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/Hawes/analyses/trimgalore-2/ Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_1_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_1_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_1_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1380.46 s (27 µs/read; 2.26 M reads/minute). === Summary === Total reads processed: 51,950,473 Reads with adapters: 22,538,617 (43.4%) Reads written (passing filters): 51,950,473 (100.0%) Total basepairs processed: 5,475,353,592 bp Quality-trimmed: 6,215,557 bp (0.1%) Total written (filtered): 5,443,726,454 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22538617 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.5% C: 10.3% G: 6.6% T: 37.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20574469 12987618.2 0 20574469 2 1281458 3246904.6 0 1281458 3 464321 811726.1 0 464321 4 215633 202931.5 0 215633 5 1239 50732.9 0 1239 6 459 12683.2 0 459 7 150 3170.8 0 150 8 35 792.7 0 35 9 243 198.2 0 22 221 10 503 49.5 1 4 499 11 84 12.4 1 0 84 12 18 3.1 1 0 18 13 5 0.8 1 0 5 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_1_R1_val_1.fq.gz ============================================= 51950473 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/Hawes/analyses/trimgalore-2/zr3644_1_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_1_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_1_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1487.11 s (29 µs/read; 2.10 M reads/minute). === Summary === Total reads processed: 51,950,473 Reads with adapters: 22,677,249 (43.7%) Reads written (passing filters): 51,950,473 (100.0%) Total basepairs processed: 5,474,149,564 bp Quality-trimmed: 11,112,152 bp (0.2%) Total written (filtered): 5,437,608,277 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22677249 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.8% C: 10.4% G: 6.4% T: 37.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20832854 12987618.2 0 20832854 2 1164953 3246904.6 0 1164953 3 459994 811726.1 0 459994 4 215556 202931.5 0 215556 5 2455 50732.9 0 2455 6 462 12683.2 0 462 7 148 3170.8 0 148 8 34 792.7 0 34 9 242 198.2 0 34 208 10 445 49.5 1 9 436 11 87 12.4 1 1 86 12 18 3.1 1 0 18 13 1 0.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_1_R2_val_2.fq.gz ============================================= 51950473 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_1_R1_val_1_trimmed.fq.gz and zr3644_1_R2_val_2_trimmed.fq.gz file_1: zr3644_1_R1_val_1_trimmed.fq.gz, file_2: zr3644_1_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_1_R1_val_1_trimmed.fq.gz and zr3644_1_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_1_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_1_R2_val_2_val_2.fq.gz Total number of sequences analysed: 51950473 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 34186 (0.07%) >>> Now running FastQC on the validated data zr3644_1_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_1_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_1_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_1_R1_val_1_val_1.fq.gz Analysis complete for zr3644_1_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_1_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_1_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_1_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_1_R2_val_2_val_2.fq.gz Analysis complete for zr3644_1_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_1_R1_val_1_trimmed.fq.gz and zr3644_1_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_2_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_2_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_2_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1512.05 s (27 µs/read; 2.21 M reads/minute). === Summary === Total reads processed: 55,664,369 Reads with adapters: 24,412,986 (43.9%) Reads written (passing filters): 55,664,369 (100.0%) Total basepairs processed: 5,975,803,867 bp Quality-trimmed: 7,086,800 bp (0.1%) Total written (filtered): 5,941,256,825 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24412986 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 10.2% G: 6.4% T: 37.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22325079 13916092.2 0 22325079 2 1365072 3479023.1 0 1365072 3 494372 869755.8 0 494372 4 225572 217438.9 0 225572 5 1283 54359.7 0 1283 6 562 13589.9 0 562 7 156 3397.5 0 156 8 37 849.4 0 37 9 241 212.3 0 24 217 10 524 53.1 1 4 520 11 69 13.3 1 2 67 12 14 3.3 1 0 14 16 1 0.8 1 0 1 18 2 0.8 1 0 2 26 2 0.8 1 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_2_R1_val_1.fq.gz ============================================= 55664369 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/Hawes/analyses/trimgalore-2/zr3644_2_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_2_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_2_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1547.14 s (28 µs/read; 2.16 M reads/minute). === Summary === Total reads processed: 55,664,369 Reads with adapters: 24,450,667 (43.9%) Reads written (passing filters): 55,664,369 (100.0%) Total basepairs processed: 5,972,628,915 bp Quality-trimmed: 10,635,459 bp (0.2%) Total written (filtered): 5,934,603,445 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24450667 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.0% C: 10.2% G: 6.2% T: 37.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22474453 13916092.2 0 22474453 2 1253246 3479023.1 0 1253246 3 491137 869755.8 0 491137 4 228272 217438.9 0 228272 5 2056 54359.7 0 2056 6 529 13589.9 0 529 7 143 3397.5 0 143 8 35 849.4 0 35 9 251 212.3 0 19 232 10 439 53.1 1 2 437 11 90 13.3 1 0 90 12 15 3.3 1 0 15 13 1 0.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_2_R2_val_2.fq.gz ============================================= 55664369 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_2_R1_val_1_trimmed.fq.gz and zr3644_2_R2_val_2_trimmed.fq.gz file_1: zr3644_2_R1_val_1_trimmed.fq.gz, file_2: zr3644_2_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_2_R1_val_1_trimmed.fq.gz and zr3644_2_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_2_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_2_R2_val_2_val_2.fq.gz Total number of sequences analysed: 55664369 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 27982 (0.05%) >>> Now running FastQC on the validated data zr3644_2_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_2_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_2_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_2_R1_val_1_val_1.fq.gz Analysis complete for zr3644_2_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_2_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_2_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_2_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_2_R2_val_2_val_2.fq.gz Analysis complete for zr3644_2_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_2_R1_val_1_trimmed.fq.gz and zr3644_2_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_3_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_3_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 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/Hawes/analyses/trimgalore/zr3644_3_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1069.32 s (27 µs/read; 2.21 M reads/minute). === Summary === Total reads processed: 39,446,621 Reads with adapters: 17,287,588 (43.8%) Reads written (passing filters): 39,446,621 (100.0%) Total basepairs processed: 4,198,659,045 bp Quality-trimmed: 5,258,040 bp (0.1%) Total written (filtered): 4,173,950,912 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17287588 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.4% G: 6.5% T: 37.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15807468 9861655.2 0 15807468 2 966064 2465413.8 0 966064 3 351561 616353.5 0 351561 4 160330 154088.4 0 160330 5 1021 38522.1 0 1021 6 389 9630.5 0 389 7 123 2407.6 0 123 8 25 601.9 0 25 9 187 150.5 0 7 180 10 342 37.6 1 6 336 11 60 9.4 1 2 58 12 13 2.4 1 0 13 13 2 0.6 1 0 2 14 1 0.6 1 0 1 17 1 0.6 1 0 1 18 1 0.6 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_3_R1_val_1.fq.gz ============================================= 39446621 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/Hawes/analyses/trimgalore-2/zr3644_3_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_3_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 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/Hawes/analyses/trimgalore/zr3644_3_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1090.85 s (28 µs/read; 2.17 M reads/minute). === Summary === Total reads processed: 39,446,621 Reads with adapters: 17,252,522 (43.7%) Reads written (passing filters): 39,446,621 (100.0%) Total basepairs processed: 4,198,098,999 bp Quality-trimmed: 7,062,296 bp (0.2%) Total written (filtered): 4,171,657,724 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17252522 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.8% C: 10.2% G: 6.4% T: 37.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15817158 9861655.2 0 15817158 2 916634 2465413.8 0 916634 3 352886 616353.5 0 352886 4 163089 154088.4 0 163089 5 1565 38522.1 0 1565 6 395 9630.5 0 395 7 141 2407.6 0 141 8 28 601.9 0 28 9 213 150.5 0 11 202 10 339 37.6 1 1 338 11 65 9.4 1 1 64 12 6 2.4 1 0 6 13 3 0.6 1 0 3 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_3_R2_val_2.fq.gz ============================================= 39446621 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_3_R1_val_1_trimmed.fq.gz and zr3644_3_R2_val_2_trimmed.fq.gz file_1: zr3644_3_R1_val_1_trimmed.fq.gz, file_2: zr3644_3_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_3_R1_val_1_trimmed.fq.gz and zr3644_3_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_3_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_3_R2_val_2_val_2.fq.gz Total number of sequences analysed: 39446621 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21679 (0.05%) >>> Now running FastQC on the validated data zr3644_3_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_3_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_3_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_3_R1_val_1_val_1.fq.gz Analysis complete for zr3644_3_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_3_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_3_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_3_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_3_R2_val_2_val_2.fq.gz Analysis complete for zr3644_3_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_3_R1_val_1_trimmed.fq.gz and zr3644_3_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_4_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_4_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_4_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1432.70 s (29 µs/read; 2.09 M reads/minute). === Summary === Total reads processed: 50,012,460 Reads with adapters: 21,979,123 (43.9%) Reads written (passing filters): 50,012,460 (100.0%) Total basepairs processed: 5,318,299,419 bp Quality-trimmed: 8,005,212 bp (0.2%) Total written (filtered): 5,285,592,524 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21979123 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.4% G: 6.4% T: 37.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20114892 12503115.0 0 20114892 2 1216212 3125778.8 0 1216212 3 445120 781444.7 0 445120 4 200071 195361.2 0 200071 5 1394 48840.3 0 1394 6 511 12210.1 0 511 7 165 3052.5 0 165 8 22 763.1 0 22 9 196 190.8 0 14 182 10 424 47.7 1 4 420 11 97 11.9 1 1 96 12 11 3.0 1 0 11 13 1 0.7 1 0 1 14 1 0.7 1 0 1 16 1 0.7 1 0 1 17 1 0.7 1 0 1 19 1 0.7 1 0 1 22 1 0.7 1 0 1 25 1 0.7 1 0 1 27 1 0.7 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_4_R1_val_1.fq.gz ============================================= 50012460 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/Hawes/analyses/trimgalore-2/zr3644_4_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_4_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_4_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1348.15 s (27 µs/read; 2.23 M reads/minute). === Summary === Total reads processed: 50,012,460 Reads with adapters: 21,882,879 (43.8%) Reads written (passing filters): 50,012,460 (100.0%) Total basepairs processed: 5,316,873,875 bp Quality-trimmed: 7,825,202 bp (0.1%) Total written (filtered): 5,284,547,154 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21882879 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.0% C: 10.1% G: 6.2% T: 37.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20120821 12503115.0 0 20120821 2 1120477 3125778.8 0 1120477 3 433542 781444.7 0 433542 4 205117 195361.2 0 205117 5 1655 48840.3 0 1655 6 429 12210.1 0 429 7 134 3052.5 0 134 8 36 763.1 0 36 9 200 190.8 0 20 180 10 387 47.7 1 4 383 11 68 11.9 1 0 68 12 12 3.0 1 0 12 13 1 0.7 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_4_R2_val_2.fq.gz ============================================= 50012460 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_4_R1_val_1_trimmed.fq.gz and zr3644_4_R2_val_2_trimmed.fq.gz file_1: zr3644_4_R1_val_1_trimmed.fq.gz, file_2: zr3644_4_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_4_R1_val_1_trimmed.fq.gz and zr3644_4_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_4_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_4_R2_val_2_val_2.fq.gz Total number of sequences analysed: 50012460 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 24805 (0.05%) >>> Now running FastQC on the validated data zr3644_4_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_4_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_4_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_4_R1_val_1_val_1.fq.gz Analysis complete for zr3644_4_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_4_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_4_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_4_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_4_R2_val_2_val_2.fq.gz Analysis complete for zr3644_4_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_4_R1_val_1_trimmed.fq.gz and zr3644_4_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_5_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_5_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore/zr3644_5_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1337.69 s (30 µs/read; 2.00 M reads/minute). === Summary === Total reads processed: 44,694,095 Reads with adapters: 19,627,250 (43.9%) Reads written (passing filters): 44,694,095 (100.0%) Total basepairs processed: 4,764,654,231 bp Quality-trimmed: 8,509,712 bp (0.2%) Total written (filtered): 4,734,049,862 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19627250 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.4% C: 10.6% G: 6.5% T: 37.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17930802 11173523.8 0 17930802 2 1112005 2793380.9 0 1112005 3 404928 698345.2 0 404928 4 176645 174586.3 0 176645 5 1571 43646.6 0 1571 6 452 10911.6 0 452 7 139 2727.9 0 139 8 28 682.0 0 28 9 215 170.5 0 21 194 10 356 42.6 1 8 348 11 90 10.7 1 0 90 12 17 2.7 1 0 17 13 1 0.7 1 0 1 15 1 0.7 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_5_R1_val_1.fq.gz ============================================= 44694095 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/Hawes/analyses/trimgalore-2/zr3644_5_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_5_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore/zr3644_5_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1214.85 s (27 µs/read; 2.21 M reads/minute). === Summary === Total reads processed: 44,694,095 Reads with adapters: 19,510,418 (43.7%) Reads written (passing filters): 44,694,095 (100.0%) Total basepairs processed: 4,765,186,193 bp Quality-trimmed: 7,003,157 bp (0.1%) Total written (filtered): 4,736,283,447 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19510418 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.9% C: 10.1% G: 6.3% T: 37.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17898954 11173523.8 0 17898954 2 1028183 2793380.9 0 1028183 3 395616 698345.2 0 395616 4 184975 174586.3 0 184975 5 1418 43646.6 0 1418 6 453 10911.6 0 453 7 104 2727.9 0 104 8 34 682.0 0 34 9 200 170.5 0 13 187 10 387 42.6 1 4 383 11 86 10.7 1 0 86 12 7 2.7 1 0 7 13 1 0.7 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_5_R2_val_2.fq.gz ============================================= 44694095 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_5_R1_val_1_trimmed.fq.gz and zr3644_5_R2_val_2_trimmed.fq.gz file_1: zr3644_5_R1_val_1_trimmed.fq.gz, file_2: zr3644_5_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_5_R1_val_1_trimmed.fq.gz and zr3644_5_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_5_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_5_R2_val_2_val_2.fq.gz Total number of sequences analysed: 44694095 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 22579 (0.05%) >>> Now running FastQC on the validated data zr3644_5_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_5_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_5_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_5_R1_val_1_val_1.fq.gz Analysis complete for zr3644_5_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_5_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_5_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_5_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_5_R2_val_2_val_2.fq.gz Analysis complete for zr3644_5_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_5_R1_val_1_trimmed.fq.gz and zr3644_5_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_6_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_6_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_6_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1473.86 s (27 µs/read; 2.20 M reads/minute). === Summary === Total reads processed: 54,032,664 Reads with adapters: 23,593,118 (43.7%) Reads written (passing filters): 54,032,664 (100.0%) Total basepairs processed: 5,745,290,893 bp Quality-trimmed: 7,309,874 bp (0.1%) Total written (filtered): 5,711,425,985 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23593118 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.3% G: 6.5% T: 37.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21565962 13508166.0 0 21565962 2 1323130 3377041.5 0 1323130 3 481295 844260.4 0 481295 4 219675 211065.1 0 219675 5 1549 52766.3 0 1549 6 491 13191.6 0 491 7 149 3297.9 0 149 8 40 824.5 0 40 9 238 206.1 0 21 217 10 484 51.5 1 2 482 11 92 12.9 1 0 92 12 8 3.2 1 0 8 13 2 0.8 1 0 2 15 1 0.8 1 0 1 17 1 0.8 1 0 1 25 1 0.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_6_R1_val_1.fq.gz ============================================= 54032664 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/Hawes/analyses/trimgalore-2/zr3644_6_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_6_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_6_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1465.48 s (27 µs/read; 2.21 M reads/minute). === Summary === Total reads processed: 54,032,664 Reads with adapters: 23,564,542 (43.6%) Reads written (passing filters): 54,032,664 (100.0%) Total basepairs processed: 5,744,903,513 bp Quality-trimmed: 9,195,296 bp (0.2%) Total written (filtered): 5,709,275,896 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23564542 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.9% C: 10.2% G: 6.3% T: 37.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21632860 13508166.0 0 21632860 2 1230197 3377041.5 0 1230197 3 475335 844260.4 0 475335 4 222590 211065.1 0 222590 5 2056 52766.3 0 2056 6 484 13191.6 0 484 7 172 3297.9 0 172 8 41 824.5 0 41 9 237 206.1 0 13 224 10 447 51.5 1 8 439 11 96 12.9 1 2 94 12 24 3.2 1 0 24 13 3 0.8 1 0 3 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_6_R2_val_2.fq.gz ============================================= 54032664 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_6_R1_val_1_trimmed.fq.gz and zr3644_6_R2_val_2_trimmed.fq.gz file_1: zr3644_6_R1_val_1_trimmed.fq.gz, file_2: zr3644_6_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_6_R1_val_1_trimmed.fq.gz and zr3644_6_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_6_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_6_R2_val_2_val_2.fq.gz Total number of sequences analysed: 54032664 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 28525 (0.05%) >>> Now running FastQC on the validated data zr3644_6_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_6_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_6_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_6_R1_val_1_val_1.fq.gz Analysis complete for zr3644_6_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_6_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_6_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_6_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_6_R2_val_2_val_2.fq.gz Analysis complete for zr3644_6_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_6_R1_val_1_trimmed.fq.gz and zr3644_6_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_7_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_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 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/Hawes/analyses/trimgalore/zr3644_7_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2226.53 s (27 µs/read; 2.23 M reads/minute). === Summary === Total reads processed: 82,575,967 Reads with adapters: 36,222,656 (43.9%) Reads written (passing filters): 82,575,967 (100.0%) Total basepairs processed: 8,807,444,499 bp Quality-trimmed: 10,576,903 bp (0.1%) Total written (filtered): 8,756,123,651 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36222656 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 10.3% G: 6.5% T: 37.