0 2 1939 928 1313 21 3850 0.0 2 1856 883 1111 22 3403 0.0 2 1717 736 950 23 3238 0.0 2 1591 806 841 24 3337 0.0 2 1678 815 844 25 3053 0.0 2 1567 746 740 26 2630 0.0 2 1329 663 638 27 2556 0.0 2 1388 605 563 28 2403 0.0 2 1349 594 460 29 2235 0.0 2 1284 544 407 30 2766 0.0 3 1244 578 367 577 31 2596 0.0 3 1116 508 429 543 32 2566 0.0 3 1094 521 419 532 33 2525 0.0 3 1127 540 384 474 34 2425 0.0 3 1073 517 363 472 35 2390 0.0 3 1044 509 374 463 36 2361 0.0 3 1063 508 358 432 37 2240 0.0 3 1037 484 325 394 38 1955 0.0 3 966 467 282 240 39 1963 0.0 3 916 498 309 240 40 2293 0.0 4 909 438 298 263 385 41 2412 0.0 4 948 453 317 294 400 42 2434 0.0 4 1018 462 315 253 386 43 2346 0.0 4 926 488 307 256 369 44 2329 0.0 4 920 467 317 246 379 45 2065 0.0 4 876 379 225 237 348 46 2211 0.0 4 939 453 258 248 313 47 2164 0.0 4 991 462 274 185 252 48 2469 0.0 4 1072 531 367 279 220 49 4643 0.0 4 2035 1048 686 485 389 50 4889 0.0 5 2003 1010 673 488 396 319 51 3690 0.0 5 2022 669 410 250 185 154 52 3186 0.0 5 1807 577 297 212 174 119 53 2985 0.0 5 1855 505 271 174 110 70 54 2880 0.0 5 1818 481 257 165 93 66 55 2764 0.0 5 1794 452 248 130 81 59 56 2846 0.0 5 1965 419 203 129 78 52 57 3086 0.0 5 2290 371 209 105 68 43 58 3402 0.0 5 2635 371 187 96 68 45 59 3310 0.0 5 2692 306 135 79 69 29 60 2305 0.0 5 1692 317 135 82 43 36 61 2211 0.0 5 1688 268 128 62 41 24 62 2621 0.0 5 2105 285 107 64 28 32 63 3277 0.0 5 2820 227 115 58 31 26 64 3821 0.0 5 3285 299 112 56 41 28 65 2292 0.0 5 1792 244 135 76 23 22 66 2589 0.0 5 2133 259 97 54 31 15 67 2294 0.0 5 1844 263 94 43 34 16 68 2461 0.0 5 2018 260 83 56 30 14 69 3201 0.0 5 2722 280 103 54 27 15 70 5481 0.0 5 5053 240 85 49 34 20 71 14421 0.0 5 13979 276 77 51 26 12 72 63317 0.0 5 62847 308 87 43 23 9 73 204838 0.0 5 204340 326 78 44 33 17 74 969623 0.0 5 969148 290 83 51 31 20 75 47299 0.0 5 46893 238 75 46 33 14 76 57319 0.0 5 56971 211 56 44 21 16 77 202036 0.0 5 201682 218 67 34 24 11 78 29232 0.0 5 28911 167 67 40 28 19 79 120785 0.0 5 120501 150 67 31 13 23 80 29689 0.0 5 29402 159 65 27 24 12 81 20327 0.0 5 20043 148 62 33 23 18 82 36983 0.0 5 36742 109 56 40 27 9 83 9014 0.0 5 8787 115 53 29 15 15 84 15364 0.0 5 15135 130 54 18 13 14 85 3288 0.0 5 3093 108 50 18 13 6 86 823 0.0 5 641 92 41 26 11 12 87 793 0.0 5 605 103 33 27 13 12 88 720 0.0 5 551 94 42 14 12 7 89 653 0.0 5 497 78 32 22 8 16 90 655 0.0 5 516 79 33 13 8 6 91 635 0.0 5 451 86 45 25 20 8 92 569 0.0 5 432 62 39 17 14 5 93 539 0.0 5 384 75 33 21 16 10 94 468 0.0 5 333 59 30 19 17 10 95 438 0.0 5 319 55 25 21 15 3 96 400 0.0 5 289 50 31 6 13 11 97 403 0.0 5 288 52 25 13 14 11 98 345 0.0 5 246 44 26 11 9 9 99 322 0.0 5 242 31 18 12 9 10 100 280 0.0 5 196 28 24 13 14 5 101 251 0.0 5 185 18 19 10 9 10 102 225 0.0 5 172 24 12 4 6 7 103 183 0.0 5 147 15 6 8 5 2 104 176 0.0 5 118 30 10 10 3 5 105 163 0.0 5 108 22 12 8 6 7 106 119 0.0 5 91 16 4 2 3 3 107 101 0.0 5 75 3 5 11 3 4 108 92 0.0 5 68 6 4 3 4 7 109 84 0.0 5 61 5 5 2 7 4 110 77 0.0 5 56 3 5 4 6 3 111 64 0.0 5 42 6 5 4 4 3 112 53 0.0 5 39 7 1 2 1 3 113 40 0.0 5 30 5 1 1 2 1 114 46 0.0 5 42 2 0 1 1 115 171 0.0 5 164 2 2 3 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_8_R1_val_1_val_1.fq.gz ============================================= 161309784 