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 33128262 20643991.8 0 33128262 2 2018455 5160997.9 0 2018455 3 736707 1290249.5 0 736707 4 335009 322562.4 0 335009 5 1927 80640.6 0 1927 6 763 20160.1 0 763 7 214 5040.0 0 214 8 60 1260.0 0 60 9 363 315.0 0 34 329 10 742 78.8 1 4 738 11 132 19.7 1 2 130 12 17 4.9 1 0 17 13 2 1.2 1 0 2 14 1 1.2 1 0 1 18 1 1.2 1 0 1 24 1 1.2 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_7_R1_val_1.fq.gz ============================================= 82575967 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/Hawes/analyses/trimgalore-2/zr3644_7_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_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 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/Hawes/analyses/trimgalore/zr3644_7_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2318.43 s (28 µs/read; 2.14 M reads/minute). === Summary === Total reads processed: 82,575,967 Reads with adapters: 36,247,525 (43.9%) Reads written (passing filters): 82,575,967 (100.0%) Total basepairs processed: 8,804,136,896 bp Quality-trimmed: 16,290,671 bp (0.2%) Total written (filtered): 8,747,217,431 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36247525 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.0% C: 10.1% G: 6.3% T: 37.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 33298978 20643991.8 0 33298978 2 1873842 5160997.9 0 1873842 3 729535 1290249.5 0 729535 4 339564 322562.4 0 339564 5 3410 80640.6 0 3410 6 700 20160.1 0 700 7 216 5040.0 0 216 8 60 1260.0 0 60 9 374 315.0 0 25 349 10 672 78.8 1 4 668 11 147 19.7 1 4 143 12 25 4.9 1 0 25 13 2 1.2 1 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_7_R2_val_2.fq.gz ============================================= 82575967 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_7_R1_val_1_trimmed.fq.gz and zr3644_7_R2_val_2_trimmed.fq.gz file_1: zr3644_7_R1_val_1_trimmed.fq.gz, file_2: zr3644_7_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_7_R1_val_1_trimmed.fq.gz and zr3644_7_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_7_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_7_R2_val_2_val_2.fq.gz Total number of sequences analysed: 82575967 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 48898 (0.06%) >>> Now running FastQC on the validated data zr3644_7_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_7_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_7_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_7_R1_val_1_val_1.fq.gz Analysis complete for zr3644_7_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_7_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_7_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_7_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_7_R2_val_2_val_2.fq.gz Analysis complete for zr3644_7_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_7_R1_val_1_trimmed.fq.gz and zr3644_7_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_8_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_8_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore/zr3644_8_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1157.87 s (27 µs/read; 2.23 M reads/minute). === Summary === Total reads processed: 42,944,059 Reads with adapters: 18,771,452 (43.7%) Reads written (passing filters): 42,944,059 (100.0%) Total basepairs processed: 4,553,628,990 bp Quality-trimmed: 5,628,517 bp (0.1%) Total written (filtered): 4,526,859,091 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18771452 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.4% G: 6.6% T: 37.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17148689 10736014.8 0 17148689 2 1061835 2684003.7 0 1061835 3 381925 671000.9 0 381925 4 175925 167750.2 0 175925 5 1790 41937.6 0 1790 6 435 10484.4 0 435 7 125 2621.1 0 125 8 31 655.3 0 31 9 202 163.8 0 14 188 10 411 41.0 1 4 407 11 72 10.2 1 1 71 12 11 2.6 1 0 11 13 1 0.6 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_8_R1_val_1.fq.gz ============================================= 42944059 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/Hawes/analyses/trimgalore-2/zr3644_8_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore/zr3644_8_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore/zr3644_8_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1198.73 s (28 µs/read; 2.15 M reads/minute). === Summary === Total reads processed: 42,944,059 Reads with adapters: 18,798,887 (43.8%) Reads written (passing filters): 42,944,059 (100.0%) Total basepairs processed: 4,552,516,502 bp Quality-trimmed: 8,191,924 bp (0.2%) Total written (filtered): 4,523,218,672 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18798887 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.8% C: 10.3% G: 6.4% T: 37.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17247458 10736014.8 0 17247458 2 984900 2684003.7 0 984900 3 384804 671000.9 0 384804 4 178516 167750.2 0 178516 5 1921 41937.6 0 1921 6 433 10484.4 0 433 7 133 2621.1 0 133 8 25 655.3 0 25 9 229 163.8 0 23 206 10 385 41.0 1 3 382 11 69 10.2 1 0 69 12 14 2.6 1 0 14 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_8_R2_val_2.fq.gz ============================================= 42944059 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_8_R1_val_1_trimmed.fq.gz and zr3644_8_R2_val_2_trimmed.fq.gz file_1: zr3644_8_R1_val_1_trimmed.fq.gz, file_2: zr3644_8_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_8_R1_val_1_trimmed.fq.gz and zr3644_8_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_8_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_8_R2_val_2_val_2.fq.gz Total number of sequences analysed: 42944059 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 25551 (0.06%) >>> Now running FastQC on the validated data zr3644_8_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_8_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_8_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_8_R1_val_1_val_1.fq.gz Analysis complete for zr3644_8_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_8_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_8_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_8_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_8_R2_val_2_val_2.fq.gz Analysis complete for zr3644_8_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_8_R1_val_1_trimmed.fq.gz and zr3644_8_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_9_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_9_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/Hawes/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 zr3644_9_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/Hawes/analyses/trimgalore/zr3644_9_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore/zr3644_9_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1260.95 s (26 µs/read; 2.32 M reads/minute). === Summary === Total reads processed: 48,759,846 Reads with adapters: 21,011,128 (43.1%) Reads written (passing filters): 48,759,846 (100.0%) Total basepairs processed: 5,064,756,755 bp Quality-trimmed: 6,267,373 bp (0.1%) Total written (filtered): 5,034,775,359 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21011128 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.4% G: 6.7% T: 37.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19166103 12189961.5 0 19166103 2 1200841 3047490.4 0 1200841 3 437953 761872.6 0 437953 4 203481 190468.1 0 203481 5 1267 47617.0 0 1267 6 512 11904.3 0 512 7 162 2976.1 0 162 8 25 744.0 0 25 9 255 186.0 0 15 240 10 419 46.5 1 5 414 11 92 11.6 1 3 89 12 17 2.9 1 0 17 13 1 0.7 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_9_R1_val_1.fq.gz ============================================= 48759846 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/Hawes/analyses/trimgalore-2/zr3644_9_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_9_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/Hawes/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 zr3644_9_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/Hawes/analyses/trimgalore/zr3644_9_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore/zr3644_9_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1284.44 s (26 µs/read; 2.28 M reads/minute). === Summary === Total reads processed: 48,759,846 Reads with adapters: 21,069,884 (43.2%) Reads written (passing filters): 48,759,846 (100.0%) Total basepairs processed: 5,063,886,112 bp Quality-trimmed: 8,852,793 bp (0.2%) Total written (filtered): 5,031,356,233 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21069884 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.9% C: 10.4% G: 6.5% T: 37.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19312484 12189961.5 0 19312484 2 1120955 3047490.4 0 1120955 3 431035 761872.6 0 431035 4 201907 190468.1 0 201907 5 2087 47617.0 0 2087 6 491 11904.3 0 491 7 154 2976.1 0 154 8 50 744.0 0 50 9 212 186.0 0 10 202 10 422 46.5 1 5 417 11 72 11.6 1 0 72 12 15 2.9 1 0 15 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_9_R2_val_2.fq.gz ============================================= 48759846 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_9_R1_val_1_trimmed.fq.gz and zr3644_9_R2_val_2_trimmed.fq.gz file_1: zr3644_9_R1_val_1_trimmed.fq.gz, file_2: zr3644_9_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_9_R1_val_1_trimmed.fq.gz and zr3644_9_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_9_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_9_R2_val_2_val_2.fq.gz Total number of sequences analysed: 48759846 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 36189 (0.07%) >>> Now running FastQC on the validated data zr3644_9_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_9_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_9_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_9_R1_val_1_val_1.fq.gz Analysis complete for zr3644_9_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_9_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_9_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_9_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_9_R2_val_2_val_2.fq.gz Analysis complete for zr3644_9_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_9_R1_val_1_trimmed.fq.gz and zr3644_9_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_10_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_10_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/Hawes/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 zr3644_10_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/Hawes/analyses/trimgalore/zr3644_10_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_10_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1408.41 s (27 µs/read; 2.24 M reads/minute). === Summary === Total reads processed: 52,592,877 Reads with adapters: 22,973,068 (43.7%) Reads written (passing filters): 52,592,877 (100.0%) Total basepairs processed: 5,572,077,675 bp Quality-trimmed: 6,744,016 bp (0.1%) Total written (filtered): 5,539,415,510 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22973068 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.4% G: 6.6% T: 37.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20956973 13148219.2 0 20956973 2 1316084 3287054.8 0 1316084 3 478983 821763.7 0 478983 4 218148 205440.9 0 218148 5 1294 51360.2 0 1294 6 545 12840.1 0 545 7 155 3210.0 0 155 8 50 802.5 0 50 9 275 200.6 0 19 256 10 443 50.2 1 5 438 11 93 12.5 1 1 92 12 24 3.1 1 0 24 26 1 0.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_10_R1_val_1.fq.gz ============================================= 52592877 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/Hawes/analyses/trimgalore-2/zr3644_10_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_10_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/Hawes/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 zr3644_10_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/Hawes/analyses/trimgalore/zr3644_10_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_10_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1438.95 s (27 µs/read; 2.19 M reads/minute). === Summary === Total reads processed: 52,592,877 Reads with adapters: 23,007,562 (43.7%) Reads written (passing filters): 52,592,877 (100.0%) Total basepairs processed: 5,570,349,840 bp Quality-trimmed: 9,621,008 bp (0.2%) Total written (filtered): 5,534,917,787 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23007562 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.9% C: 10.3% G: 6.4% T: 37.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21121296 13148219.2 0 21121296 2 1199383 3287054.8 0 1199383 3 465040 821763.7 0 465040 4 218106 205440.9 0 218106 5 2211 51360.2 0 2211 6 551 12840.1 0 551 7 160 3210.0 0 160 8 41 802.5 0 41 9 228 200.6 0 20 208 10 443 50.2 1 2 441 11 88 12.5 1 1 87 12 15 3.1 1 0 15 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_10_R2_val_2.fq.gz ============================================= 52592877 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_10_R1_val_1_trimmed.fq.gz and zr3644_10_R2_val_2_trimmed.fq.gz file_1: zr3644_10_R1_val_1_trimmed.fq.gz, file_2: zr3644_10_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_10_R1_val_1_trimmed.fq.gz and zr3644_10_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_10_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_10_R2_val_2_val_2.fq.gz Total number of sequences analysed: 52592877 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 30396 (0.06%) >>> Now running FastQC on the validated data zr3644_10_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_10_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_10_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_10_R1_val_1_val_1.fq.gz Analysis complete for zr3644_10_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_10_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_10_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_10_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_10_R2_val_2_val_2.fq.gz Analysis complete for zr3644_10_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_10_R1_val_1_trimmed.fq.gz and zr3644_10_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_11_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_11_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/Hawes/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 zr3644_11_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/Hawes/analyses/trimgalore/zr3644_11_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_11_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1524.75 s (27 µs/read; 2.24 M reads/minute). === Summary === Total reads processed: 56,807,549 Reads with adapters: 24,870,380 (43.8%) Reads written (passing filters): 56,807,549 (100.0%) Total basepairs processed: 6,015,552,738 bp Quality-trimmed: 7,496,241 bp (0.1%) Total written (filtered): 5,980,049,550 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24870380 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.4% G: 6.5% T: 37.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22722576 14201887.2 0 22722576 2 1403696 3550471.8 0 1403696 3 507852 887618.0 0 507852 4 233162 221904.5 0 233162 5 1413 55476.1 0 1413 6 604 13869.0 0 604 7 149 3467.3 0 149 8 42 866.8 0 42 9 275 216.7 0 22 253 10 508 54.2 1 7 501 11 91 13.5 1 0 91 12 10 3.4 1 0 10 15 1 0.8 1 0 1 16 1 0.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_11_R1_val_1.fq.gz ============================================= 56807549 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/Hawes/analyses/trimgalore-2/zr3644_11_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_11_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/Hawes/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 zr3644_11_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/Hawes/analyses/trimgalore/zr3644_11_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_11_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1554.98 s (27 µs/read; 2.19 M reads/minute). === Summary === Total reads processed: 56,807,549 Reads with adapters: 24,841,448 (43.7%) Reads written (passing filters): 56,807,549 (100.0%) Total basepairs processed: 6,013,778,082 bp Quality-trimmed: 10,231,800 bp (0.2%) Total written (filtered): 5,975,677,543 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24841448 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.9% C: 10.2% G: 6.4% T: 37.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22805353 14201887.2 0 22805353 2 1293971 3550471.8 0 1293971 3 502162 887618.0 0 502162 4 236139 221904.5 0 236139 5 2178 55476.1 0 2178 6 550 13869.0 0 550 7 182 3467.3 0 182 8 44 866.8 0 44 9 248 216.7 0 20 228 10 509 54.2 1 3 506 11 83 13.5 1 1 82 12 26 3.4 1 0 26 13 3 0.8 1 0 3 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_11_R2_val_2.fq.gz ============================================= 56807549 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_11_R1_val_1_trimmed.fq.gz and zr3644_11_R2_val_2_trimmed.fq.gz file_1: zr3644_11_R1_val_1_trimmed.fq.gz, file_2: zr3644_11_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_11_R1_val_1_trimmed.fq.gz and zr3644_11_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_11_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_11_R2_val_2_val_2.fq.gz Total number of sequences analysed: 56807549 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 33290 (0.06%) >>> Now running FastQC on the validated data zr3644_11_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_11_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_11_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_11_R1_val_1_val_1.fq.gz Analysis complete for zr3644_11_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_11_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_11_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_11_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_11_R2_val_2_val_2.fq.gz Analysis complete for zr3644_11_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_11_R1_val_1_trimmed.fq.gz and zr3644_11_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_12_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_12_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/Hawes/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 zr3644_12_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/Hawes/analyses/trimgalore/zr3644_12_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore/zr3644_12_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1270.40 s (27 µs/read; 2.25 M reads/minute). === Summary === Total reads processed: 47,672,940 Reads with adapters: 20,907,864 (43.9%) Reads written (passing filters): 47,672,940 (100.0%) Total basepairs processed: 5,057,370,806 bp Quality-trimmed: 5,436,445 bp (0.1%) Total written (filtered): 5,028,568,661 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20907864 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.1% C: 10.2% G: 6.1% T: 37.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19232385 11918235.0 0 19232385 2 1088137 2979558.8 0 1088137 3 398188 744889.7 0 398188 4 186980 186222.4 0 186980 5 1039 46555.6 0 1039 6 370 11638.9 0 370 7 124 2909.7 0 124 8 38 727.4 0 38 9 160 181.9 0 13 147 10 368 45.5 1 8 360 11 61 11.4 1 1 60 12 11 2.8 1 0 11 13 2 0.7 1 0 2 21 1 0.7 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_12_R1_val_1.fq.gz ============================================= 47672940 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/Hawes/analyses/trimgalore-2/zr3644_12_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_12_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/Hawes/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 zr3644_12_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/Hawes/analyses/trimgalore/zr3644_12_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore/zr3644_12_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1303.79 s (27 µs/read; 2.19 M reads/minute). === Summary === Total reads processed: 47,672,940 Reads with adapters: 20,886,033 (43.8%) Reads written (passing filters): 47,672,940 (100.0%) Total basepairs processed: 5,056,045,086 bp Quality-trimmed: 8,049,156 bp (0.2%) Total written (filtered): 5,024,697,872 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20886033 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.2% C: 10.0% G: 6.0% T: 37.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19271195 11918235.0 0 19271195 2 1018652 2979558.8 0 1018652 3 401475 744889.7 0 401475 4 191842 186222.4 0 191842 5 1817 46555.6 0 1817 6 353 11638.9 0 353 7 94 2909.7 0 94 8 32 727.4 0 32 9 176 181.9 0 20 156 10 319 45.5 1 2 317 11 63 11.4 1 0 63 12 13 2.8 1 0 13 13 2 0.7 1 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_12_R2_val_2.fq.gz ============================================= 47672940 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_12_R1_val_1_trimmed.fq.gz and zr3644_12_R2_val_2_trimmed.fq.gz file_1: zr3644_12_R1_val_1_trimmed.fq.gz, file_2: zr3644_12_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_12_R1_val_1_trimmed.fq.gz and zr3644_12_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_12_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_12_R2_val_2_val_2.fq.gz Total number of sequences analysed: 47672940 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 23117 (0.05%) >>> Now running FastQC on the validated data zr3644_12_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_12_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_12_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_12_R1_val_1_val_1.fq.gz Analysis complete for zr3644_12_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_12_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_12_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_12_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_12_R2_val_2_val_2.fq.gz Analysis complete for zr3644_12_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_12_R1_val_1_trimmed.fq.gz and zr3644_12_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_13_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_13_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/Hawes/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 zr3644_13_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/Hawes/analyses/trimgalore/zr3644_13_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_13_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1458.05 s (27 µs/read; 2.22 M reads/minute). === Summary === Total reads processed: 53,911,566 Reads with adapters: 23,651,701 (43.9%) Reads written (passing filters): 53,911,566 (100.0%) Total basepairs processed: 5,759,871,046 bp Quality-trimmed: 6,988,047 bp (0.1%) Total written (filtered): 5,726,266,859 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23651701 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 10.3% G: 6.4% T: 37.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21623159 13477891.5 0 21623159 2 1323589 3369472.9 0 1323589 3 481744 842368.2 0 481744 4 220391 210592.1 0 220391 5 1296 52648.0 0 1296 6 512 13162.0 0 512 7 157 3290.5 0 157 8 42 822.6 0 42 9 228 205.7 0 15 213 10 466 51.4 1 8 458 11 101 12.9 1 5 96 12 14 3.2 1 0 14 13 1 0.8 1 0 1 16 1 0.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_13_R1_val_1.fq.gz ============================================= 53911566 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/Hawes/analyses/trimgalore-2/zr3644_13_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_13_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/Hawes/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 zr3644_13_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/Hawes/analyses/trimgalore/zr3644_13_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_13_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1494.17 s (28 µs/read; 2.16 M reads/minute). === Summary === Total reads processed: 53,911,566 Reads with adapters: 23,665,801 (43.9%) Reads written (passing filters): 53,911,566 (100.0%) Total basepairs processed: 5,758,774,314 bp Quality-trimmed: 9,848,920 bp (0.2%) Total written (filtered): 5,722,402,739 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23665801 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.0% C: 10.1% G: 6.3% T: 37.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21744851 13477891.5 0 21744851 2 1219138 3369472.9 0 1219138 3 475872 842368.2 0 475872 4 222580 210592.1 0 222580 5 1892 52648.0 0 1892 6 481 13162.0 0 481 7 135 3290.5 0 135 8 49 822.6 0 49 9 246 205.7 0 9 237 10 453 51.4 1 5 448 11 84 12.9 1 0 84 12 19 3.2 1 0 19 13 1 0.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_13_R2_val_2.fq.gz ============================================= 53911566 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_13_R1_val_1_trimmed.fq.gz and zr3644_13_R2_val_2_trimmed.fq.gz file_1: zr3644_13_R1_val_1_trimmed.fq.gz, file_2: zr3644_13_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_13_R1_val_1_trimmed.fq.gz and zr3644_13_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_13_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_13_R2_val_2_val_2.fq.gz Total number of sequences analysed: 53911566 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 28311 (0.05%) >>> Now running FastQC on the validated data zr3644_13_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_13_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_13_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_13_R1_val_1_val_1.fq.gz Analysis complete for zr3644_13_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_13_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_13_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_13_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_13_R2_val_2_val_2.fq.gz Analysis complete for zr3644_13_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_13_R1_val_1_trimmed.fq.gz and zr3644_13_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_14_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_14_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/Hawes/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 zr3644_14_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/Hawes/analyses/trimgalore/zr3644_14_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 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/Hawes/analyses/trimgalore/zr3644_14_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1083.91 s (29 µs/read; 2.04 M reads/minute). === Summary === Total reads processed: 36,871,756 Reads with adapters: 16,142,874 (43.8%) Reads written (passing filters): 36,871,756 (100.0%) Total basepairs processed: 3,913,478,219 bp Quality-trimmed: 6,690,699 bp (0.2%) Total written (filtered): 3,888,601,182 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16142874 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.2% C: 10.5% G: 6.6% T: 37.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 14740280 9217939.0 0 14740280 2 917217 2304484.8 0 917217 3 335971 576121.2 0 335971 4 146884 144030.3 0 146884 5 1359 36007.6 0 1359 6 420 9001.9 0 420 7 134 2250.5 0 134 8 35 562.6 0 35 9 199 140.7 0 16 183 10 299 35.2 1 4 295 11 64 8.8 1 1 63 12 10 2.2 1 0 10 13 1 0.5 1 0 1 24 1 0.5 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_14_R1_val_1.fq.gz ============================================= 36871756 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/Hawes/analyses/trimgalore-2/zr3644_14_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_14_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/Hawes/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 zr3644_14_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/Hawes/analyses/trimgalore/zr3644_14_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 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/Hawes/analyses/trimgalore/zr3644_14_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 990.19 s (27 µs/read; 2.23 M reads/minute). === Summary === Total reads processed: 36,871,756 Reads with adapters: 16,076,590 (43.6%) Reads written (passing filters): 36,871,756 (100.0%) Total basepairs processed: 3,913,759,881 bp Quality-trimmed: 5,533,727 bp (0.1%) Total written (filtered): 3,890,189,244 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16076590 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.9% C: 10.1% G: 6.3% T: 37.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 14757826 9217939.0 0 14757826 2 839052 2304484.8 0 839052 3 323487 576121.2 0 323487 4 153983 144030.3 0 153983 5 1202 36007.6 0 1202 6 352 9001.9 0 352 7 99 2250.5 0 99 8 27 562.6 0 27 9 176 140.7 0 13 163 10 292 35.2 1 2 290 11 77 8.8 1 0 77 12 16 2.2 1 0 16 13 1 0.5 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_14_R2_val_2.fq.gz ============================================= 36871756 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_14_R1_val_1_trimmed.fq.gz and zr3644_14_R2_val_2_trimmed.fq.gz file_1: zr3644_14_R1_val_1_trimmed.fq.gz, file_2: zr3644_14_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_14_R1_val_1_trimmed.fq.gz and zr3644_14_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_14_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_14_R2_val_2_val_2.fq.gz Total number of sequences analysed: 36871756 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 19172 (0.05%) >>> Now running FastQC on the validated data zr3644_14_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_14_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_14_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_14_R1_val_1_val_1.fq.gz Analysis complete for zr3644_14_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_14_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_14_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_14_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_14_R2_val_2_val_2.fq.gz Analysis complete for zr3644_14_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_14_R1_val_1_trimmed.fq.gz and zr3644_14_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_15_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_15_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/Hawes/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 zr3644_15_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/Hawes/analyses/trimgalore/zr3644_15_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_15_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1618.49 s (27 µs/read; 2.19 M reads/minute). === Summary === Total reads processed: 59,137,561 Reads with adapters: 25,905,284 (43.8%) Reads written (passing filters): 59,137,561 (100.0%) Total basepairs processed: 6,290,652,174 bp Quality-trimmed: 7,940,179 bp (0.1%) Total written (filtered): 6,253,550,020 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25905284 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 10.3% G: 6.5% T: 37.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 23677624 14784390.2 0 23677624 2 1453224 3696097.6 0 1453224 3 528809 924024.4 0 528809 4 242203 231006.1 0 242203 5 1675 57751.5 0 1675 6 610 14437.9 0 610 7 166 3609.5 0 166 8 55 902.4 0 55 9 287 225.6 0 18 269 10 517 56.4 1 4 513 11 94 14.1 1 0 94 12 20 3.5 1 0 20 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_15_R1_val_1.fq.gz ============================================= 59137561 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/Hawes/analyses/trimgalore-2/zr3644_15_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_15_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/Hawes/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 zr3644_15_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/Hawes/analyses/trimgalore/zr3644_15_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_15_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1622.12 s (27 µs/read; 2.19 M reads/minute). === Summary === Total reads processed: 59,137,561 Reads with adapters: 25,893,265 (43.8%) Reads written (passing filters): 59,137,561 (100.0%) Total basepairs processed: 6,290,547,044 bp Quality-trimmed: 10,043,561 bp (0.2%) Total written (filtered): 6,251,454,303 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25893265 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.0% C: 10.1% G: 6.3% T: 37.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 23768673 14784390.2 0 23768673 2 1352013 3696097.6 0 1352013 3 522926 924024.4 0 522926 4 245795 231006.1 0 245795 5 2231 57751.5 0 2231 6 578 14437.9 0 578 7 136 3609.5 0 136 8 41 902.4 0 41 9 259 225.6 0 24 235 10 479 56.4 1 3 476 11 110 14.1 1 4 106 12 23 3.5 1 0 23 13 1 0.9 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_15_R2_val_2.fq.gz ============================================= 59137561 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_15_R1_val_1_trimmed.fq.gz and zr3644_15_R2_val_2_trimmed.fq.gz file_1: zr3644_15_R1_val_1_trimmed.fq.gz, file_2: zr3644_15_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_15_R1_val_1_trimmed.fq.gz and zr3644_15_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_15_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_15_R2_val_2_val_2.fq.gz Total number of sequences analysed: 59137561 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 31899 (0.05%) >>> Now running FastQC on the validated data zr3644_15_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_15_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_15_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_15_R1_val_1_val_1.fq.gz Analysis complete for zr3644_15_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_15_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_15_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_15_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_15_R2_val_2_val_2.fq.gz Analysis complete for zr3644_15_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_15_R1_val_1_trimmed.fq.gz and zr3644_15_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_16_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_16_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/Hawes/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 zr3644_16_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/Hawes/analyses/trimgalore/zr3644_16_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_16_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1421.46 s (28 µs/read; 2.18 M reads/minute). === Summary === Total reads processed: 51,615,953 Reads with adapters: 22,358,370 (43.3%) Reads written (passing filters): 51,615,953 (100.0%) Total basepairs processed: 5,398,887,438 bp Quality-trimmed: 7,587,870 bp (0.1%) Total written (filtered): 5,366,099,765 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22358370 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.5% C: 10.5% G: 6.7% T: 37.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20416303 12903988.2 0 20416303 2 1263682 3225997.1 0 1263682 3 465476 806499.3 0 465476 4 209912 201624.8 0 209912 5 1454 50406.2 0 1454 6 467 12601.6 0 467 7 180 3150.4 0 180 8 44 787.6 0 44 9 278 196.9 0 35 243 10 461 49.2 1 7 454 11 96 12.3 1 0 96 12 13 3.1 1 0 13 13 4 0.8 1 0 4 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_16_R1_val_1.fq.gz ============================================= 51615953 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/Hawes/analyses/trimgalore-2/zr3644_16_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_16_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/Hawes/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 zr3644_16_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/Hawes/analyses/trimgalore/zr3644_16_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_16_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1393.63 s (27 µs/read; 2.22 M reads/minute). === Summary === Total reads processed: 51,615,953 Reads with adapters: 22,307,149 (43.2%) Reads written (passing filters): 51,615,953 (100.0%) Total basepairs processed: 5,398,402,113 bp Quality-trimmed: 9,050,977 bp (0.2%) Total written (filtered): 5,364,300,606 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22307149 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.8% C: 10.3% G: 6.5% T: 37.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20464399 12903988.2 0 20464399 2 1169773 3225997.1 0 1169773 3 453692 806499.3 0 453692 4 215709 201624.8 0 215709 5 2078 50406.2 0 2078 6 491 12601.6 0 491 7 177 3150.4 0 177 8 31 787.6 0 31 9 248 196.9 0 26 222 10 459 49.2 1 3 456 11 78 12.3 1 0 78 12 12 3.1 1 0 12 13 2 0.8 1 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_16_R2_val_2.fq.gz ============================================= 51615953 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_16_R1_val_1_trimmed.fq.gz and zr3644_16_R2_val_2_trimmed.fq.gz file_1: zr3644_16_R1_val_1_trimmed.fq.gz, file_2: zr3644_16_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_16_R1_val_1_trimmed.fq.gz and zr3644_16_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_16_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_16_R2_val_2_val_2.fq.gz Total number of sequences analysed: 51615953 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 31598 (0.06%) >>> Now running FastQC on the validated data zr3644_16_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_16_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_16_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_16_R1_val_1_val_1.fq.gz Analysis complete for zr3644_16_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_16_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_16_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_16_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_16_R2_val_2_val_2.fq.gz Analysis complete for zr3644_16_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_16_R1_val_1_trimmed.fq.gz and zr3644_16_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_17_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_17_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/Hawes/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 zr3644_17_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/Hawes/analyses/trimgalore/zr3644_17_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_17_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1556.05 s (27 µs/read; 2.25 M reads/minute). === Summary === Total reads processed: 58,307,693 Reads with adapters: 25,412,767 (43.6%) Reads written (passing filters): 58,307,693 (100.0%) Total basepairs processed: 6,158,828,348 bp Quality-trimmed: 7,031,454 bp (0.1%) Total written (filtered): 6,123,151,465 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25412767 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.5% G: 6.6% T: 37.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 23203313 14576923.2 0 23203313 2 1440507 3644230.8 0 1440507 3 523661 911057.7 0 523661 4 241985 227764.4 0 241985 5 1584 56941.1 0 1584 6 542 14235.3 0 542 7 179 3558.8 0 179 8 44 889.7 0 44 9 291 222.4 0 21 270 10 544 55.6 1 6 538 11 93 13.9 1 1 92 12 17 3.5 1 0 17 13 3 0.9 1 0 3 17 1 0.9 1 0 1 19 2 0.9 1 0 2 22 1 0.9 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_17_R1_val_1.fq.gz ============================================= 58307693 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/Hawes/analyses/trimgalore-2/zr3644_17_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_17_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/Hawes/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 zr3644_17_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/Hawes/analyses/trimgalore/zr3644_17_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_17_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1586.41 s (27 µs/read; 2.21 M reads/minute). === Summary === Total reads processed: 58,307,693 Reads with adapters: 25,366,685 (43.5%) Reads written (passing filters): 58,307,693 (100.0%) Total basepairs processed: 6,158,132,185 bp Quality-trimmed: 9,852,766 bp (0.2%) Total written (filtered): 6,119,780,472 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 25366685 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.8% C: 10.3% G: 6.5% T: 37.