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G/zr3616_8_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_8_R2_val_2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.6 Cutadapt version: 3.1 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' (user defined) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_8_R2_val_2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG' from file /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_8_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_8_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 3712.28 s (23 µs/read; 2.61 M reads/minute). === Summary === Total reads processed: 161,309,784 Reads with adapters: 16,896,270 (10.5%) Reads written (passing filters): 161,309,784 (100.0%) Total basepairs processed: 15,578,772,993 bp Quality-trimmed: 3,804,929 bp (0.0%) Total written (filtered): 15,335,395,137 bp (98.4%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 16896270 times No. of allowed errors: 1-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50 bp: 5 Bases preceding removed adapters: A: 13.9% C: 5.5% G: 0.0% T: 80.1% none/other: 0.5% WARNING: The adapter is preceded by "T" extremely often. The provided adapter sequence could be incomplete at its 5' end. Overview of removed sequences length count expect max.err error counts 1 10728037 40327446.0 0 10728037 2 3180063 10081861.5 0 3180063 3 691498 2520465.4 0 691498 4 197818 630116.3 0 197818 5 57457 157529.1 0 57457 6 14925 39382.3 0 14925 7 4931 9845.6 0 4931 8 2970 2461.4 0 2970 9 2471 615.3 0 2471 10 7191 153.8 1 2354 4837 11 6228 38.5 1 2128 4100 12 4726 9.6 1 1910 2816 13 4051 2.4 1 1635 2416 14 3706 0.6 1 1490 2216 15 3246 0.2 1 1309 1937 16 2653 0.0 1 1157 1496 17 2166 0.0 1 958 1208 18 1769 0.0 1 973 796 19 1532 0.0 1 802 730 20 3450 0.0 2 1284 747 1419 21 3180 0.0 2 1108 663 1409 22 2895 0.0 2 1071 593 1231 23 2833 0.0 2 1050 569 1214 24 2456 0.0 2 874 518 1064 25 2467 0.0 2 861 536 1070 26 2066 0.0 2 814 434 818 27 1864 0.0 2 779 402 683 28 1632 0.0 2 815 358 459 29 1580 0.0 2 734 401 445 30 2562 0.0 3 768 358 435 1001 31 2434 0.0 3 718 369 431 916 32 2228 0.0 3 711 317 359 841 33 2276 0.0 3 757 329 375 815 34 2236 0.0 3 704 351 383 798 35 2068 0.0 3 614 347 365 742 36 1840 0.0 3 654 305 324 557 37 1696 0.0 3 597 309 272 518 38 1509 0.0 3 641 288 253 327 39 1472 0.0 3 576 285 270 341 40 2241 0.0 4 666 285 282 346 662 41 2041 0.0 4 512 291 260 312 666 42 2161 0.0 4 619 283 258 335 666 43 1948 0.0 4 449 261 247 324 667 44 1987 0.0 4 588 275 256 314 554 45 1967 0.0 4 558 278 228 327 576 46 1794 0.0 4 607 254 213 283 437 47 1933 0.0 4 632 311 295 221 474 48 2119 0.0 4 755 408 356 296 304 49 4916 0.0 4 1461 1110 903 806 636 50 5146 0.0 5 1361 1044 802 788 608 543 51 3975 0.0 5 1470 790 601 468 344 302 52 3305 0.0 5 1337 648 486 373 268 193 53 2886 0.0 5 1208 576 399 302 242 159 54 2707 0.0 5 1290 506 332 252 183 144 55 2434 0.0 5 1219 460 280 209 149 117 56 2350 0.0 5 1217 439 250 194 138 112 57 2227 0.0 5 1235 411 226 147 115 93 58 2143 0.0 5 1243 357 221 150 100 72 59 1834 0.0 5 1033 324 179 132 106 60 60 1724 0.0 5 1013 292 167 115 81 56 61 1663 0.0 5 1030 264 139 98 83 49 62 1748 0.0 5 1109 286 163 83 52 55 63 1624 0.0 5 1010 289 141 96 59 29 64 1591 0.0 5 1029 267 114 90 55 36 65 1494 0.0 5 989 216 130 74 51 34 66 1428 