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 23256715 14576923.2 0 23256715 2 1345228 3644230.8 0 1345228 3 516661 911057.7 0 516661 4 244222 227764.4 0 244222 5 2194 56941.1 0 2194 6 506 14235.3 0 506 7 167 3558.8 0 167 8 41 889.7 0 41 9 263 222.4 0 16 247 10 558 55.6 1 3 555 11 105 13.9 1 1 104 12 25 3.5 1 0 25 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_17_R2_val_2.fq.gz ============================================= 58307693 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_17_R1_val_1_trimmed.fq.gz and zr3644_17_R2_val_2_trimmed.fq.gz file_1: zr3644_17_R1_val_1_trimmed.fq.gz, file_2: zr3644_17_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_17_R1_val_1_trimmed.fq.gz and zr3644_17_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_17_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_17_R2_val_2_val_2.fq.gz Total number of sequences analysed: 58307693 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 33047 (0.06%) >>> Now running FastQC on the validated data zr3644_17_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_17_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_17_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_17_R1_val_1_val_1.fq.gz Analysis complete for zr3644_17_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_17_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_17_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_17_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_17_R2_val_2_val_2.fq.gz Analysis complete for zr3644_17_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_17_R1_val_1_trimmed.fq.gz and zr3644_17_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_18_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_18_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/Hawes/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 zr3644_18_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/Hawes/analyses/trimgalore/zr3644_18_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_18_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1378.13 s (27 µs/read; 2.25 M reads/minute). === Summary === Total reads processed: 51,713,176 Reads with adapters: 22,562,188 (43.6%) Reads written (passing filters): 51,713,176 (100.0%) Total basepairs processed: 5,465,399,814 bp Quality-trimmed: 6,523,423 bp (0.1%) Total written (filtered): 5,433,434,497 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22562188 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.4% G: 6.6% T: 37.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20591166 12928294.0 0 20591166 2 1288102 3232073.5 0 1288102 3 464974 808018.4 0 464974 4 215050 202004.6 0 215050 5 1399 50501.1 0 1399 6 504 12625.3 0 504 7 141 3156.3 0 141 8 34 789.1 0 34 9 237 197.3 0 19 218 10 446 49.3 1 6 440 11 110 12.3 1 0 110 12 16 3.1 1 0 16 13 7 0.8 1 0 7 18 1 0.8 1 0 1 20 1 0.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_18_R1_val_1.fq.gz ============================================= 51713176 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/Hawes/analyses/trimgalore-2/zr3644_18_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_18_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/Hawes/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 zr3644_18_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/Hawes/analyses/trimgalore/zr3644_18_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_18_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1403.98 s (27 µs/read; 2.21 M reads/minute). === Summary === Total reads processed: 51,713,176 Reads with adapters: 22,554,093 (43.6%) Reads written (passing filters): 51,713,176 (100.0%) Total basepairs processed: 5,464,527,560 bp Quality-trimmed: 8,896,205 bp (0.2%) Total written (filtered): 5,430,306,583 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22554093 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.8% C: 10.3% G: 6.4% T: 37.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20689709 12928294.0 0 20689709 2 1185957 3232073.5 0 1185957 3 458368 808018.4 0 458368 4 216584 202004.6 0 216584 5 2083 50501.1 0 2083 6 499 12625.3 0 499 7 145 3156.3 0 145 8 45 789.1 0 45 9 226 197.3 0 15 211 10 379 49.3 1 1 378 11 77 12.3 1 0 77 12 19 3.1 1 0 19 13 2 0.8 1 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_18_R2_val_2.fq.gz ============================================= 51713176 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_18_R1_val_1_trimmed.fq.gz and zr3644_18_R2_val_2_trimmed.fq.gz file_1: zr3644_18_R1_val_1_trimmed.fq.gz, file_2: zr3644_18_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_18_R1_val_1_trimmed.fq.gz and zr3644_18_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_18_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_18_R2_val_2_val_2.fq.gz Total number of sequences analysed: 51713176 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 28799 (0.06%) >>> Now running FastQC on the validated data zr3644_18_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_18_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_18_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_18_R1_val_1_val_1.fq.gz Analysis complete for zr3644_18_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_18_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_18_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_18_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_18_R2_val_2_val_2.fq.gz Analysis complete for zr3644_18_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_18_R1_val_1_trimmed.fq.gz and zr3644_18_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_19_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_19_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/Hawes/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 zr3644_19_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/Hawes/analyses/trimgalore/zr3644_19_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore/zr3644_19_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1337.65 s (27 µs/read; 2.21 M reads/minute). === Summary === Total reads processed: 49,363,404 Reads with adapters: 21,587,602 (43.7%) Reads written (passing filters): 49,363,404 (100.0%) Total basepairs processed: 5,228,373,046 bp Quality-trimmed: 6,488,759 bp (0.1%) Total written (filtered): 5,197,575,816 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21587602 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 10.4% G: 6.5% T: 37.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19724367 12340851.0 0 19724367 2 1217336 3085212.8 0 1217336 3 441387 771303.2 0 441387 4 201787 192825.8 0 201787 5 1348 48206.4 0 1348 6 457 12051.6 0 457 7 154 3012.9 0 154 8 32 753.2 0 32 9 203 188.3 0 11 192 10 415 47.1 1 5 410 11 101 11.8 1 0 101 12 10 2.9 1 0 10 13 1 0.7 1 0 1 18 1 0.7 1 0 1 22 2 0.7 1 0 2 24 1 0.7 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_19_R1_val_1.fq.gz ============================================= 49363404 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/Hawes/analyses/trimgalore-2/zr3644_19_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_19_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/Hawes/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 zr3644_19_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/Hawes/analyses/trimgalore/zr3644_19_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore/zr3644_19_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1355.33 s (27 µs/read; 2.19 M reads/minute). === Summary === Total reads processed: 49,363,404 Reads with adapters: 21,525,774 (43.6%) Reads written (passing filters): 49,363,404 (100.0%) Total basepairs processed: 5,226,810,807 bp Quality-trimmed: 9,035,389 bp (0.2%) Total written (filtered): 5,193,590,463 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 21525774 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.8% C: 10.2% G: 6.4% T: 37.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19733513 12340851.0 0 19733513 2 1141973 3085212.8 0 1141973 3 440982 771303.2 0 440982 4 205989 192825.8 0 205989 5 2042 48206.4 0 2042 6 446 12051.6 0 446 7 141 3012.9 0 141 8 31 753.2 0 31 9 203 188.3 0 18 185 10 360 47.1 1 2 358 11 83 11.8 1 0 83 12 10 2.9 1 0 10 13 1 0.7 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_19_R2_val_2.fq.gz ============================================= 49363404 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_19_R1_val_1_trimmed.fq.gz and zr3644_19_R2_val_2_trimmed.fq.gz file_1: zr3644_19_R1_val_1_trimmed.fq.gz, file_2: zr3644_19_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_19_R1_val_1_trimmed.fq.gz and zr3644_19_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_19_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_19_R2_val_2_val_2.fq.gz Total number of sequences analysed: 49363404 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 29484 (0.06%) >>> Now running FastQC on the validated data zr3644_19_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_19_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_19_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_19_R1_val_1_val_1.fq.gz Analysis complete for zr3644_19_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_19_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_19_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_19_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_19_R2_val_2_val_2.fq.gz Analysis complete for zr3644_19_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_19_R1_val_1_trimmed.fq.gz and zr3644_19_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_20_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_20_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/Hawes/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 zr3644_20_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/Hawes/analyses/trimgalore/zr3644_20_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_20_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1767.68 s (33 µs/read; 1.84 M reads/minute). === Summary === Total reads processed: 54,084,897 Reads with adapters: 23,814,058 (44.0%) Reads written (passing filters): 54,084,897 (100.0%) Total basepairs processed: 5,774,617,900 bp Quality-trimmed: 13,543,407 bp (0.2%) Total written (filtered): 5,734,279,099 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23814058 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 11.2% G: 6.6% T: 37.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21758968 13521224.2 0 21758968 2 1347678 3380306.1 0 1347678 3 498483 845076.5 0 498483 4 204292 211269.1 0 204292 5 2906 52817.3 0 2906 6 655 13204.3 0 655 7 197 3301.1 0 197 8 43 825.3 0 43 9 254 206.3 0 29 225 10 452 51.6 1 5 447 11 109 12.9 1 1 108 12 15 3.2 1 0 15 13 5 0.8 1 0 5 20 1 0.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_20_R1_val_1.fq.gz ============================================= 54084897 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/Hawes/analyses/trimgalore-2/zr3644_20_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_20_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/Hawes/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 zr3644_20_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/Hawes/analyses/trimgalore/zr3644_20_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_20_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1464.11 s (27 µs/read; 2.22 M reads/minute). === Summary === Total reads processed: 54,084,897 Reads with adapters: 23,535,860 (43.5%) Reads written (passing filters): 54,084,897 (100.0%) Total basepairs processed: 5,775,645,485 bp Quality-trimmed: 7,729,128 bp (0.1%) Total written (filtered): 5,741,438,443 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23535860 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 9.8% G: 6.5% T: 38.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21554107 13521224.2 0 21554107 2 1263041 3380306.1 0 1263041 3 485137 845076.5 0 485137 4 230530 211269.1 0 230530 5 1531 52817.3 0 1531 6 476 13204.3 0 476 7 154 3301.1 0 154 8 35 825.3 0 35 9 285 206.3 0 13 272 10 462 51.6 1 1 461 11 86 12.9 1 0 86 12 14 3.2 1 0 14 13 2 0.8 1 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_20_R2_val_2.fq.gz ============================================= 54084897 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_20_R1_val_1_trimmed.fq.gz and zr3644_20_R2_val_2_trimmed.fq.gz file_1: zr3644_20_R1_val_1_trimmed.fq.gz, file_2: zr3644_20_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_20_R1_val_1_trimmed.fq.gz and zr3644_20_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_20_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_20_R2_val_2_val_2.fq.gz Total number of sequences analysed: 54084897 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 25663 (0.05%) >>> Now running FastQC on the validated data zr3644_20_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_20_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_20_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_20_R1_val_1_val_1.fq.gz Analysis complete for zr3644_20_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_20_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_20_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_20_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_20_R2_val_2_val_2.fq.gz Analysis complete for zr3644_20_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_20_R1_val_1_trimmed.fq.gz and zr3644_20_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_21_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_21_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/Hawes/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 zr3644_21_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/Hawes/analyses/trimgalore/zr3644_21_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_21_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1452.77 s (28 µs/read; 2.11 M reads/minute). === Summary === Total reads processed: 51,112,555 Reads with adapters: 22,461,462 (43.9%) Reads written (passing filters): 51,112,555 (100.0%) Total basepairs processed: 5,444,180,217 bp Quality-trimmed: 8,179,226 bp (0.2%) Total written (filtered): 5,410,714,043 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22461462 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.4% G: 6.5% T: 37.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20526296 12778138.8 0 20526296 2 1264712 3194534.7 0 1264712 3 459041 798633.7 0 459041 4 207720 199658.4 0 207720 5 2173 49914.6 0 2173 6 562 12478.7 0 562 7 143 3119.7 0 143 8 37 779.9 0 37 9 250 195.0 0 18 232 10 431 48.7 1 5 426 11 74 12.2 1 0 74 12 16 3.0 1 0 16 13 1 0.8 1 0 1 16 1 0.8 1 0 1 17 2 0.8 1 0 2 20 1 0.8 1 0 1 21 2 0.8 1 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_21_R1_val_1.fq.gz ============================================= 51112555 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/Hawes/analyses/trimgalore-2/zr3644_21_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_21_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/Hawes/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 zr3644_21_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/Hawes/analyses/trimgalore/zr3644_21_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_21_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1399.67 s (27 µs/read; 2.19 M reads/minute). === Summary === Total reads processed: 51,112,555 Reads with adapters: 22,379,133 (43.8%) Reads written (passing filters): 51,112,555 (100.0%) Total basepairs processed: 5,444,089,562 bp Quality-trimmed: 8,820,277 bp (0.2%) Total written (filtered): 5,410,194,746 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22379133 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.0% C: 10.2% G: 6.3% T: 37.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20565028 12778138.8 0 20565028 2 1153680 3194534.7 0 1153680 3 446995 798633.7 0 446995 4 210217 199658.4 0 210217 5 1879 49914.6 0 1879 6 458 12478.7 0 458 7 132 3119.7 0 132 8 39 779.9 0 39 9 234 195.0 0 24 210 10 385 48.7 1 3 382 11 71 12.2 1 1 70 12 13 3.0 1 0 13 13 2 0.8 1 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_21_R2_val_2.fq.gz ============================================= 51112555 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_21_R1_val_1_trimmed.fq.gz and zr3644_21_R2_val_2_trimmed.fq.gz file_1: zr3644_21_R1_val_1_trimmed.fq.gz, file_2: zr3644_21_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_21_R1_val_1_trimmed.fq.gz and zr3644_21_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_21_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_21_R2_val_2_val_2.fq.gz Total number of sequences analysed: 51112555 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 27784 (0.05%) >>> Now running FastQC on the validated data zr3644_21_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_21_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_21_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_21_R1_val_1_val_1.fq.gz Analysis complete for zr3644_21_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_21_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_21_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_21_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_21_R2_val_2_val_2.fq.gz Analysis complete for zr3644_21_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_21_R1_val_1_trimmed.fq.gz and zr3644_21_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_22_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_22_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/Hawes/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 zr3644_22_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/Hawes/analyses/trimgalore/zr3644_22_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore/zr3644_22_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1280.27 s (27 µs/read; 2.24 M reads/minute). === Summary === Total reads processed: 47,725,182 Reads with adapters: 20,805,835 (43.6%) Reads written (passing filters): 47,725,182 (100.0%) Total basepairs processed: 5,065,667,631 bp Quality-trimmed: 6,033,168 bp (0.1%) Total written (filtered): 5,036,195,933 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20805835 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.4% G: 6.6% T: 37.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19005070 11931295.5 0 19005070 2 1174162 2982823.9 0 1174162 3 428230 745706.0 0 428230 4 195781 186426.5 0 195781 5 1281 46606.6 0 1281 6 437 11651.7 0 437 7 112 2912.9 0 112 8 35 728.2 0 35 9 211 182.1 0 15 196 10 404 45.5 1 4 400 11 89 11.4 1 1 88 12 16 2.8 1 0 16 13 3 0.7 1 0 3 16 1 0.7 1 0 1 18 1 0.7 1 0 1 24 2 0.7 1 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_22_R1_val_1.fq.gz ============================================= 47725182 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/Hawes/analyses/trimgalore-2/zr3644_22_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_22_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/Hawes/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 zr3644_22_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/Hawes/analyses/trimgalore/zr3644_22_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore/zr3644_22_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1304.96 s (27 µs/read; 2.19 M reads/minute). === Summary === Total reads processed: 47,725,182 Reads with adapters: 20,746,534 (43.5%) Reads written (passing filters): 47,725,182 (100.0%) Total basepairs processed: 5,064,153,931 bp Quality-trimmed: 8,600,269 bp (0.2%) Total written (filtered): 5,032,244,815 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20746534 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 10.3% G: 6.4% T: 37.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19018813 11931295.5 0 19018813 2 1102799 2982823.9 0 1102799 3 422330 745706.0 0 422330 4 199471 186426.5 0 199471 5 1874 46606.6 0 1874 6 427 11651.7 0 427 7 136 2912.9 0 136 8 34 728.2 0 34 9 193 182.1 0 12 181 10 376 45.5 1 2 374 11 65 11.4 1 0 65 12 14 2.8 1 0 14 13 2 0.7 1 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_22_R2_val_2.fq.gz ============================================= 47725182 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_22_R1_val_1_trimmed.fq.gz and zr3644_22_R2_val_2_trimmed.fq.gz file_1: zr3644_22_R1_val_1_trimmed.fq.gz, file_2: zr3644_22_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_22_R1_val_1_trimmed.fq.gz and zr3644_22_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_22_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_22_R2_val_2_val_2.fq.gz Total number of sequences analysed: 47725182 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 26554 (0.06%) >>> Now running FastQC on the validated data zr3644_22_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_22_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_22_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_22_R1_val_1_val_1.fq.gz Analysis complete for zr3644_22_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_22_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_22_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_22_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_22_R2_val_2_val_2.fq.gz Analysis complete for zr3644_22_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_22_R1_val_1_trimmed.fq.gz and zr3644_22_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_23_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_23_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/Hawes/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 zr3644_23_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/Hawes/analyses/trimgalore/zr3644_23_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore/zr3644_23_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1080.05 s (27 µs/read; 2.25 M reads/minute). === Summary === Total reads processed: 40,539,021 Reads with adapters: 17,674,203 (43.6%) Reads written (passing filters): 40,539,021 (100.0%) Total basepairs processed: 4,280,801,776 bp Quality-trimmed: 5,104,755 bp (0.1%) Total written (filtered): 4,255,781,741 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17674203 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.4% G: 6.6% T: 37.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16143667 10134755.2 0 16143667 2 996474 2533688.8 0 996474 3 363897 633422.2 0 363897 4 167893 158355.6 0 167893 5 1059 39588.9 0 1059 6 368 9897.2 0 368 7 134 2474.3 0 134 8 30 618.6 0 30 9 207 154.6 0 20 187 10 376 38.7 1 3 373 11 81 9.7 1 0 81 12 14 2.4 1 0 14 13 3 0.6 1 0 3 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_23_R1_val_1.fq.gz ============================================= 40539021 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/Hawes/analyses/trimgalore-2/zr3644_23_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_23_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/Hawes/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 zr3644_23_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/Hawes/analyses/trimgalore/zr3644_23_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore/zr3644_23_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1116.39 s (28 µs/read; 2.18 M reads/minute). === Summary === Total reads processed: 40,539,021 Reads with adapters: 17,635,972 (43.5%) Reads written (passing filters): 40,539,021 (100.0%) Total basepairs processed: 4,279,858,954 bp Quality-trimmed: 7,142,575 bp (0.2%) Total written (filtered): 4,252,914,909 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17635972 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.8% C: 10.3% G: 6.4% T: 37.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16178776 10134755.2 0 16178776 2 927146 2533688.8 0 927146 3 358259 633422.2 0 358259 4 169076 158355.6 0 169076 5 1577 39588.9 0 1577 6 361 9897.2 0 361 7 118 2474.3 0 118 8 22 618.6 0 22 9 196 154.6 0 12 184 10 356 38.7 1 2 354 11 76 9.7 1 0 76 12 9 2.4 1 0 9 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_23_R2_val_2.fq.gz ============================================= 40539021 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_23_R1_val_1_trimmed.fq.gz and zr3644_23_R2_val_2_trimmed.fq.gz file_1: zr3644_23_R1_val_1_trimmed.fq.gz, file_2: zr3644_23_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_23_R1_val_1_trimmed.fq.gz and zr3644_23_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_23_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_23_R2_val_2_val_2.fq.gz Total number of sequences analysed: 40539021 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 23114 (0.06%) >>> Now running FastQC on the validated data zr3644_23_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_23_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_23_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_23_R1_val_1_val_1.fq.gz Analysis complete for zr3644_23_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_23_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_23_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_23_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_23_R2_val_2_val_2.fq.gz Analysis complete for zr3644_23_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_23_R1_val_1_trimmed.fq.gz and zr3644_23_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_24_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_24_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/Hawes/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 zr3644_24_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/Hawes/analyses/trimgalore/zr3644_24_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_24_R1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1461.67 s (28 µs/read; 2.17 M reads/minute). === Summary === Total reads processed: 52,922,544 Reads with adapters: 23,174,909 (43.8%) Reads written (passing filters): 52,922,544 (100.0%) Total basepairs processed: 5,625,540,317 bp Quality-trimmed: 7,113,215 bp (0.1%) Total written (filtered): 5,592,330,989 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23174909 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 10.4% G: 6.5% T: 37.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21176762 13230636.0 0 21176762 2 1303077 3307659.0 0 1303077 3 474958 826914.8 0 474958 4 217209 206728.7 0 217209 5 1352 51682.2 0 1352 6 526 12920.5 0 526 7 159 3230.1 0 159 8 46 807.5 0 46 9 242 201.9 0 22 220 10 465 50.5 1 8 457 11 98 12.6 1 0 98 12 13 3.2 1 0 13 13 1 0.8 1 0 1 15 1 0.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_24_R1_val_1.fq.gz ============================================= 52922544 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/Hawes/analyses/trimgalore-2/zr3644_24_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_24_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/Hawes/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 zr3644_24_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/Hawes/analyses/trimgalore/zr3644_24_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore/zr3644_24_R2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1460.85 s (28 µs/read; 2.17 M reads/minute). === Summary === Total reads processed: 52,922,544 Reads with adapters: 23,136,470 (43.7%) Reads written (passing filters): 52,922,544 (100.0%) Total basepairs processed: 5,624,990,440 bp Quality-trimmed: 8,998,238 bp (0.2%) Total written (filtered): 5,590,031,647 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23136470 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.9% C: 10.2% G: 6.4% T: 37.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21235591 13230636.0 0 21235591 2 1208767 3307659.0 0 1208767 3 469015 826914.8 0 469015 4 219623 206728.7 0 219623 5 2038 51682.2 0 2038 6 484 12920.5 0 484 7 178 3230.1 0 178 8 30 807.5 0 30 9 237 201.9 0 22 215 10 415 50.5 1 1 414 11 75 12.6 1 1 74 12 16 3.2 1 0 16 13 1 0.8 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore/zr3644_24_R2_val_2.fq.gz ============================================= 52922544 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_24_R1_val_1_trimmed.fq.gz and zr3644_24_R2_val_2_trimmed.fq.gz file_1: zr3644_24_R1_val_1_trimmed.fq.gz, file_2: zr3644_24_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_24_R1_val_1_trimmed.fq.gz and zr3644_24_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_24_R1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_24_R2_val_2_val_2.fq.gz Total number of sequences analysed: 52922544 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 27654 (0.05%) >>> Now running FastQC on the validated data zr3644_24_R1_val_1_val_1.fq.gz<<< Started analysis of zr3644_24_R1_val_1_val_1.fq.gz Approx 5% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 10% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 15% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 20% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 25% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 30% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 35% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 40% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 45% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 50% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 55% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 60% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 65% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 70% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 75% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 80% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 85% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 90% complete for zr3644_24_R1_val_1_val_1.fq.gz Approx 95% complete for zr3644_24_R1_val_1_val_1.fq.gz Analysis complete for zr3644_24_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_24_R2_val_2_val_2.fq.gz<<< Started analysis of zr3644_24_R2_val_2_val_2.fq.gz Approx 5% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 10% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 15% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 20% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 25% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 30% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 35% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 40% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 45% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 50% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 55% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 60% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 65% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 70% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 75% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 80% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 85% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 90% complete for zr3644_24_R2_val_2_val_2.fq.gz Approx 95% complete for zr3644_24_R2_val_2_val_2.fq.gz Analysis complete for zr3644_24_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_24_R1_val_1_trimmed.fq.gz and zr3644_24_R2_val_2_trimmed.fq.gz ==================================================================================================== [INFO ] multiqc : This is MultiQC v1.8 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching : /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2 [INFO ] cutadapt : Found 48 reports [INFO ] fastqc : Found 48 reports [INFO ] multiqc : Compressing plot data [INFO ] multiqc : Report : multiqc_report.html [INFO ] multiqc : Data : multiqc_data [INFO ] multiqc : MultiQC 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/Hawes/analyses/trimgalore-2/poly-G/ Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_1_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_1_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_1_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1374.14 s (26 µs/read; 2.27 M reads/minute). === Summary === Total reads processed: 51,916,287 Reads with adapters: 5,525,580 (10.6%) Reads written (passing filters): 51,916,287 (100.0%) Total basepairs processed: 5,441,948,956 bp Quality-trimmed: 1,820,838 bp (0.0%) Total written (filtered): 5,364,161,939 bp (98.6%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5525580 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: 24.1% C: 4.3% G: 0.0% T: 71.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3344083 12979071.8 0 3344083 2 938405 3244767.9 0 938405 3 200770 811192.0 0 200770 4 56454 202798.0 0 56454 5 16140 50699.5 0 16140 6 4880 12674.9 0 4880 7 2090 3168.7 0 2090 8 1412 792.2 0 1412 9 1244 198.0 0 1244 10 2764 49.5 1 1216 1548 11 2405 12.4 1 1134 1271 12 2126 3.1 1 1047 1079 13 1965 0.8 1 993 972 14 1668 0.2 1 809 859 15 1464 0.0 1 724 740 16 1262 0.0 1 613 649 17 1032 0.0 1 484 548 18 816 0.0 1 487 329 19 757 0.0 1 458 299 20 1190 0.0 2 472 294 424 21 1075 0.0 2 459 257 359 22 981 0.0 2 413 252 316 23 950 0.0 2 424 211 315 24 890 0.0 2 380 234 276 25 853 0.0 2 377 236 240 26 706 0.0 2 318 195 193 27 679 0.0 2 322 188 169 28 615 0.0 2 300 196 119 29 564 0.0 2 274 174 116 30 805 0.0 3 272 191 136 206 31 767 0.0 3 252 190 149 176 32 688 0.0 3 238 157 113 180 33 652 0.0 3 246 141 106 159 34 639 0.0 3 222 146 118 153 35 593 0.0 3 214 136 112 131 36 608 0.0 3 230 138 97 143 37 598 0.0 3 242 121 100 135 38 525 0.0 3 210 131 93 91 39 534 0.0 3 229 110 103 92 40 628 0.0 4 196 131 91 68 142 41 593 0.0 4 208 112 112 51 110 42 683 0.0 4 242 134 88 86 133 43 615 0.0 4 182 120 101 82 130 44 606 0.0 4 193 123 92 78 120 45 547 0.0 4 180 95 83 91 98 46 581 0.0 4 188 129 74 85 105 47 519 0.0 4 188 113 74 61 83 48 616 0.0 4 220 133 111 84 68 49 1366 0.0 4 542 307 234 161 122 50 1526 0.0 5 699 290 195 132 104 106 51 1226 0.0 5 652 211 145 98 78 42 52 1114 0.0 5 630 191 110 77 48 58 53 981 0.0 5 579 175 98 65 38 26 54 1063 0.0 5 658 184 94 60 42 25 55 1172 0.0 5 746 202 101 60 37 26 56 1267 0.0 5 879 199 93 49 31 16 57 1085 0.0 5 774 151 76 45 29 10 58 1261 0.0 5 956 157 65 33 24 26 59 1637 0.0 5 1306 174 69 33 29 26 60 1084 0.0 5 756 180 77 36 24 11 61 1101 0.0 5 837 138 60 32 22 12 62 1320 0.0 5 1018 171 65 40 20 6 63 1479 0.0 5 1222 139 55 30 20 13 64 2353 0.0 5 2085 151 64 30 14 9 65 1359 0.0 5 1092 164 58 22 16 7 66 1636 0.0 5 1367 153 56 33 21 6 67 1846 0.0 5 1558 186 56 26 13 7 68 2452 0.0 5 2143 196 70 23 12 8 69 3238 0.0 5 2882 258 62 22 10 4 70 5512 0.0 5 5153 219 89 24 15 12 71 10803 0.0 5 10383 301 75 26 14 4 72 36337 0.0 5 35773 437 71 32 15 9 73 99386 0.0 5 98658 586 79 36 15 12 74 453790 0.0 5 452230 1346 170 22 10 12 75 28799 0.0 5 28461 258 45 16 6 13 76 26299 0.0 5 26071 166 34 15 7 6 77 100319 0.0 5 99951 291 43 16 10 8 78 12885 0.0 5 12739 88 35 8 12 3 79 58910 0.0 5 58698 161 24 13 10 4 80 16620 0.0 5 16482 87 33 9 5 4 81 9264 0.0 5 9162 53 26 8 12 3 82 20012 0.0 5 19889 89 16 8 6 4 83 3412 0.0 5 3286 78 23 9 9 7 84 6088 0.0 5 5962 96 13 7 7 3 85 1162 0.0 5 1093 34 13 11 8 3 86 205 0.0 5 141 21 24 8 7 4 87 193 0.0 5 118 27 20 10 8 10 88 168 0.0 5 115 30 7 6 5 5 89 151 0.0 5 96 26 15 3 5 6 90 146 0.0 5 92 22 11 9 8 4 91 156 0.0 5 91 27 19 8 6 5 92 131 0.0 5 91 20 7 5 6 2 93 135 0.0 5 82 23 11 12 5 2 94 107 0.0 5 75 13 9 3 2 5 95 104 0.0 5 63 16 10 7 5 3 96 103 0.0 5 58 20 13 4 4 4 97 102 0.0 5 58 15 16 4 3 6 98 80 0.0 5 48 17 4 5 5 1 99 61 0.0 5 37 6 6 7 3 2 100 66 0.0 5 46 5 6 4 3 2 101 62 0.0 5 39 8 5 4 5 1 102 50 0.0 5 30 6 6 5 1 2 103 31 0.0 5 20 4 1 2 2 2 104 38 0.0 5 23 4 4 2 3 2 105 28 0.0 5 19 0 4 4 1 106 27 0.0 5 20 3 2 0 2 107 20 0.0 5 15 2 0 2 0 1 108 18 0.0 5 11 2 1 1 2 1 109 22 0.0 5 9 3 3 2 2 3 110 11 0.0 5 8 1 0 0 1 1 111 13 0.0 5 9 2 0 0 1 1 112 11 0.0 5 8 1 1 1 113 7 0.0 5 4 2 0 0 0 1 114 13 0.0 5 9 0 2 1 0 1 115 120 0.0 5 116 2 1 0 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_1_R1_val_1_val_1.fq.gz ============================================= 51916287 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_1_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_1_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_1_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1473.29 s (28 µs/read; 2.11 M reads/minute). === Summary === Total reads processed: 51,916,287 Reads with adapters: 5,160,649 (9.9%) Reads written (passing filters): 51,916,287 (100.0%) Total basepairs processed: 5,436,783,419 bp Quality-trimmed: 3,184,149 bp (0.1%) Total written (filtered): 5,320,849,423 bp (97.9%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5160649 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: 13.4% C: 5.1% G: 0.0% T: 81.5% 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 3094599 12979071.8 0 3094599 2 831227 3244767.9 0 831227 3 185194 811192.0 0 185194 4 52681 202798.0 0 52681 5 15524 50699.5 0 15524 6 4454 12674.9 0 4454 7 1731 3168.7 0 1731 8 886 792.2 0 886 9 743 198.0 0 743 10 2784 49.5 1 640 2144 11 2344 12.4 1 622 1722 12 1895 3.1 1 544 1351 13 1637 0.8 1 483 1154 14 1377 0.2 1 399 978 15 1242 0.0 1 390 852 16 1059 0.0 1 356 703 17 747 0.0 1 283 464 18 567 0.0 1 245 322 19 502 0.0 1 239 263 20 1377 0.0 2 341 258 778 21 1277 0.0 2 328 277 672 22 1139 0.0 2 294 220 625 23 999 0.0 2 279 200 520 24 919 0.0 2 262 172 485 25 820 0.0 2 242 186 392 26 697 0.0 2 231 164 302 27 665 0.0 2 254 142 269 28 515 0.0 2 216 145 154 29 410 0.0 2 179 95 136 30 905 0.0 3 200 135 148 422 31 813 0.0 3 190 118 123 382 32 802 0.0 3 200 104 132 366 33 705 0.0 3 159 98 113 335 34 715 0.0 3 186 104 108 317 35 643 0.0 3 160 118 111 254 36 626 0.0 3 173 100 103 250 37 539 0.0 3 167 103 94 175 38 489 0.0 3 169 107 93 120 39 415 0.0 3 154 76 80 105 40 720 0.0 4 150 86 79 115 290 41 741 0.0 4 177 104 69 93 298 42 657 0.0 4 129 75 80 107 266 43 638 0.0 4 154 79 70 100 235 44 610 0.0 4 129 81 75 98 227 45 613 0.0 4 141 95 92 83 202 46 580 0.0 4 164 79 87 89 161 47 533 0.0 4 171 101 72 58 131 48 564 0.0 4 174 105 101 97 87 49 1604 0.0 4 481 328 262 285 248 50 1783 0.0 5 453 317 306 238 230 239 51 1292 0.0 5 395 239 194 180 150 134 52 1261 0.0 5 430 241 197 146 120 127 53 1132 0.0 5 434 205 172 129 116 76 54 1008 0.0 5 407 196 158 96 83 68 55 914 0.0 5 362 187 125 101 73 66 56 952 0.0 5 444 186 112 94 66 50 57 886 0.0 5 426 158 124 73 56 49 58 752 0.0 5 320 172 100 67 51 42 59 683 0.0 5 329 145 73 57 39 40 60 715 0.0 5 361 151 71 67 41 24 61 649 0.0 5 351 112 81 40 31 34 62 643 0.0 5 335 123 65 47 48 25 63 735 0.0 5 427 129 69 39 38 33 64 698 0.0 5 362 132 83 47 44 30 65 748 0.0 5 445 135 80 35 34 19 66 641 0.0 5 398 118 55 27 27 16 67 662 0.0 5 425 115 47 31 21 23 68 697 0.0 5 466 113 38 32 27 21 69 827 0.0 5 600 122 38 34 17 16 70 785 0.0 5 574 83 49 39 25 15 71 570 0.0 5 400 81 32 25 17 15 72 607 0.0 5 412 86 39 24 25 21 73 599 0.0 5 431 74 43 23 15 13 74 647 0.0 5 456 77 48 34 18 14 75 852 0.0 5 647 95 50 20 19 21 76 627 0.0 5 458 89 38 18 16 8 77 633 0.0 5 495 70 23 13 19 13 78 572 0.0 5 426 70 25 23 19 9 79 671 0.0 5 528 54 34 20 24 11 80 559 0.0 5 416 70 30 24 5 14 81 539 0.0 5 414 55 22 20 16 12 82 478 0.0 5 349 59 26 14 15 15 83 453 0.0 5 351 43 28 11 13 7 84 508 0.0 5 392 49 22 24 9 12 85 503 0.0 5 380 56 21 16 17 13 86 512 0.0 5 413 41 24 13 15 6 87 407 0.0 5 312 42 17 17 10 9 88 550 0.0 5 455 43 20 9 10 13 89 503 0.0 5 402 46 20 17 13 5 90 469 0.0 5 356 51 27 18 6 11 91 395 0.0 5 300 43 16 16 11 9 92 446 0.0 5 366 42 13 11 8 6 93 360 0.0 5 288 39 15 5 9 4 94 346 0.0 5 277 39 14 6 6 4 95 461 0.0 5 374 39 17 14 8 9 96 429 0.0 5 327 54 18 13 7 10 97 362 0.0 5 275 38 23 12 6 8 98 346 0.0 5 269 31 14 10 16 6 99 429 0.0 5 359 29 20 8 5 8 100 312 0.0 5 225 39 15 15 12 6 101 528 0.0 5 448 39 16 10 9 6 102 508 0.0 5 418 49 17 7 6 11 103 446 0.0 5 381 28 16 6 8 7 104 343 0.0 5 272 31 19 8 6 7 105 513 0.0 5 420 49 12 11 13 8 106 396 0.0 5 319 40 12 11 7 7 107 425 0.0 5 353 31 15 8 4 14 108 404 0.0 5 327 43 8 14 8 4 109 596 0.0 5 441 70 54 13 12 6 110 622 0.0 5 506 63 21 11 11 10 111 445 0.0 5 339 37 27 17 11 14 112 1050 0.0 5 878 77 34 24 13 24 113 1232 0.0 5 1018 108 48 17 22 19 114 4675 0.0 5 4303 204 72 36 36 24 115 890935 0.0 5 889535 1077 177 60 48 38 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/Hawes/analyses/trimgalore-2/zr3644_1_R2_val_2_val_2.fq.gz ============================================= 51916287 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_1_R1_val_1_val_1_trimmed.fq.gz and zr3644_1_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_1_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_1_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_1_R1_val_1_val_1_trimmed.fq.gz and zr3644_1_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_1_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_1_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 51916287 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 922836 (1.78%) >>> Now running FastQC on the validated data zr3644_1_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_1_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_1_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_1_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_1_R1_val_1_val_1_trimmed.fq.gz and zr3644_1_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_2_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_2_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_2_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1503.70 s (27 µs/read; 2.22 M reads/minute). === Summary === Total reads processed: 55,636,387 Reads with adapters: 5,493,428 (9.9%) Reads written (passing filters): 55,636,387 (100.0%) Total basepairs processed: 5,939,768,268 bp Quality-trimmed: 2,052,719 bp (0.0%) Total written (filtered): 5,884,926,750 bp (99.1%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5493428 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: 20.5% C: 4.4% G: 0.0% T: 75.