0.0 5 986 212 106 59 43 22 67 1450 0.0 5 1025 195 86 65 40 39 68 1575 0.0 5 1147 214 106 39 45 24 69 1440 0.0 5 1021 192 101 66 39 21 70 1287 0.0 5 950 172 66 52 23 24 71 1204 0.0 5 872 164 71 46 28 23 72 1277 0.0 5 975 149 61 43 25 24 73 1162 0.0 5 893 121 72 31 24 21 74 1068 0.0 5 801 134 59 31 18 25 75 999 0.0 5 781 107 48 20 24 19 76 1043 0.0 5 829 107 40 26 26 15 77 1028 0.0 5 797 120 52 22 21 16 78 919 0.0 5 720 92 47 24 22 14 79 824 0.0 5 645 89 43 18 18 11 80 957 0.0 5 748 98 52 26 16 17 81 889 0.0 5 727 80 39 23 10 10 82 777 0.0 5 626 71 40 22 12 6 83 708 0.0 5 567 63 30 21 12 15 84 702 0.0 5 545 71 35 27 12 12 85 738 0.0 5 591 72 21 22 21 11 86 684 0.0 5 576 53 20 15 12 8 87 650 0.0 5 518 60 30 21 12 9 88 640 0.0 5 535 48 25 12 8 12 89 583 0.0 5 462 47 25 22 16 11 90 583 0.0 5 475 53 26 7 9 13 91 505 0.0 5 403 38 22 19 13 10 92 495 0.0 5 387 43 22 16 13 14 93 540 0.0 5 437 52 17 15 11 8 94 522 0.0 5 440 40 17 13 9 3 95 509 0.0 5 414 33 24 17 11 10 96 449 0.0 5 365 31 20 9 14 10 97 459 0.0 5 359 36 27 13 17 7 98 415 0.0 5 335 34 17 13 6 10 99 451 0.0 5 368 31 20 11 12 9 100 404 0.0 5 328 30 21 8 12 5 101 399 0.0 5 319 31 20 12 10 7 102 381 0.0 5 300 30 18 11 10 12 103 375 0.0 5 300 28 17 11 5 14 104 376 0.0 5 297 33 15 13 11 7 105 404 0.0 5 320 37 18 11 7 11 106 346 0.0 5 284 24 11 11 11 5 107 400 0.0 5 319 34 9 14 14 10 108 349 0.0 5 276 34 6 12 7 14 109 473 0.0 5 384 31 24 14 10 10 110 568 0.0 5 456 31 18 25 18 20 111 564 0.0 5 459 35 24 18 13 15 112 983 0.0 5 792 69 24 31 33 34 113 1309 0.0 5 1098 64 39 39 34 35 114 4066 0.0 5 3711 151 69 56 39 40 115 1831773 0.0 5 1831021 391 142 89 78 52 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/zr3616_8_R2_val_2_val_2.fq.gz ============================================= 161309784 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_8_R1_val_1_val_1_trimmed.fq.gz and zr3616_8_R2_val_2_val_2_trimmed.fq.gz file_1: zr3616_8_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3616_8_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_8_R1_val_1_val_1_trimmed.fq.gz and zr3616_8_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_8_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_8_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 161309784 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1927048 (1.19%) >>> Now running FastQC on the validated data zr3616_8_R1_val_1_val_1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 5471610392. >>> Now running FastQC on the validated data zr3616_8_R2_val_2_val_2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 5471610392. Deleting both intermediate output files zr3616_8_R1_val_1_val_1_trimmed.fq.gz and zr3616_8_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== TrimGalore 3 complete [INFO ] multiqc : This is MultiQC v1.8 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching : /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore-2/poly-G [INFO ] cutadapt : Found 16 reports [INFO ] multiqc : Compressing plot data [WARNING] multiqc : Previous MultiQC output found! Adjusting filenames.. [WARNING] multiqc : Use -f or --force to overwrite existing reports instead [INFO ] multiqc : Report : multiqc_report_2.html [INFO ] multiqc : Data : multiqc_data_2 [INFO ] multiqc : MultiQC complete MultiQC 3 complete