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3577011 13909096.8 0 3577011 2 977192 3477274.2 0 977192 3 207866 869318.5 0 207866 4 57278 217329.6 0 57278 5 16597 54332.4 0 16597 6 5064 13583.1 0 5064 7 2198 3395.8 0 2198 8 1504 848.9 0 1504 9 1363 212.2 0 1363 10 3023 53.1 1 1376 1647 11 2630 13.3 1 1241 1389 12 2226 3.3 1 1140 1086 13 2114 0.8 1 1079 1035 14 1897 0.2 1 952 945 15 1602 0.1 1 826 776 16 1374 0.0 1 735 639 17 1107 0.0 1 576 531 18 938 0.0 1 546 392 19 873 0.0 1 531 342 20 1263 0.0 2 479 313 471 21 1178 0.0 2 500 281 397 22 1171 0.0 2 512 295 364 23 1050 0.0 2 436 266 348 24 968 0.0 2 440 251 277 25 883 0.0 2 410 210 263 26 781 0.0 2 351 230 200 27 732 0.0 2 361 172 199 28 652 0.0 2 315 198 139 29 669 0.0 2 327 190 152 30 841 0.0 3 276 207 157 201 31 826 0.0 3 318 166 143 199 32 788 0.0 3 343 153 119 173 33 773 0.0 3 305 181 122 165 34 722 0.0 3 292 146 118 166 35 717 0.0 3 269 167 132 149 36 676 0.0 3 264 173 90 149 37 666 0.0 3 273 143 124 126 38 620 0.0 3 258 159 112 91 39 556 0.0 3 221 129 110 96 40 719 0.0 4 259 148 95 97 120 41 603 0.0 4 187 119 101 78 118 42 693 0.0 4 211 148 84 99 151 43 643 0.0 4 211 147 92 69 124 44 588 0.0 4 184 130 95 80 99 45 586 0.0 4 199 107 93 87 100 46 621 0.0 4 195 153 90 91 92 47 617 0.0 4 230 134 84 67 102 48 691 0.0 4 272 149 112 73 85 49 1286 0.0 4 517 314 197 134 124 50 1406 0.0 5 637 250 190 135 111 83 51 1035 0.0 5 583 185 106 71 56 34 52 1046 0.0 5 604 188 102 72 45 35 53 861 0.0 5 513 168 71 51 40 18 54 882 0.0 5 566 143 78 47 29 19 55 981 0.0 5 632 150 104 39 34 22 56 1050 0.0 5 708 173 76 48 21 24 57 1002 0.0 5 683 157 77 40 32 13 58 959 0.0 5 702 125 57 41 22 12 59 1091 0.0 5 855 125 54 20 22 15 60 841 0.0 5 586 135 59 34 17 10 61 879 0.0 5 652 136 46 24 14 7 62 1070 0.0 5 778 154 71 30 21 16 63 1099 0.0 5 896 115 39 18 14 17 64 1447 0.0 5 1247 110 42 20 16 12 65 952 0.0 5 748 117 48 26 10 3 66 1204 0.0 5 977 122 53 31 14 7 67 1277 0.0 5 1040 151 43 27 10 6 68 1536 0.0 5 1309 129 55 22 16 5 69 2053 0.0 5 1792 158 51 25 16 11 70 3409 0.0 5 3115 188 51 29 14 12 71 6713 0.0 5 6419 202 60 21 9 2 72 26540 0.0 5 26146 305 56 23 7 3 73 49904 0.0 5 49400 380 72 36 10 6 74 307788 0.0 5 306711 898 132 25 10 12 75 24973 0.0 5 24748 164 36 13 5 7 76 13669 0.0 5 13482 125 30 16 6 10 77 61628 0.0 5 61357 204 34 15 9 9 78 8039 0.0 5 7894 85 26 14 14 6 79 37020 0.0 5 36839 123 19 21 10 8 80 10133 0.0 5 10009 76 24 9 7 8 81 5413 0.0 5 5301 65 23 11 8 5 82 12783 0.0 5 12668 71 18 12 11 3 83 3282 0.0 5 3164 70 27 15 2 4 84 7678 0.0 5 7556 85 18 6 6 7 85 1799 0.0 5 1711 46 13 15 8 6 86 247 0.0 5 175 36 15 10 7 4 87 194 0.0 5 143 28 11 5 5 2 88 167 0.0 5 108 30 12 8 2 7 89 167 0.0 5 117 26 8 3 5 8 90 177 0.0 5 123 26 11 8 8 1 91 143 0.0 5 96 22 10 7 5 3 92 153 0.0 5 105 22 9 9 1 7 93 138 0.0 5 89 19 10 11 4 5 94 103 0.0 5 62 21 10 3 5 2 95 117 0.0 5 74 14 12 9 4 4 96 117 0.0 5 73 18 15 5 4 2 97 100 0.0 5 66 14 6 6 2 6 98 87 0.0 5 59 12 6 6 2 2 99 61 0.0 5 43 5 5 1 4 3 100 79 0.0 5 57 7 7 4 2 2 101 88 0.0 5 57 10 5 8 2 6 102 51 0.0 5 38 5 5 1 1 1 103 40 0.0 5 27 6 4 1 1 1 104 34 0.0 5 19 7 1 3 4 105 39 0.0 5 18 7 4 7 1 2 106 35 0.0 5 23 3 2 2 4 1 107 26 0.0 5 18 2 1 1 2 2 108 22 0.0 5 17 2 2 0 0 1 109 18 0.0 5 8 1 1 3 3 2 110 9 0.0 5 5 2 2 111 12 0.0 5 10 1 0 0 1 112 14 0.0 5 10 2 1 0 1 113 5 0.0 5 2 1 0 1 0 1 114 6 0.0 5 5 0 0 0 1 115 101 0.0 5 98 2 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_2_R1_val_1_val_1.fq.gz ============================================= 55636387 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_2_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_2_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_2_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1548.23 s (28 µs/read; 2.16 M reads/minute). === Summary === Total reads processed: 55,636,387 Reads with adapters: 5,105,352 (9.2%) Reads written (passing filters): 55,636,387 (100.0%) Total basepairs processed: 5,933,849,217 bp Quality-trimmed: 3,009,323 bp (0.1%) Total written (filtered): 5,853,819,703 bp (98.7%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5105352 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: 13.3% C: 5.0% G: 0.0% T: 81.6% 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 3303790 13909096.8 0 3303790 2 873751 3477274.2 0 873751 3 190959 869318.5 0 190959 4 53102 217329.6 0 53102 5 15368 54332.4 0 15368 6 4429 13583.1 0 4429 7 1706 3395.8 0 1706 8 962 848.9 0 962 9 800 212.2 0 800 10 2884 53.1 1 801 2083 11 2428 13.3 1 683 1745 12 1921 3.3 1 606 1315 13 1669 0.8 1 535 1134 14 1463 0.2 1 443 1020 15 1296 0.1 1 446 850 16 1120 0.0 1 399 721 17 841 0.0 1 325 516 18 619 0.0 1 317 302 19 535 0.0 1 253 282 20 1319 0.0 2 378 286 655 21 1288 0.0 2 369 279 640 22 1157 0.0 2 361 247 549 23 1027 0.0 2 305 228 494 24 951 0.0 2 285 225 441 25 921 0.0 2 306 204 411 26 807 0.0 2 289 187 331 27 671 0.0 2 269 145 257 28 596 0.0 2 270 138 188 29 542 0.0 2 245 125 172 30 887 0.0 3 240 111 154 382 31 875 0.0 3 239 155 145 336 32 845 0.0 3 213 147 134 351 33 764 0.0 3 225 97 121 321 34 713 0.0 3 191 108 117 297 35 668 0.0 3 181 108 122 257 36 629 0.0 3 201 115 108 205 37 572 0.0 3 214 88 107 163 38 581 0.0 3 214 110 119 138 39 509 0.0 3 213 83 92 121 40 769 0.0 4 187 104 94 109 275 41 765 0.0 4 196 101 77 103 288 42 743 0.0 4 180 99 86 110 268 43 704 0.0 4 178 81 93 117 235 44 665 0.0 4 172 96 84 98 215 45 671 0.0 4 150 121 81 108 211 46 606 0.0 4 166 80 79 103 178 47 581 0.0 4 195 117 54 67 148 48 651 0.0 4 199 120 145 84 103 49 1650 0.0 4 503 325 297 256 269 50 1692 0.0 5 419 308 273 263 221 208 51 1341 0.0 5 439 264 209 173 140 116 52 1248 0.0 5 424 249 176 158 126 115 53 1136 0.0 5 428 236 150 124 110 88 54 1041 0.0 5 442 178 142 111 79 89 55 870 0.0 5 382 185 117 84 67 35 56 933 0.0 5 488 159 100 84 62 40 57 809 0.0 5 403 155 75 81 61 34 58 764 0.0 5 387 135 96 53 48 45 59 741 0.0 5 416 144 71 46 33 31 60 742 0.0 5 417 121 76 51 42 35 61 669 0.0 5 364 124 74 53 29 25 62 628 0.0 5 366 108 63 40 30 21 63 623 0.0 5 363 102 60 41 28 29 64 713 0.0 5 414 134 65 52 27 21 65 720 0.0 5 472 111 55 33 31 18 66 654 0.0 5 408 112 50 29 27 28 67 687 0.0 5 469 97 46 42 19 14 68 693 0.0 5 447 103 63 39 19 22 69 688 0.0 5 496 93 46 24 15 14 70 702 0.0 5 510 86 44 30 19 13 71 560 0.0 5 394 85 31 25 12 13 72 515 0.0 5 371 66 33 25 13 7 73 555 0.0 5 409 66 26 31 15 8 74 519 0.0 5 393 59 24 15 21 7 75 588 0.0 5 461 64 26 12 13 12 76 537 0.0 5 404 63 27 13 21 9 77 527 0.0 5 421 59 25 8 7 7 78 452 0.0 5 338 47 28 20 11 8 79 493 0.0 5 399 56 20 8 5 5 80 422 0.0 5 326 62 13 7 6 8 81 431 0.0 5 313 47 25 28 10 8 82 384 0.0 5 302 46 16 10 6 4 83 397 0.0 5 310 45 18 11 6 7 84 387 0.0 5 310 31 19 11 7 9 85 355 0.0 5 273 43 19 7 8 5 86 390 0.0 5 315 34 16 11 10 4 87 315 0.0 5 243 31 20 7 6 8 88 386 0.0 5 319 38 11 5 7 6 89 323 0.0 5 245 36 20 11 8 3 90 317 0.0 5 258 24 12 8 6 9 91 290 0.0 5 233 26 16 6 5 4 92 337 0.0 5 273 28 15 16 4 1 93 276 0.0 5 217 32 6 11 6 4 94 239 0.0 5 196 19 7 8 6 3 95 324 0.0 5 255 38 14 6 8 3 96 339 0.0 5 254 41 18 10 6 10 97 302 0.0 5 243 33 13 6 2 5 98 222 0.0 5 187 10 9 6 4 6 99 310 0.0 5 261 20 10 11 3 5 100 198 0.0 5 166 12 9 3 6 2 101 349 0.0 5 310 15 6 8 6 4 102 322 0.0 5 266 31 11 6 5 3 103 283 0.0 5 239 19 7 6 9 3 104 227 0.0 5 178 21 10 6 7 5 105 306 0.0 5 258 23 5 7 3 10 106 242 0.0 5 197 16 6 6 7 10 107 287 0.0 5 222 31 14 14 3 3 108 260 0.0 5 207 17 12 9 9 6 109 419 0.0 5 316 31 48 8 9 7 110 408 0.0 5 325 39 20 8 9 7 111 382 0.0 5 309 23 10 11 17 12 112 823 0.0 5 704 39 23 18 21 18 113 967 0.0 5 832 60 15 20 23 17 114 3145 0.0 5 2913 106 46 29 30 21 115 583378 0.0 5 582633 569 89 49 20 18 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/Hawes/analyses/trimgalore-2/zr3644_2_R2_val_2_val_2.fq.gz ============================================= 55636387 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_2_R1_val_1_val_1_trimmed.fq.gz and zr3644_2_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_2_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_2_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_2_R1_val_1_val_1_trimmed.fq.gz and zr3644_2_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_2_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_2_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 55636387 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 610473 (1.10%) >>> Now running FastQC on the validated data zr3644_2_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_2_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_2_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_2_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_2_R1_val_1_val_1_trimmed.fq.gz and zr3644_2_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_3_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_3_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 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/Hawes/analyses/trimgalore-2/zr3644_3_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1068.54 s (27 µs/read; 2.21 M reads/minute). === Summary === Total reads processed: 39,424,942 Reads with adapters: 3,969,102 (10.1%) Reads written (passing filters): 39,424,942 (100.0%) Total basepairs processed: 4,172,882,554 bp Quality-trimmed: 1,505,900 bp (0.0%) Total written (filtered): 4,127,815,733 bp (98.9%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 3969102 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: 21.3% C: 4.6% G: 0.0% T: 74.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2524910 9856235.5 0 2524910 2 692538 2464058.9 0 692538 3 149039 616014.7 0 149039 4 41295 154003.7 0 41295 5 12096 38500.9 0 12096 6 3598 9625.2 0 3598 7 1633 2406.3 0 1633 8 1114 601.6 0 1114 9 1064 150.4 0 1064 10 2233 37.6 1 983 1250 11 1936 9.4 1 920 1016 12 1764 2.3 1 909 855 13 1543 0.6 1 769 774 14 1339 0.1 1 695 644 15 1158 0.0 1 590 568 16 1056 0.0 1 547 509 17 821 0.0 1 412 409 18 698 0.0 1 420 278 19 689 0.0 1 413 276 20 976 0.0 2 388 239 349 21 920 0.0 2 376 230 314 22 856 0.0 2 369 214 273 23 861 0.0 2 351 226 284 24 753 0.0 2 337 220 196 25 717 0.0 2 304 200 213 26 627 0.0 2 287 175 165 27 564 0.0 2 250 144 170 28 529 0.0 2 271 153 105 29 429 0.0 2 208 125 96 30 703 0.0 3 244 145 122 192 31 665 0.0 3 265 118 107 175 32 601 0.0 3 214 134 90 163 33 632 0.0 3 239 141 112 140 34 588 0.0 3 205 130 99 154 35 558 0.0 3 206 140 91 121 36 493 0.0 3 200 105 77 111 37 495 0.0 3 178 137 71 109 38 485 0.0 3 195 117 83 90 39 475 0.0 3 185 115 96 79 40 514 0.0 4 149 115 78 71 101 41 576 0.0 4 204 101 103 74 94 42 545 0.0 4 177 116 80 71 101 43 509 0.0 4 160 111 84 58 96 44 460 0.0 4 134 104 71 61 90 45 468 0.0 4 157 88 69 71 83 46 493 0.0 4 142 99 96 65 91 47 453 0.0 4 168 110 54 56 65 48 524 0.0 4 188 122 80 69 65 49 1075 0.0 4 426 251 159 125 114 50 1086 0.0 5 447 221 145 114 92 67 51 863 0.0 5 476 153 82 62 56 34 52 746 0.0 5 432 121 83 47 35 28 53 689 0.0 5 398 126 62 40 42 21 54 723 0.0 5 460 103 71 42 27 20 55 826 0.0 5 561 119 64 38 30 14 56 849 0.0 5 604 115 59 36 22 13 57 771 0.0 5 542 126 46 33 14 10 58 781 0.0 5 589 113 35 20 14 10 59 886 0.0 5 690 107 47 14 17 11 60 738 0.0 5 518 124 48 25 16 7 61 763 0.0 5 561 120 41 21 13 7 62 854 0.0 5 650 110 41 25 18 10 63 913 0.0 5 738 104 33 16 12 10 64 1212 0.0 5 1024 111 34 23 16 4 65 854 0.0 5 681 99 36 24 10 4 66 1021 0.0 5 826 117 43 17 10 8 67 1177 0.0 5 965 113 53 32 6 8 68 1433 0.0 5 1244 123 32 19 11 4 69 1957 0.0 5 1742 150 39 15 6 5 70 3313 0.0 5 3105 119 44 22 12 11 71 7097 0.0 5 6848 179 38 20 8 4 72 24252 0.0 5 23909 268 47 16 6 6 73 54768 0.0 5 54352 341 46 16 7 6 74 237740 0.0 5 236969 657 81 17 11 5 75 20158 0.0 5 19973 121 35 20 6 3 76 14627 0.0 5 14478 104 22 8 10 5 77 45849 0.0 5 45652 147 28 12 3 7 78 8204 0.0 5 8092 74 20 9 7 2 79 27712 0.0 5 27543 119 20 14 13 3 80 8046 0.0 5 7947 54 22 10 8 5 81 5759 0.0 5 5675 55 17 6 5 1 82 10351 0.0 5 10267 58 10 6 8 2 83 6208 0.0 5 6115 51 21 12 4 5 84 12035 0.0 5 11925 77 18 5 5 5 85 2281 0.0 5 2207 45 17 5 4 3 86 339 0.0 5 272 29 23 4 6 5 87 162 0.0 5 118 19 8 10 5 2 88 178 0.0 5 126 27 9 8 3 5 89 139 0.0 5 94 17 12 11 5 90 180 0.0 5 125 22 12 8 10 3 91 132 0.0 5 91 16 9 5 7 4 92 115 0.0 5 81 18 5 7 2 2 93 143 0.0 5 102 19 11 4 3 4 94 107 0.0 5 70 22 6 4 3 2 95 84 0.0 5 62 10 6 1 3 2 96 103 0.0 5 69 16 8 4 6 97 88 0.0 5 57 15 7 3 2 4 98 63 0.0 5 38 9 5 7 2 2 99 66 0.0 5 43 8 6 3 3 3 100 71 0.0 5 45 10 6 4 4 2 101 78 0.0 5 51 13 4 4 4 2 102 56 0.0 5 35 11 2 2 5 1 103 43 0.0 5 26 7 3 2 2 3 104 42 0.0 5 28 4 7 1 1 1 105 31 0.0 5 23 4 2 1 1 106 33 0.0 5 18 3 6 1 5 107 32 0.0 5 22 6 1 1 1 1 108 30 0.0 5 23 4 1 1 1 109 28 0.0 5 18 4 1 3 1 1 110 11 0.0 5 8 0 1 0 1 1 111 17 0.0 5 15 1 0 0 0 1 112 6 0.0 5 4 0 0 2 113 13 0.0 5 9 0 2 0 2 114 8 0.0 5 4 1 1 1 1 115 94 0.0 5 90 1 1 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_3_R1_val_1_val_1.fq.gz ============================================= 39424942 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_3_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_3_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 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/Hawes/analyses/trimgalore-2/zr3644_3_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1086.16 s (28 µs/read; 2.18 M reads/minute). === Summary === Total reads processed: 39,424,942 Reads with adapters: 3,790,019 (9.6%) Reads written (passing filters): 39,424,942 (100.0%) Total basepairs processed: 4,171,077,084 bp Quality-trimmed: 1,996,418 bp (0.0%) Total written (filtered): 4,105,329,141 bp (98.4%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 3790019 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: 13.5% C: 5.1% G: 0.0% T: 81.4% 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 2400622 9856235.5 0 2400622 2 644501 2464058.9 0 644501 3 141199 616014.7 0 141199 4 39191 154003.7 0 39191 5 11553 38500.9 0 11553 6 3424 9625.2 0 3424 7 1285 2406.3 0 1285 8 684 601.6 0 684 9 578 150.4 0 578 10 2145 37.6 1 587 1558 11 1660 9.4 1 465 1195 12 1385 2.3 1 401 984 13 1266 0.6 1 399 867 14 1043 0.1 1 332 711 15 897 0.0 1 315 582 16 738 0.0 1 237 501 17 608 0.0 1 211 397 18 410 0.0 1 213 197 19 399 0.0 1 194 205 20 969 0.0 2 240 212 517 21 943 0.0 2 240 206 497 22 888 0.0 2 218 177 493 23 787 0.0 2 201 164 422 24 694 0.0 2 196 146 352 25 635 0.0 2 201 142 292 26 554 0.0 2 173 118 263 27 471 0.0 2 169 96 206 28 374 0.0 2 165 91 118 29 402 0.0 2 174 86 142 30 660 0.0 3 167 90 102 301 31 679 0.0 3 145 100 116 318 32 563 0.0 3 122 76 119 246 33 522 0.0 3 116 71 111 224 34 526 0.0 3 114 100 79 233 35 464 0.0 3 117 67 71 209 36 456 0.0 3 119 83 84 170 37 373 0.0 3 105 63 68 137 38 351 0.0 3 108 91 67 85 39 358 0.0 3 105 72 69 112 40 567 0.0 4 124 68 72 72 231 41 528 0.0 4 100 60 49 87 232 42 494 0.0 4 102 57 55 66 214 43 490 0.0 4 97 74 71 84 164 44 452 0.0 4 90 53 67 74 168 45 434 0.0 4 100 47 60 64 163 46 422 0.0 4 112 51 51 71 137 47 413 0.0 4 119 55 69 49 121 48 407 0.0 4 129 68 93 62 55 49 1183 0.0 4 323 249 235 198 178 50 1336 0.0 5 326 228 238 191 174 179 51 1027 0.0 5 306 190 174 128 123 106 52 909 0.0 5 310 193 130 95 100 81 53 783 0.0 5 301 146 111 84 78 63 54 676 0.0 5 275 113 111 72 60 45 55 715 0.0 5 322 123 114 55 59 42 56 684 0.0 5 305 154 86 65 42 32 57 635 0.0 5 294 123 87 46 45 40 58 588 0.0 5 301 112 66 46 33 30 59 534 0.0 5 243 103 64 53 38 33 60 506 0.0 5 264 87 63 42 35 15 61 462 0.0 5 249 75 37 43 31 27 62 440 0.0 5 224 98 41 32 22 23 63 474 0.0 5 259 92 55 34 19 15 64 483 0.0 5 288 85 45 21 24 20 65 487 0.0 5 282 86 59 28 15 17 66 468 0.0 5 287 74 43 28 19 17 67 517 0.0 5 340 80 47 22 19 9 68 505 0.0 5 343 68 39 24 19 12 69 548 0.0 5 395 68 32 26 15 12 70 469 0.0 5 353 53 23 19 12 9 71 408 0.0 5 295 43 20 24 17 9 72 390 0.0 5 277 50 25 13 9 16 73 380 0.0 5 266 63 21 13 6 11 74 403 0.0 5 287 50 23 19 10 14 75 445 0.0 5 336 62 15 10 11 11 76 367 0.0 5 266 37 23 20 13 8 77 382 0.0 5 301 32 16 12 8 13 78 303 0.0 5 216 37 19 14 10 7 79 346 0.0 5 277 31 16 5 10 7 80 338 0.0 5 257 37 16 14 4 10 81 275 0.0 5 198 36 13 10 10 8 82 288 0.0 5 209 38 14 11 10 6 83 293 0.0 5 214 32 24 11 3 9 84 288 0.0 5 229 26 12 8 8 5 85 241 0.0 5 191 22 16 5 5 2 86 287 0.0 5 227 26 10 13 6 5 87 287 0.0 5 227 30 13 7 6 4 88 279 0.0 5 222 30 5 11 5 6 89 253 0.0 5 197 27 14 8 4 3 90 251 0.0 5 200 18 10 10 11 2 91 246 0.0 5 178 35 14 9 2 8 92 254 0.0 5 206 18 13 10 5 2 93 193 0.0 5 147 26 7 3 5 5 94 187 0.0 5 141 16 7 10 8 5 95 211 0.0 5 176 12 9 10 2 2 96 230 0.0 5 172 26 15 7 5 5 97 210 0.0 5 166 21 12 4 6 1 98 154 0.0 5 112 22 8 7 4 1 99 254 0.0 5 205 26 6 7 3 7 100 161 0.0 5 110 23 12 8 5 3 101 250 0.0 5 205 15 9 10 5 6 102 218 0.0 5 182 15 6 5 6 4 103 213 0.0 5 176 21 4 2 8 2 104 162 0.0 5 125 12 5 7 7 6 105 266 0.0 5 223 24 7 6 4 2 106 187 0.0 5 146 18 5 8 6 4 107 200 0.0 5 149 24 12 6 3 6 108 201 0.0 5 155 20 8 5 8 5 109 305 0.0 5 211 29 42 7 8 8 110 316 0.0 5 241 34 13 8 6 14 111 242 0.0 5 188 23 5 16 5 5 112 612 0.0 5 496 51 20 22 10 13 113 684 0.0 5 569 52 23 22 8 10 114 2290 0.0 5 2098 90 45 26 19 12 115 491376 0.0 5 490730 437 111 43 35 20 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/Hawes/analyses/trimgalore-2/zr3644_3_R2_val_2_val_2.fq.gz ============================================= 39424942 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_3_R1_val_1_val_1_trimmed.fq.gz and zr3644_3_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_3_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_3_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_3_R1_val_1_val_1_trimmed.fq.gz and zr3644_3_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_3_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_3_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 39424942 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 511333 (1.30%) >>> Now running FastQC on the validated data zr3644_3_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_3_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_3_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_3_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_3_R1_val_1_val_1_trimmed.fq.gz and zr3644_3_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_4_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_4_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_4_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1441.06 s (29 µs/read; 2.08 M reads/minute). === Summary === Total reads processed: 49,987,655 Reads with adapters: 5,107,946 (10.2%) Reads written (passing filters): 49,987,655 (100.0%) Total basepairs processed: 5,284,463,398 bp Quality-trimmed: 2,504,037 bp (0.0%) Total written (filtered): 5,224,475,371 bp (98.9%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5107946 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: 21.3% C: 4.6% G: 0.0% T: 74.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3247085 12496913.8 0 3247085 2 881441 3124228.4 0 881441 3 188904 781057.1 0 188904 4 52089 195264.3 0 52089 5 15650 48816.1 0 15650 6 4534 12204.0 0 4534 7 1953 3051.0 0 1953 8 1264 762.8 0 1264 9 1204 190.7 0 1204 10 2699 47.7 1 1141 1558 11 2287 11.9 1 1033 1254 12 1991 3.0 1 915 1076 13 1918 0.7 1 887 1031 14 1578 0.2 1 763 815 15 1508 0.0 1 712 796 16 1192 0.0 1 557 635 17 983 0.0 1 497 486 18 730 0.0 1 425 305 19 789 0.0 1 459 330 20 1202 0.0 2 433 302 467 21 1106 0.0 2 410 275 421 22 1013 0.0 2 394 247 372 23 900 0.0 2 335 252 313 24 852 0.0 2 329 222 301 25 819 0.0 2 335 234 250 26 679 0.0 2 294 195 190 27 588 0.0 2 267 167 154 28 598 0.0 2 286 180 132 29 578 0.0 2 268 181 129 30 863 0.0 3 302 184 143 234 31 758 0.0 3 249 180 122 207 32 719 0.0 3 237 166 111 205 33 663 0.0 3 206 161 113 183 34 665 0.0 3 232 149 124 160 35 618 0.0 3 204 128 128 158 36 586 0.0 3 215 137 114 120 37 518 0.0 3 175 155 88 100 38 514 0.0 3 211 136 91 76 39 498 0.0 3 209 113 98 78 40 605 0.0 4 182 113 91 90 129 41 651 0.0 4 200 127 89 80 155 42 640 0.0 4 180 142 99 73 146 43 563 0.0 4 175 123 80 83 102 44 503 0.0 4 140 87 76 68 132 45 520 0.0 4 170 95 81 69 105 46 573 0.0 4 187 133 73 70 110 47 508 0.0 4 182 110 71 59 86 48 547 0.0 4 200 126 101 64 56 49 1253 0.0 4 509 271 208 156 109 50 1448 0.0 5 586 313 181 136 123 109 51 1151 0.0 5 585 202 139 97 70 58 52 1102 0.0 5 578 213 133 67 55 56 53 912 0.0 5 485 181 108 66 31 41 54 1003 0.0 5 595 185 102 56 37 28 55 1043 0.0 5 637 181 96 63 34 32 56 1114 0.0 5 744 182 78 52 33 25 57 1116 0.0 5 713 193 104 44 37 25 58 1198 0.0 5 833 164 86 50 38 27 59 1248 0.0 5 937 163 68 39 32 9 60 965 0.0 5 628 193 64 39 22 19 61 972 0.0 5 678 153 54 41 31 15 62 1117 0.0 5 782 185 79 34 23 14 63 1172 0.0 5 894 140 65 40 22 11 64 1629 0.0 5 1322 157 69 35 27 19 65 1158 0.0 5 838 168 80 40 14 18 66 1371 0.0 5 1069 169 55 36 23 19 67 1615 0.0 5 1287 197 65 37 19 10 68 2012 0.0 5 1700 194 61 25 14 18 69 2590 0.0 5 2218 237 67 35 18 15 70 4464 0.0 5 4096 212 75 35 33 13 71 8766 0.0 5 8319 285 105 32 19 6 72 30770 0.0 5 30098 490 120 36 18 8 73 63254 0.0 5 62489 600 99 37 16 13 74 311508 0.0 5 309748 1463 218 54 13 12 75 32616 0.0 5 32253 260 62 21 13 7 76 15197 0.0 5 14992 125 45 14 9 12 77 69799 0.0 5 69481 239 47 15 12 5 78 9355 0.0 5 9208 79 33 24 5 6 79 44277 0.0 5 44081 138 31 17 6 4 80 12438 0.0 5 12295 82 29 14 9 9 81 6967 0.0 5 6840 70 29 13 5 10 82 15666 0.0 5 15540 67 26 10 14 9 83 5186 0.0 5 5078 53 19 21 7 8 84 15046 0.0 5 14864 121 20 20 15 6 85 3377 0.0 5 3283 47 14 20 5 8 86 375 0.0 5 288 35 24 8 11 9 87 164 0.0 5 91 25 16 13 12 7 88 160 0.0 5 95 25 22 8 9 1 89 159 0.0 5 86 30 19 10 11 3 90 141 0.0 5 73 25 20 8 10 5 91 104 0.0 5 50 21 22 6 3 2 92 125 0.0 5 52 36 23 7 5 2 93 135 0.0 5 75 28 14 12 5 1 94 116 0.0 5 58 21 15 10 9 3 95 98 0.0 5 53 16 12 9 3 5 96 86 0.0 5 42 19 8 9 2 6 97 107 0.0 5 51 27 12 8 7 2 98 76 0.0 5 35 13 9 8 6 5 99 65 0.0 5 34 12 4 6 6 3 100 68 0.0 5 35 9 5 6 6 7 101 53 0.0 5 30 5 6 8 2 2 102 48 0.0 5 28 6 2 6 6 103 29 0.0 5 14 3 5 3 3 1 104 30 0.0 5 14 4 2 1 4 5 105 35 0.0 5 23 2 3 2 3 2 106 16 0.0 5 10 2 1 1 1 1 107 35 0.0 5 20 7 2 1 2 3 108 19 0.0 5 10 3 1 1 3 1 109 19 0.0 5 13 1 0 2 0 3 110 17 0.0 5 10 2 1 0 3 1 111 16 0.0 5 10 3 1 0 0 2 112 12 0.0 5 4 4 0 1 0 3 113 10 0.0 5 5 0 1 1 0 3 114 7 0.0 5 5 0 0 2 115 100 0.0 5 96 2 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_4_R1_val_1_val_1.fq.gz ============================================= 49987655 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_4_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_4_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_4_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1345.03 s (27 µs/read; 2.23 M reads/minute). === Summary === Total reads processed: 49,987,655 Reads with adapters: 4,731,085 (9.5%) Reads written (passing filters): 49,987,655 (100.0%) Total basepairs processed: 5,283,854,168 bp Quality-trimmed: 2,218,382 bp (0.0%) Total written (filtered): 5,197,304,876 bp (98.4%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4731085 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: 13.0% C: 5.0% G: 0.0% T: 81.9% 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 2980620 12496913.8 0 2980620 2 792865 3124228.4 0 792865 3 170737 781057.1 0 170737 4 46700 195264.3 0 46700 5 13367 48816.1 0 13367 6 3577 12204.0 0 3577 7 1297 3051.0 0 1297 8 719 762.8 0 719 9 607 190.7 0 607 10 2120 47.7 1 604 1516 11 1705 11.9 1 534 1171 12 1409 3.0 1 471 938 13 1268 0.7 1 450 818 14 1118 0.2 1 384 734 15 953 0.0 1 295 658 16 843 0.0 1 309 534 17 595 0.0 1 216 379 18 435 0.0 1 200 235 19 424 0.0 1 207 217 20 1065 0.0 2 297 219 549 21 936 0.0 2 271 217 448 22 913 0.0 2 294 204 415 23 837 0.0 2 267 183 387 24 742 0.0 2 256 161 325 25 724 0.0 2 238 174 312 26 627 0.0 2 206 169 252 27 516 0.0 2 192 102 222 28 468 0.0 2 219 106 143 29 463 0.0 2 217 100 146 30 722 0.0 3 197 112 105 308 31 730 0.0 3 188 112 138 292 32 666 0.0 3 182 98 110 276 33 609 0.0 3 206 77 111 215 34 567 0.0 3 143 96 104 224 35 571 0.0 3 185 75 94 217 36 554 0.0 3 188 89 86 191 37 466 0.0 3 164 80 82 140 38 409 0.0 3 159 76 77 97 39 420 0.0 3 161 75 83 101 40 624 0.0 4 136 76 68 101 243 41 610 0.0 4 173 70 66 100 201 42 593 0.0 4 146 67 74 97 209 43 576 0.0 4 135 77 79 92 193 44 500 0.0 4 118 59 61 90 172 45 523 0.0 4 116 76 68 98 165 46 484 0.0 4 140 69 63 62 150 47 498 0.0 4 157 87 63 61 130 48 556 0.0 4 178 108 105 84 81 49 1386 0.0 4 417 313 263 216 177 50 1409 0.0 5 367 266 239 184 189 164 51 1113 0.0 5 399 205 164 120 133 92 52 1007 0.0 5 378 215 147 103 92 72 53 878 0.0 5 395 169 103 80 76 55 54 771 0.0 5 338 145 104 76 49 59 55 789 0.0 5 383 152 106 63 50 35 56 851 0.0 5 441 151 109 67 43 40 57 710 0.0 5 380 133 75 49 51 22 58 616 0.0 5 310 115 79 45 39 28 59 590 0.0 5 312 115 63 41 33 26 60 562 0.0 5 312 90 51 51 30 28 61 579 0.0 5 336 114 54 39 25 11 62 524 0.0 5 312 77 57 32 26 20 63 662 0.0 5 417 100 54 44 26 21 64 553 0.0 5 351 85 38 27 25 27 65 650 0.0 5 419 97 68 26 27 13 66 552 0.0 5 380 76 40 28 20 8 67 598 0.0 5 416 96 37 24 14 11 68 602 0.0 5 429 79 47 21 16 10 69 643 0.0 5 478 85 37 15 15 13 70 598 0.0 5 458 65 33 22 13 7 71 487 0.0 5 327 73 35 25 19 8 72 505 0.0 5 361 62 31 27 9 15 73 486 0.0 5 363 56 26 16 13 12 74 474 0.0 5 368 52 23 19 7 5 75 546 0.0 5 434 57 27 11 12 5 76 478 0.0 5 339 67 29 15 16 12 77 494 0.0 5 393 44 29 14 8 6 78 422 0.0 5 326 40 23 11 13 9 79 443 0.0 5 348 45 28 4 11 7 80 364 0.0 5 270 42 26 12 8 6 81 380 0.0 5 298 34 19 8 11 10 82 369 0.0 5 285 40 16 13 9 6 83 318 0.0 5 244 39 10 16 6 3 84 343 0.0 5 289 18 13 10 8 5 85 311 0.0 5 233 38 18 9 5 8 86 321 0.0 5 262 25 16 6 4 8 87 317 0.0 5 251 28 17 12 6 3 88 378 0.0 5 321 17 19 11 7 3 89 313 0.0 5 256 35 10 7 3 2 90 287 0.0 5 235 20 14 12 5 1 91 244 0.0 5 191 31 5 7 5 5 92 285 0.0 5 230 24 13 6 7 5 93 234 0.0 5 183 32 8 6 4 1 94 255 0.0 5 189 37 8 5 10 6 95 246 0.0 5 217 15 6 7 1 96 256 0.0 5 182 40 17 9 5 3 97 238 0.0 5 189 21 10 2 12 4 98 205 0.0 5 154 26 12 4 1 8 99 314 0.0 5 260 24 14 7 7 2 100 174 0.0 5 140 15 12 2 4 1 101 326 0.0 5 285 22 7 4 6 2 102 317 0.0 5 271 24 12 2 4 4 103 302 0.0 5 247 23 12 4 4 12 104 218 0.0 5 174 22 7 6 5 4 105 346 0.0 5 281 28 16 10 2 9 106 239 0.0 5 195 18 7 6 8 5 107 276 0.0 5 217 27 14 8 6 4 108 270 0.0 5 217 21 11 10 5 6 109 380 0.0 5 252 50 53 14 7 4 110 415 0.0 5 329 33 20 11 14 8 111 331 0.0 5 233 36 25 14 15 8 112 787 0.0 5 652 43 33 22 18 19 113 906 0.0 5 732 74 40 22 22 16 114 2908 0.0 5 2627 133 51 48 27 22 115 656606 0.0 5 655651 718 121 51 35 30 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/Hawes/analyses/trimgalore-2/zr3644_4_R2_val_2_val_2.fq.gz ============================================= 49987655 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_4_R1_val_1_val_1_trimmed.fq.gz and zr3644_4_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_4_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_4_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_4_R1_val_1_val_1_trimmed.fq.gz and zr3644_4_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_4_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_4_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 49987655 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 681407 (1.36%) >>> Now running FastQC on the validated data zr3644_4_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_4_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_4_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_4_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_4_R1_val_1_val_1_trimmed.fq.gz and zr3644_4_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_5_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_5_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_5_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1336.53 s (30 µs/read; 2.01 M reads/minute). === Summary === Total reads processed: 44,671,516 Reads with adapters: 4,652,727 (10.4%) Reads written (passing filters): 44,671,516 (100.0%) Total basepairs processed: 4,732,991,538 bp Quality-trimmed: 2,611,057 bp (0.1%) Total written (filtered): 4,680,445,149 bp (98.9%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4652727 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: 21.0% C: 4.8% G: 0.0% T: 74.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2965124 11167879.0 0 2965124 2 815311 2791969.8 0 815311 3 177687 697992.4 0 177687 4 50063 174498.1 0 50063 5 14973 43624.5 0 14973 6 4303 10906.1 0 4303 7 1979 2726.5 0 1979 8 1325 681.6 0 1325 9 1179 170.4 0 1179 10 2731 42.6 1 1071 1660 11 2401 10.7 1 1034 1367 12 2043 2.7 1 935 1108 13 1869 0.7 1 849 1020 14 1666 0.2 1 732 934 15 1448 0.0 1 664 784 16 1244 0.0 1 574 670 17 1021 0.0 1 492 529 18 783 0.0 1 433 350 19 764 0.0 1 442 322 20 1239 0.0 2 423 303 513 21 1153 0.0 2 419 291 443 22 1054 0.0 2 369 275 410 23 998 0.0 2 366 253 379 24 881 0.0 2 343 237 301 25 796 0.0 2 285 238 273 26 713 0.0 2 263 191 259 27 654 0.0 2 256 175 223 28 569 0.0 2 242 174 153 29 559 0.0 2 234 175 150 30 760 0.0 3 253 147 135 225 31 776 0.0 3 233 189 124 230 32 698 0.0 3 234 157 113 194 33 645 0.0 3 219 146 90 190 34 673 0.0 3 234 140 112 187 35 671 0.0 3 219 159 130 163 36 583 0.0 3 218 143 101 121 37 599 0.0 3 198 147 106 148 38 523 0.0 3 213 118 93 99 39 528 0.0 3 193 135 105 95 40 593 0.0 4 148 143 94 65 143 41 609 0.0 4 182 133 85 78 131 42 647 0.0 4 174 155 88 90 140 43 615 0.0 4 163 123 90 99 140 44 542 0.0 4 135 114 100 67 126 45 534 0.0 4 156 114 79 72 113 46 575 0.0 4 161 137 85 89 103 47 553 0.0 4 205 121 78 58 91 48 564 0.0 4 175 133 92 79 85 49 1196 0.0 4 440 277 204 157 118 50 1431 0.0 5 556 284 186 172 146 87 51 1067 0.0 5 511 219 119 103 57 58 52 1009 0.0 5 491 209 118 87 64 40 53 861 0.0 5 433 165 117 63 47 36 54 941 0.0 5 535 161 101 60 53 31 55 1041 0.0 5 635 182 101 55 44 24 56 1120 0.0 5 702 204 87 59 39 29 57 956 0.0 5 609 145 96 51 38 17 58 1030 0.0 5 698 163 72 44 34 19 59 1082 0.0 5 770 133 83 43 38 15 60 910 0.0 5 579 172 65 41 34 19 61 934 0.0 5 643 156 61 41 15 18 62 1076 0.0 5 733 193 66 46 28 10 63 1134 0.0 5 862 136 79 29 14 14 64 1537 0.0 5 1258 149 57 40 21 12 65 1085 0.0 5 792 165 68 36 14 10 66 1261 0.0 5 977 155 65 31 18 15 67 1483 0.0 5 1167 176 64 35 24 17 68 1768 0.0 5 1427 196 74 42 18 11 69 2285 0.0 5 2004 164 53 26 26 12 70 4228 0.0 5 3879 218 61 38 19 13 71 8085 0.0 5 7650 291 76 41 15 12 72 28140 0.0 5 27502 457 106 48 16 11 73 59137 0.0 5 58348 588 127 42 21 11 74 262016 0.0 5 260463 1292 186 42 17 16 75 30690 0.0 5 30343 229 67 24 18 9 76 14512 0.0 5 14271 147 41 23 17 13 77 60145 0.0 5 59880 181 42 24 9 9 78 8481 0.0 5 8303 94 40 24 15 5 79 37424 0.0 5 37211 132 37 16 20 8 80 10590 0.0 5 10432 84 36 11 19 8 81 5962 0.0 5 5827 67 26 22 11 9 82 13264 0.0 5 13142 65 21 19 10 7 83 4046 0.0 5 3934 58 26 15 8 5 84 8622 0.0 5 8459 90 28 17 19 9 85 1856 0.0 5 1749 55 18 19 11 4 86 207 0.0 5 122 38 21 9 12 5 87 161 0.0 5 86 27 17 15 7 9 88 140 0.0 5 69 31 17 6 10 7 89 134 0.0 5 79 22 10 10 6 7 90 129 0.0 5 64 27 20 9 7 2 91 116 0.0 5 72 13 9 13 6 3 92 115 0.0 5 62 19 16 7 4 7 93 95 0.0 5 45 23 6 9 9 3 94 85 0.0 5 37 19 8 5 9 7 95 102 0.0 5 47 22 16 5 5 7 96 78 0.0 5 45 13 11 2 5 2 97 68 0.0 5 39 8 5 4 8 4 98 79 0.0 5 41 17 9 7 3 2 99 63 0.0 5 29 13 5 7 5 4 100 73 0.0 5 43 13 5 6 4 2 101 67 0.0 5 39 10 4 6 5 3 102 38 0.0 5 22 3 6 4 1 2 103 37 0.0 5 18 6 2 5 3 3 104 39 0.0 5 21 6 2 4 4 2 105 26 0.0 5 11 7 5 0 3 106 25 0.0 5 14 3 3 1 3 1 107 19 0.0 5 9 4 1 1 2 2 108 17 0.0 5 11 1 0 3 1 1 109 18 0.0 5 8 2 2 4 1 1 110 24 0.0 5 17 2 3 1 1 111 11 0.0 5 7 1 0 2 1 112 10 0.0 5 6 3 1 113 9 0.0 5 7 1 1 114 9 0.0 5 4 2 2 0 1 115 110 0.0 5 105 3 0 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_5_R1_val_1_val_1.fq.gz ============================================= 44671516 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_5_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_5_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_5_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1214.61 s (27 µs/read; 2.21 M reads/minute). === Summary === Total reads processed: 44,671,516 Reads with adapters: 4,275,485 (9.6%) Reads written (passing filters): 44,671,516 (100.0%) Total basepairs processed: 4,735,632,086 bp Quality-trimmed: 2,019,882 bp (0.0%) Total written (filtered): 4,660,595,509 bp (98.4%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4275485 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: 13.3% C: 5.1% G: 0.0% T: 81.5% 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 2703253 11167879.0 0 2703253 2 727624 2791969.8 0 727624 3 158840 697992.4 0 158840 4 43460 174498.1 0 43460 5 12522 43624.5 0 12522 6 3501 10906.1 0 3501 7 1177 2726.5 0 1177 8 681 681.6 0 681 9 640 170.4 0 640 10 2066 42.6 1 608 1458 11 1697 10.7 1 530 1167 12 1364 2.7 1 431 933 13 1262 0.7 1 426 836 14 1114 0.2 1 380 734 15 923 0.0 1 350 573 16 864 0.0 1 331 533 17 687 0.0 1 250 437 18 453 0.0 1 221 232 19 369 0.0 1 181 188 20 940 0.0 2 271 201 468 21 904 0.0 2 265 201 438 22 896 0.0 2 247 209 440 23 808 0.0 2 250 179 379 24 759 0.0 2 250 174 335 25 719 0.0 2 240 162 317 26 611 0.0 2 224 129 258 27 490 0.0 2 201 109 180 28 446 0.0 2 199 99 148 29 430 0.0 2 185 113 132 30 686 0.0 3 169 89 128 300 31 651 0.0 3 162 92 138 259 32 623 0.0 3 159 95 112 257 33 594 0.0 3 166 89 91 248 34 535 0.0 3 147 84 103 201 35 541 0.0 3 147 90 109 195 36 497 0.0 3 161 87 75 174 37 459 0.0 3 169 88 71 131 38 396 0.0 3 128 77 77 114 39 395 0.0 3 145 87 78 85 40 605 0.0 4 141 75 84 102 203 41 591 0.0 4 163 76 64 90 198 42 523 0.0 4 123 68 70 79 183 43 509 0.0 4 120 85 59 74 171 44 488 0.0 4 114 68 49 73 184 45 502 0.0 4 125 68 65 82 162 46 457 0.0 4 130 76 62 63 126 47 448 0.0 4 162 81 48 52 105 48 490 0.0 4 151 86 92 91 70 49 1162 0.0 4 341 250 232 193 146 50 1257 0.0 5 355 250 218 160 141 133 51 1011 0.0 5 354 211 148 106 100 92 52 880 0.0 5 325 191 124 110 64 66 53 770 0.0 5 351 145 106 84 40 44 54 741 0.0 5 347 144 96 58 52 44 55 652 0.0 5 324 143 72 54 31 28 56 678 0.0 5 366 123 79 42 27 41 57 608 0.0 5 319 122 63 53 32 19 58 546 0.0 5 274 107 68 42 29 26 59 514 0.0 5 284 83 61 30 31 25 60 518 0.0 5 309 82 49 30 23 25 61 480 0.0 5 292 81 41 27 23 16 62 463 0.0 5 281 88 33 24 19 18 63 523 0.0 5 325 75 44 32 25 22 64 448 0.0 5 270 69 44 36 19 10 65 492 0.0 5 329 84 34 21 14 10 66 434 0.0 5 281 68 44 18 7 16 67 504 0.0 5 333 79 45 19 15 13 68 452 0.0 5 309 63 29 20 22 9 69 572 0.0 5 427 59 35 24 11 16 70 465 0.0 5 353 51 28 15 12 6 71 447 0.0 5 331 59 24 19 9 5 72 433 0.0 5 320 45 24 23 13 8 73 386 0.0 5 263 55 22 16 12 18 74 383 0.0 5 286 37 31 11 6 12 75 478 0.0 5 369 47 23 10 22 7 76 414 0.0 5 319 50 20 11 5 9 77 366 0.0 5 285 34 20 13 6 8 78 320 0.0 5 234 43 18 14 4 7 79 381 0.0 5 312 30 14 11 6 8 80 339 0.0 5 259 49 13 7 7 4 81 318 0.0 5 239 32 16 12 11 8 82 309 0.0 5 236 34 13 13 10 3 83 265 0.0 5 201 34 8 10 8 4 84 318 0.0 5 245 31 22 7 6 7 85 265 0.0 5 209 27 11 6 5 7 86 301 0.0 5 225 30 13 12 12 9 87 261 0.0 5 213 23 4 10 7 4 88 329 0.0 5 271 18 19 7 6 8 89 266 0.0 5 215 20 14 8 6 3 90 265 0.0 5 210 24 11 9 6 5 91 203 0.0 5 155 24 7 8 5 4 92 267 0.0 5 212 25 4 8 11 7 93 203 0.0 5 155 19 6 10 7 6 94 220 0.0 5 171 15 17 5 5 7 95 224 0.0 5 185 19 7 6 5 2 96 208 0.0 5 142 27 18 10 6 5 97 210 0.0 5 150 37 10 7 4 2 98 167 0.0 5 126 15 6 11 3 6 99 234 0.0 5 203 9 7 4 6 5 100 151 0.0 5 114 15 11 3 5 3 101 284 0.0 5 250 10 11 2 7 4 102 279 0.0 5 224 24 8 6 10 7 103 251 0.0 5 205 22 10 6 2 6 104 160 0.0 5 116 18 9 5 3 9 105 281 0.0 5 233 19 14 6 7 2 106 180 0.0 5 130 22 10 4 9 5 107 245 0.0 5 194 13 8 8 13 9 108 203 0.0 5 160 15 6 10 8 4 109 330 0.0 5 215 39 51 10 11 4 110 329 0.0 5 255 35 14 8 12 5 111 309 0.0 5 223 37 13 12 12 12 112 632 0.0 5 525 31 21 22 13 20 113 784 0.0 5 658 51 28 18 10 19 114 2374 0.0 5 2157 100 49 40 14 14 115 566253 0.0 5 565569 500 93 47 24 20 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/Hawes/analyses/trimgalore-2/zr3644_5_R2_val_2_val_2.fq.gz ============================================= 44671516 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_5_R1_val_1_val_1_trimmed.fq.gz and zr3644_5_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_5_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_5_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_5_R1_val_1_val_1_trimmed.fq.gz and zr3644_5_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_5_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_5_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 44671516 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 587860 (1.32%) >>> Now running FastQC on the validated data zr3644_5_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_5_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_5_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_5_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_5_R1_val_1_val_1_trimmed.fq.gz and zr3644_5_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_6_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_6_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_6_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1476.24 s (27 µs/read; 2.19 M reads/minute). === Summary === Total reads processed: 54,004,139 Reads with adapters: 5,593,686 (10.4%) Reads written (passing filters): 54,004,139 (100.0%) Total basepairs processed: 5,710,082,467 bp Quality-trimmed: 2,138,241 bp (0.0%) Total written (filtered): 5,638,540,446 bp (98.7%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5593686 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: 21.7% C: 4.6% G: 0.0% T: 73.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3476905 13501034.8 0 3476905 2 955395 3375258.7 0 955395 3 205964 843814.7 0 205964 4 56369 210953.7 0 56369 5 16760 52738.4 0 16760 6 4888 13184.6 0 4888 7 2140 3296.2 0 2140 8 1418 824.0 0 1418 9 1374 206.0 0 1374 10 2856 51.5 1 1268 1588 11 2551 12.9 1 1199 1352 12 2271 3.2 1 1094 1177 13 1992 0.8 1 946 1046 14 1804 0.2 1 907 897 15 1522 0.1 1 755 767 16 1373 0.0 1 725 648 17 1112 0.0 1 572 540 18 856 0.0 1 506 350 19 855 0.0 1 525 330 20 1326 0.0 2 492 327 507 21 1181 0.0 2 468 309 404 22 1145 0.0 2 488 307 350 23 1051 0.0 2 428 267 356 24 921 0.0 2 377 258 286 25 920 0.0 2 398 254 268 26 779 0.0 2 329 225 225 27 803 0.0 2 391 204 208 28 655 0.0 2 347 188 120 29 607 0.0 2 290 177 140 30 855 0.0 3 322 181 154 198 31 862 0.0 3 308 181 146 227 32 768 0.0 3 303 165 116 184 33 773 0.0 3 281 168 150 174 34 760 0.0 3 258 181 147 174 35 748 0.0 3 282 178 119 169 36 681 0.0 3 265 157 119 140 37 604 0.0 3 280 128 81 115 38 602 0.0 3 274 145 91 92 39 592 0.0 3 240 146 112 94 40 647 0.0 4 222 124 90 77 134 41 704 0.0 4 229 135 99 96 145 42 686 0.0 4 225 140 101 87 133 43 626 0.0 4 187 135 84 91 129 44 617 0.0 4 211 115 95 74 122 45 611 0.0 4 203 129 89 102 88 46 580 0.0 4 178 143 77 81 101 47 569 0.0 4 207 130 85 67 80 48 669 0.0 4 269 156 99 85 60 49 1348 0.0 4 580 289 192 154 133 50 1564 0.0 5 702 309 188 163 120 82 51 1111 0.0 5 612 204 126 83 45 41 52 1033 0.0 5 569 190 114 70 51 39 53 919 0.0 5 544 165 86 64 33 27 54 1021 0.0 5 678 148 93 45 45 12 55 1117 0.0 5 720 186 95 55 38 23 56 1263 0.0 5 909 186 80 42 28 18 57 1200 0.0 5 871 178 67 31 26 27 58 1293 0.0 5 966 166 79 43 24 15 59 1274 0.0 5 970 149 76 50 20 9 60 1042 0.0 5 731 166 77 27 25 16 61 1133 0.0 5 887 128 60 32 18 8 62 1398 0.0 5 1078 196 66 20 25 13 63 1538 0.0 5 1252 164 63 35 19 5 64 1673 0.0 5 1410 146 58 29 16 14 65 1295 0.0 5 1026 141 65 31 21 11 66 1539 0.0 5 1277 158 59 21 11 13 67 1913 0.0 5 1640 181 46 23 15 8 68 2682 0.0 5 2396 187 51 28 15 5 69 3810 0.0 5 3482 213 65 26 17 7 70 7478 0.0 5 7180 216 48 13 16 5 71 16724 0.0 5 16335 283 68 18 10 10 72 45944 0.0 5 45405 422 75 27 5 10 73 132899 0.0 5 132153 619 80 31 11 5 74 337676 0.0 5 336588 938 110 22 8 10 75 35715 0.0 5 35454 197 34 17 10 3 76 32404 0.0 5 32172 173 31 16 5 7 77 66429 0.0 5 66146 204 38 23 10 8 78 18498 0.0 5 18312 131 30 14 5 6 79 43062 0.0 5 42844 147 28 25 9 9 80 12994 0.0 5 12846 95 29 9 11 4 81 10660 0.0 5 10521 90 27 10 6 6 82 13833 0.0 5 13702 92 16 9 7 7 83 9941 0.0 5 9789 104 23 10 9 6 84 12373 0.0 5 12207 119 15 18 8 6 85 2157 0.0 5 2069 47 17 11 8 5 86 329 0.0 5 239 45 23 12 7 3 87 201 0.0 5 144 28 15 8 2 4 88 195 0.0 5 133 34 7 9 3 9 89 207 0.0 5 140 29 13 12 9 4 90 183 0.0 5 121 22 20 10 6 4 91 163 0.0 5 111 26 15 6 3 2 92 152 0.0 5 101 31 10 2 5 3 93 119 0.0 5 79 23 11 5 1 94 131 0.0 5 88 17 10 8 4 4 95 111 0.0 5 73 12 8 9 5 4 96 120 0.0 5 84 15 10 5 3 3 97 126 0.0 5 77 19 7 11 7 5 98 118 0.0 5 76 19 11 4 5 3 99 91 0.0 5 53 17 11 5 2 3 100 91 0.0 5 59 10 4 13 1 4 101 79 0.0 5 43 16 7 5 4 4 102 72 0.0 5 49 7 8 3 3 2 103 63 0.0 5 41 9 5 2 5 1 104 54 0.0 5 28 17 5 3 1 105 34 0.0 5 21 6 3 2 1 1 106 54 0.0 5 39 5 3 2 0 5 107 26 0.0 5 15 5 2 0 2 2 108 35 0.0 5 21 3 3 1 2 5 109 19 0.0 5 18 0 1 110 24 0.0 5 19 2 2 1 111 11 0.0 5 6 1 0 3 0 1 112 20 0.0 5 14 1 2 1 1 1 113 8 0.0 5 6 2 114 13 0.0 5 10 2 1 115 137 0.0 5 134 1 1 0 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_6_R1_val_1_val_1.fq.gz ============================================= 54004139 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_6_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_6_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_6_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1470.19 s (27 µs/read; 2.20 M reads/minute). === Summary === Total reads processed: 54,004,139 Reads with adapters: 5,249,133 (9.7%) Reads written (passing filters): 54,004,139 (100.0%) Total basepairs processed: 5,708,503,535 bp Quality-trimmed: 2,593,820 bp (0.0%) Total written (filtered): 5,603,811,375 bp (98.2%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5249133 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: 13.3% C: 5.1% G: 0.0% T: 81.5% 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 3238784 13501034.8 0 3238784 2 870740 3375258.7 0 870740 3 189501 843814.7 0 189501 4 51701 210953.7 0 51701 5 15071 52738.4 0 15071 6 4205 13184.6 0 4205 7 1475 3296.2 0 1475 8 783 824.0 0 783 9 726 206.0 0 726 10 2553 51.5 1 669 1884 11 2042 12.9 1 611 1431 12 1659 3.2 1 507 1152 13 1433 0.8 1 487 946 14 1225 0.2 1 426 799 15 1170 0.1 1 390 780 16 935 0.0 1 318 617 17 755 0.0 1 269 486 18 538 0.0 1 267 271 19 490 0.0 1 237 253 20 1235 0.0 2 359 213 663 21 1110 0.0 2 303 235 572 22 1040 0.0 2 318 228 494 23 972 0.0 2 251 228 493 24 895 0.0 2 290 191 414 25 798 0.0 2 244 180 374 26 660 0.0 2 212 148 300 27 594 0.0 2 219 128 247 28 507 0.0 2 208 128 171 29 491 0.0 2 207 140 144 30 831 0.0 3 232 113 143 343 31 786 0.0 3 215 100 120 351 32 729 0.0 3 197 109 123 300 33 662 0.0 3 182 93 104 283 34 639 0.0 3 167 100 96 276 35 635 0.0 3 167 99 119 250 36 614 0.0 3 167 103 103 241 37 509 0.0 3 188 78 79 164 38 462 0.0 3 178 81 88 115 39 470 0.0 3 179 102 86 103 40 702 0.0 4 145 84 90 120 263 41 632 0.0 4 156 83 77 88 228 42 682 0.0 4 143 79 100 95 265 43 594 0.0 4 141 92 61 107 193 44 611 0.0 4 127 97 90 94 203 45 572 0.0 4 134 76 81 91 190 46 543 0.0 4 143 89 67 95 149 47 532 0.0 4 162 90 75 65 140 48 602 0.0 4 197 125 92 96 92 49 1506 0.0 4 460 336 287 225 198 50 1701 0.0 5 439 309 278 265 198 212 51 1272 0.0 5 418 261 189 140 140 124 52 1180 0.0 5 451 219 175 131 112 92 53 1130 0.0 5 452 252 152 117 85 72 54 928 0.0 5 423 178 115 106 57 49 55 912 0.0 5 416 173 118 92 71 42 56 910 0.0 5 466 154 121 73 58 38 57 834 0.0 5 442 180 81 51 41 39 58 733 0.0 5 363 143 83 69 39 36 59 708 0.0 5 387 137 78 43 35 28 60 683 0.0 5 373 132 74 35 44 25 61 642 0.0 5 352 108 82 45 24 31 62 655 0.0 5 403 101 65 39 20 27 63 639 0.0 5 414 89 63 33 15 25 64 626 0.0 5 371 107 56 40 30 22 65 727 0.0 5 486 110 57 34 22 18 66 666 0.0 5 440 93 56 34 24 19 67 739 0.0 5 507 121 45 26 22 18 68 677 0.0 5 471 101 49 29 15 12 69 791 0.0 5 614 90 31 24 20 12 70 730 0.0 5 583 65 29 29 9 15 71 558 0.0 5 400 76 33 18 16 15 72 593 0.0 5 417 73 47 29 10 17 73 544 0.0 5 408 64 32 16 13 11 74 545 0.0 5 427 58 14 19 11 16 75 675 0.0 5 525 74 30 25 10 11 76 619 0.0 5 481 76 35 12 10 5 77 574 0.0 5 458 55 23 17 13 8 78 474 0.0 5 377 46 18 18 8 7 79 585 0.0 5 463 64 25 12 10 11 80 480 0.0 5 389 46 15 14 10 6 81 431 0.0 5 342 34 24 12 12 7 82 414 0.0 5 333 32 21 8 13 7 83 401 0.0 5 318 38 20 11 5 9 84 439 0.0 5 359 34 16 10 14 6 85 378 0.0 5 306 30 23 11 4 4 86 414 0.0 5 357 31 10 2 8 6 87 380 0.0 5 307 37 12 9 6 9 88 461 0.0 5 375 38 15 14 14 5 89 378 0.0 5 319 30 16 3 4 6 90 430 0.0 5 355 33 14 7 12 9 91 361 0.0 5 279 45 16 12 5 4 92 434 0.0 5 360 32 16 13 6 7 93 322 0.0 5 263 23 19 9 5 3 94 300 0.0 5 256 19 11 7 4 3 95 389 0.0 5 326 30 14 8 7 4 96 394 0.0 5 311 45 14 17 3 4 97 324 0.0 5 261 39 11 4 6 3 98 295 0.0 5 246 25 11 7 3 3 99 422 0.0 5 361 27 16 9 5 4 100 286 0.0 5 216 39 12 10 5 4 101 412 0.0 5 354 32 14 5 7 102 419 0.0 5 359 29 13 8 3 7 103 382 0.0 5 338 16 8 10 7 3 104 345 0.0 5 302 22 5 8 6 2 105 461 0.0 5 381 39 15 13 6 7 106 312 0.0 5 249 33 9 8 8 5 107 350 0.0 5 293 32 7 6 6 6 108 359 0.0 5 276 31 16 13 12 11 109 531 0.0 5 371 66 60 15 10 9 110 570 0.0 5 470 46 13 15 13 13 111 432 0.0 5 325 39 24 13 18 13 112 1080 0.0 5 915 75 31 21 21 17 113 1212 0.0 5 1027 72 34 32 17 30 114 4058 0.0 5 3754 169 51 32 26 26 115 799626 0.0 5 798349 976 175 60 35 31 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/Hawes/analyses/trimgalore-2/zr3644_6_R2_val_2_val_2.fq.gz ============================================= 54004139 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_6_R1_val_1_val_1_trimmed.fq.gz and zr3644_6_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_6_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_6_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_6_R1_val_1_val_1_trimmed.fq.gz and zr3644_6_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_6_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_6_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 54004139 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 829326 (1.54%) >>> Now running FastQC on the validated data zr3644_6_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_6_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_6_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_6_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_6_R1_val_1_val_1_trimmed.fq.gz and zr3644_6_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_7_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_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 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/Hawes/analyses/trimgalore-2/zr3644_7_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2224.89 s (27 µs/read; 2.23 M reads/minute). === Summary === Total reads processed: 82,527,069 Reads with adapters: 8,201,704 (9.9%) Reads written (passing filters): 82,527,069 (100.0%) Total basepairs processed: 8,753,479,148 bp Quality-trimmed: 3,061,684 bp (0.0%) Total written (filtered): 8,668,348,901 bp (99.0%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 8201704 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: 19.5% C: 4.8% G: 0.0% T: 75.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 5286872 20631767.2 0 5286872 2 1453542 5157941.8 0 1453542 3 310856 1289485.5 0 310856 4 86133 322371.4 0 86133 5 25978 80592.8 0 25978 6 7796 20148.2 0 7796 7 3816 5037.1 0 3816 8 2597 1259.3 0 2597 9 2359 314.8 0 2359 10 5076 78.7 1 2313 2763 11 4501 19.7 1 2138 2363 12 3846 4.9 1 1897 1949 13 3604 1.2 1 1828 1776 14 3350 0.3 1 1692 1658 15 2697 0.1 1 1340 1357 16 2444 0.0 1 1227 1217 17 1984 0.0 1 1021 963 18 1614 0.0 1 958 656 19 1454 0.0 1 911 543 20 2260 0.0 2 910 527 823 21 2022 0.0 2 812 472 738 22 1967 0.0 2 823 504 640 23 1808 0.0 2 739 455 614 24 1670 0.0 2 726 423 521 25 1627 0.0 2 705 422 500 26 1512 0.0 2 632 415 465 27 1277 0.0 2 577 335 365 28 1153 0.0 2 597 318 238 29 1103 0.0 2 551 301 251 30 1543 0.0 3 530 332 260 421 31 1403 0.0 3 469 337 236 361 32 1363 0.0 3 507 271 243 342 33 1258 0.0 3 462 280 192 324 34 1314 0.0 3 487 286 198 343 35 1211 0.0 3 429 303 225 254 36 1124 0.0 3 422 252 201 249 37 1113 0.0 3 460 268 176 209 38 1037 0.0 3 419 260 177 181 39 993 0.0 3 425 228 156 184 40 1201 0.0 4 383 245 148 174 251 41 1178 0.0 4 387 233 169 160 229 42 1157 0.0 4 352 209 191 165 240 43 1102 0.0 4 368 228 148 138 220 44 984 0.0 4 293 204 133 148 206 45 999 0.0 4 346 185 165 139 164 46 1034 0.0 4 384 185 128 145 192 47 1013 0.0 4 385 203 144 114 167 48 1104 0.0 4 443 261 156 134 110 49 2286 0.0 4 945 507 331 264 239 50 2521 0.0 5 1054 492 352 245 208 170 51 1813 0.0 5 930 330 210 147 114 82 52 1756 0.0 5 984 284 214 120 92 62 53 1519 0.0 5 883 261 150 93 78 54 54 1594 0.0 5 973 250 165 89 77 40 55 1753 0.0 5 1125 285 138 107 52 46 56 1908 0.0 5 1334 287 113 88 57 29 57 1795 0.0 5 1240 254 119 89 63 30 58 1685 0.0 5 1224 233 96 71 42 19 59 1696 0.0 5 1243 229 106 51 39 28 60 1585 0.0 5 1138 242 85 62 28 30 61 1686 0.0 5 1254 226 100 54 30 22 62 1972 0.0 5 1531 222 111 54 36 18 63 2150 0.0 5 1741 218 97 48 27 19 64 2347 0.0 5 1906 238 87 56 42 18 65 1949 0.0 5 1556 238 74 46 27 8 66 2327 0.0 5 1936 228 91 33 26 13 67 2951 0.0 5 2514 269 80 44 31 13 68 4082 0.0 5 3617 319 75 41 19 11 69 6056 0.0 5 5577 309 79 41 31 19 70 11441 0.0 5 10985 301 97 28 23 7 71 24969 0.0 5 24390 415 106 35 16 7 72 60617 0.0 5 59913 516 125 31 18 14 73 189729 0.0 5 188702 808 136 47 20 16 74 323808 0.0 5 322677 922 146 37 15 11 75 43132 0.0 5 42726 270 65 33 24 14 76 41577 0.0 5 41207 260 54 30 17 9 77 70089 0.0 5 69724 261 60 28 11 5 78 24523 0.0 5 24260 152 49 34 14 14 79 45274 0.0 5 45000 175 46 21 20 12 80 15397 0.0 5 15186 122 42 22 11 14 81 13115 0.0 5 12901 128 38 23 15 10 82 14891 0.0 5 14689 110 43 29 15 5 83 10095 0.0 5 9875 140 37 19 15 9 84 10109 0.0 5 9894 137 31 23 13 11 85 1654 0.0 5 1512 75 28 17 18 4 86 501 0.0 5 378 61 20 21 12 9 87 365 0.0 5 248 63 14 20 14 6 88 295 0.0 5 210 35 21 15 6 8 89 313 0.0 5 186 53 37 12 17 8 90 274 0.0 5 175 43 24 11 14 7 91 315 0.0 5 223 36 20 14 14 8 92 228 0.0 5 148 36 17 13 9 5 93 245 0.0 5 158 35 23 15 6 8 94 234 0.0 5 146 37 22 13 8 8 95 234 0.0 5 152 37 22 7 10 6 96 187 0.0 5 134 25 13 7 3 5 97 175 0.0 5 108 26 14 8 11 8 98 177 0.0 5 93 26 15 20 10 13 99 134 0.0 5 83 16 14 11 7 3 100 149 0.0 5 95 19 11 14 4 6 101 124 0.0 5 73 12 10 10 12 7 102 117 0.0 5 77 14 10 8 5 3 103 82 0.0 5 53 14 6 3 3 3 104 78 0.0 5 50 7 12 3 5 1 105 71 0.0 5 39 12 9 8 1 2 106 53 0.0 5 32 8 1 3 4 5 107 57 0.0 5 37 3 7 4 5 1 108 48 0.0 5 35 3 2 6 1 1 109 39 0.0 5 30 1 3 1 0 4 110 32 0.0 5 24 3 2 0 2 1 111 26 0.0 5 17 5 0 3 0 1 112 25 0.0 5 19 2 0 0 2 2 113 27 0.0 5 18 1 2 1 5 114 18 0.0 5 15 2 0 0 1 115 181 0.0 5 176 3 0 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_7_R1_val_1_val_1.fq.gz ============================================= 82527069 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_7_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_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 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/Hawes/analyses/trimgalore-2/zr3644_7_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 2303.78 s (28 µs/read; 2.15 M reads/minute). === Summary === Total reads processed: 82,527,069 Reads with adapters: 7,696,946 (9.3%) Reads written (passing filters): 82,527,069 (100.0%) Total basepairs processed: 8,745,942,082 bp Quality-trimmed: 4,556,505 bp (0.1%) Total written (filtered): 8,621,287,967 bp (98.6%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 7696946 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: 13.4% C: 5.4% G: 0.0% T: 81.2% 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 4938970 20631767.2 0 4938970 2 1311581 5157941.8 0 1311581 3 291073 1289485.5 0 291073 4 81617 322371.4 0 81617 5 25058 80592.8 0 25058 6 7271 20148.2 0 7271 7 2792 5037.1 0 2792 8 1512 1259.3 0 1512 9 1252 314.8 0 1252 10 4939 78.7 1 1261 3678 11 4138 19.7 1 1076 3062 12 3233 4.9 1 907 2326 13 3049 1.2 1 871 2178 14 2472 0.3 1 739 1733 15 2074 0.1 1 681 1393 16 1718 0.0 1 522 1196 17 1290 0.0 1 442 848 18 932 0.0 1 446 486 19 871 0.0 1 383 488 20 2377 0.0 2 532 521 1324 21 2116 0.0 2 496 416 1204 22 1995 0.0 2 502 384 1109 23 1674 0.0 2 447 355 872 24 1547 0.0 2 415 369 763 25 1461 0.0 2 393 322 746 26 1230 0.0 2 361 280 589 27 1015 0.0 2 344 223 448 28 827 0.0 2 344 206 277 29 753 0.0 2 319 163 271 30 1485 0.0 3 320 189 230 746 31 1484 0.0 3 357 182 260 685 32 1370 0.0 3 282 188 227 673 33 1322 0.0 3 305 185 187 645 34 1151 0.0 3 224 161 208 558 35 1104 0.0 3 268 168 184 484 36 997 0.0 3 258 158 171 410 37 892 0.0 3 285 140 144 323 38 773 0.0 3 274 137 147 215 39 683 0.0 3 233 122 130 198 40 1197 0.0 4 194 131 136 188 548 41 1168 0.0 4 230 132 122 163 521 42 1138 0.0 4 209 136 124 195 474 43 1063 0.0 4 212 121 123 169 438 44 998 0.0 4 198 125 102 161 412 45 1004 0.0 4 205 108 137 162 392 46 944 0.0 4 242 120 101 135 346 47 848 0.0 4 228 133 115 99 273 48 989 0.0 4 265 196 180 175 173 49 2839 0.0 4 717 591 540 524 467 50 3012 0.0 5 653 529 521 442 450 417 51 2289 0.0 5 668 418 368 310 272 253 52 2116 0.0 5 685 399 324 245 250 213 53 1898 0.0 5 690 358 298 214 187 151 54 1707 0.0 5 639 361 236 179 138 154 55 1483 0.0 5 623 299 178 146 128 109 56 1485 0.0 5 676 290 199 129 98 93 57 1381 0.0 5 613 254 177 130 110 97 58 1235 0.0 5 556 243 162 112 84 78 59 1186 0.0 5 577 233 133 102 73 68 60 1142 0.0 5 555 211 145 88 80 63 61 1084 0.0 5 557 209 119 96 47 56 62 1091 0.0 5 562 176 145 97 69 42 63 1107 0.0 5 582 205 125 86 58 51 64 1028 0.0 5 558 186 96 87 65 36 65 1037 0.0 5 610 173 98 70 48 38 66 1021 0.0 5 620 178 101 48 35 39 67 1062 0.0 5 653 191 81 59 40 38 68 1031 0.0 5 652 156 98 51 44 30 69 1193 0.0 5 817 183 69 51 35 38 70 1033 0.0 5 713 129 77 44 46 24 71 840 0.0 5 565 128 52 39 33 23 72 873 0.0 5 580 124 55 52 35 27 73 863 0.0 5 591 131 59 36 24 22 74 871 0.0 5 600 125 60 30 34 22 75 931 0.0 5 697 93 46 42 37 16 76 835 0.0 5 583 110 58 35 24 25 77 823 0.0 5 615 94 45 29 26 14 78 683 0.0 5 494 78 55 23 17 16 79 742 0.0 5 559 69 45 31 25 13 80 653 0.0 5 460 82 54 27 11 19 81 626 0.0 5 441 82 36 35 14 18 82 610 0.0 5 458 63 34 15 26 14 83 585 0.0 5 434 69 28 27 18 9 84 615 0.0 5 464 63 31 21 19 17 85 568 0.0 5 420 61 32 19 17 19 86 614 0.0 5 461 71 31 25 16 10 87 548 0.0 5 422 52 32 24 9 9 88 650 0.0 5 519 59 29 22 13 8 89 601 0.0 5 468 61 25 25 11 11 90 510 0.0 5 396 53 28 17 10 6 91 490 0.0 5 355 56 21 25 17 16 92 549 0.0 5 443 46 21 15 14 10 93 430 0.0 5 326 42 35 16 8 3 94 395 0.0 5 296 35 21 20 13 10 95 523 0.0 5 410 47 24 22 10 10 96 488 0.0 5 350 71 24 16 11 16 97 450 0.0 5 350 41 20 11 13 15 98 390 0.0 5 298 41 17 9 12 13 99 543 0.0 5 440 42 23 18 12 8 100 382 0.0 5 281 42 19 12 16 12 101 592 0.0 5 498 36 13 14 22 9 102 525 0.0 5 410 55 25 10 13 12 103 489 0.0 5 408 22 27 14 11 7 104 371 0.0 5 290 41 17 11 7 5 105 570 0.0 5 448 53 25 15 15 14 106 406 0.0 5 314 31 18 16 14 13 107 493 0.0 5 396 44 29 6 11 7 108 447 0.0 5 352 36 15 17 20 7 109 744 0.0 5 522 94 85 18 16 9 110 621 0.0 5 480 66 26 21 15 13 111 631 0.0 5 452 65 30 29 28 27 112 1310 0.0 5 1074 88 45 30 46 27 113 1481 0.0 5 1192 124 52 47 39 27 114 5152 0.0 5 4700 220 81 73 50 28 115 910526 0.0 5 908979 1088 235 93 62 69 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/Hawes/analyses/trimgalore-2/zr3644_7_R2_val_2_val_2.fq.gz ============================================= 82527069 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_7_R1_val_1_val_1_trimmed.fq.gz and zr3644_7_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_7_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_7_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_7_R1_val_1_val_1_trimmed.fq.gz and zr3644_7_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_7_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_7_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 82527069 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 954320 (1.16%) >>> Now running FastQC on the validated data zr3644_7_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_7_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_7_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_7_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_7_R1_val_1_val_1_trimmed.fq.gz and zr3644_7_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_8_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_8_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_8_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1155.97 s (27 µs/read; 2.23 M reads/minute). === Summary === Total reads processed: 42,918,508 Reads with adapters: 4,384,318 (10.2%) Reads written (passing filters): 42,918,508 (100.0%) Total basepairs processed: 4,525,581,956 bp Quality-trimmed: 1,647,187 bp (0.0%) Total written (filtered): 4,474,545,072 bp (98.9%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4384318 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: 4.7% G: 0.0% T: 73.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2768608 10729627.0 0 2768608 2 765069 2682406.8 0 765069 3 165244 670601.7 0 165244 4 45703 167650.4 0 45703 5 13670 41912.6 0 13670 6 3911 10478.2 0 3911 7 1880 2619.5 0 1880 8 1250 654.9 0 1250 9 1231 163.7 0 1231 10 2481 40.9 1 1116 1365 11 2224 10.2 1 1063 1161 12 1914 2.6 1 894 1020 13 1795 0.6 1 897 898 14 1571 0.2 1 822 749 15 1340 0.0 1 663 677 16 1196 0.0 1 600 596 17 960 0.0 1 476 484 18 792 0.0 1 444 348 19 765 0.0 1 458 307 20 1090 0.0 2 416 251 423 21 1029 0.0 2 399 275 355 22 929 0.0 2 377 260 292 23 940 0.0 2 410 227 303 24 834 0.0 2 370 212 252 25 782 0.0 2 328 212 242 26 716 0.0 2 326 206 184 27 639 0.0 2 276 156 207 28 596 0.0 2 277 166 153 29 569 0.0 2 269 172 128 30 753 0.0 3 256 169 139 189 31 744 0.0 3 291 158 120 175 32 680 0.0 3 244 129 129 178 33 648 0.0 3 249 155 102 142 34 687 0.0 3 248 155 118 166 35 595 0.0 3 218 137 107 133 36 574 0.0 3 218 124 101 131 37 558 0.0 3 207 131 96 124 38 501 0.0 3 184 139 90 88 39 539 0.0 3 216 126 93 104 40 595 0.0 4 172 116 81 88 138 41 624 0.0 4 213 105 92 93 121 42 630 0.0 4 210 133 84 83 120 43 518 0.0 4 151 99 84 78 106 44 491 0.0 4 163 101 73 61 93 45 503 0.0 4 176 94 82 68 83 46 523 0.0 4 173 123 84 63 80 47 505 0.0 4 169 114 74 62 86 48 634 0.0 4 238 149 98 86 63 49 1098 0.0 4 450 271 148 122 107 50 1363 0.0 5 585 239 196 140 115 88 51 959 0.0 5 515 157 116 67 58 46 52 927 0.0 5 527 162 90 53 62 33 53 846 0.0 5 532 126 86 47 35 20 54 864 0.0 5 534 146 89 41 36 18 55 918 0.0 5 619 140 69 43 30 17 56 1003 0.0 5 700 158 59 33 35 18 57 885 0.0 5 628 128 62 30 20 17 58 988 0.0 5 724 136 50 38 30 10 59 1089 0.0 5 809 148 69 22 23 18 60 876 0.0 5 611 151 52 28 20 14 61 855 0.0 5 624 125 46 31 12 17 62 1001 0.0 5 755 136 61 33 5 11 63 1057 0.0 5 877 100 40 11 13 16 64 1496 0.0 5 1271 123 46 22 20 14 65 1006 0.0 5 811 104 44 37 7 3 66 1125 0.0 5 928 105 43 25 11 13 67 1317 0.0 5 1082 137 45 28 16 9 68 1745 0.0 5 1510 153 40 22 13 7 69 2253 0.0 5 2010 165 39 20 12 7 70 3921 0.0 5 3654 179 48 20 12 8 71 8074 0.0 5 7755 221 59 17 16 6 72 26905 0.0 5 26518 296 57 18 8 8 73 66719 0.0 5 66254 334 87 24 11 9 74 274975 0.0 5 274048 761 105 35 17 9 75 19916 0.0 5 19714 134 30 22 8 8 76 16152 0.0 5 15956 140 32 10 6 8 77 57053 0.0 5 56803 188 36 5 14 7 78 9143 0.0 5 9017 79 23 14 7 3 79 37104 0.0 5 36907 132 25 20 14 6 80 10321 0.0 5 10201 70 23 16 8 3 81 5944 0.0 5 5830 71 25 4 6 8 82 12166 0.0 5 12067 61 22 8 4 4 83 2626 0.0 5 2538 48 18 12 5 5 84 5023 0.0 5 4904 76 14 12 7 10 85 1123 0.0 5 1064 32 10 7 3 7 86 211 0.0 5 158 27 9 8 3 6 87 161 0.0 5 117 21 14 6 2 1 88 192 0.0 5 125 26 18 17 6 89 165 0.0 5 118 25 9 5 4 4 90 145 0.0 5 91 25 9 9 4 7 91 141 0.0 5 104 15 7 7 6 2 92 121 0.0 5 74 17 15 4 7 4 93 125 0.0 5 83 21 10 2 8 1 94 137 0.0 5 90 17 13 10 4 3 95 104 0.0 5 60 17 12 7 3 5 96 90 0.0 5 53 15 10 7 3 2 97 98 0.0 5 53 12 14 8 7 4 98 98 0.0 5 58 10 10 9 7 4 99 80 0.0 5 47 12 8 8 2 3 100 69 0.0 5 45 11 5 5 1 2 101 70 0.0 5 48 9 4 3 3 3 102 60 0.0 5 37 9 6 2 3 3 103 44 0.0 5 24 7 4 4 2 3 104 54 0.0 5 36 11 3 1 1 2 105 34 0.0 5 24 3 1 4 2 106 28 0.0 5 19 2 1 0 3 3 107 27 0.0 5 14 4 3 1 3 2 108 27 0.0 5 23 1 1 2 109 14 0.0 5 7 3 1 1 0 2 110 17 0.0 5 9 1 3 0 2 2 111 14 0.0 5 10 4 112 11 0.0 5 8 1 1 0 0 1 113 9 0.0 5 6 1 0 1 0 1 114 9 0.0 5 6 0 0 1 1 1 115 97 0.0 5 90 3 3 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_8_R1_val_1_val_1.fq.gz ============================================= 42918508 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_8_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_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/Hawes/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 zr3644_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/Hawes/analyses/trimgalore-2/zr3644_8_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_8_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1199.79 s (28 µs/read; 2.15 M reads/minute). === Summary === Total reads processed: 42,918,508 Reads with adapters: 4,143,181 (9.7%) Reads written (passing filters): 42,918,508 (100.0%) Total basepairs processed: 4,522,542,178 bp Quality-trimmed: 2,342,546 bp (0.1%) Total written (filtered): 4,447,873,960 bp (98.3%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4143181 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: 13.5% C: 5.5% G: 0.0% T: 81.0% 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 2598487 10729627.0 0 2598487 2 704002 2682406.8 0 704002 3 155146 670601.7 0 155146 4 43172 167650.4 0 43172 5 12992 41912.6 0 12992 6 3775 10478.2 0 3775 7 1499 2619.5 0 1499 8 780 654.9 0 780 9 659 163.7 0 659 10 2409 40.9 1 547 1862 11 2056 10.2 1 535 1521 12 1660 2.6 1 455 1205 13 1419 0.6 1 414 1005 14 1160 0.2 1 363 797 15 1154 0.0 1 347 807 16 943 0.0 1 313 630 17 666 0.0 1 219 447 18 513 0.0 1 245 268 19 414 0.0 1 175 239 20 1151 0.0 2 270 225 656 21 1106 0.0 2 259 212 635 22 994 0.0 2 222 192 580 23 887 0.0 2 225 190 472 24 780 0.0 2 197 160 423 25 724 0.0 2 208 162 354 26 591 0.0 2 165 135 291 27 502 0.0 2 169 100 233 28 414 0.0 2 166 97 151 29 395 0.0 2 163 104 128 30 754 0.0 3 154 93 137 370 31 688 0.0 3 157 84 119 328 32 642 0.0 3 126 75 129 312 33 667 0.0 3 144 88 115 320 34 604 0.0 3 124 87 95 298 35 566 0.0 3 129 73 106 258 36 547 0.0 3 145 92 91 219 37 435 0.0 3 138 74 63 160 38 390 0.0 3 125 82 71 112 39 363 0.0 3 109 65 73 116 40 650 0.0 4 107 61 75 116 291 41 589 0.0 4 121 74 73 87 234 42 585 0.0 4 111 72 70 89 243 43 577 0.0 4 120 46 90 95 226 44 450 0.0 4 84 53 55 88 170 45 462 0.0 4 108 48 51 77 178 46 476 0.0 4 130 64 56 81 145 47 437 0.0 4 115 68 67 68 119 48 525 0.0 4 123 132 100 72 98 49 1308 0.0 4 340 271 277 228 192 50 1445 0.0 5 311 270 236 232 209 187 51 1154 0.0 5 351 223 185 156 112 127 52 1068 0.0 5 343 194 167 143 122 99 53 960 0.0 5 358 191 123 122 91 75 54 837 0.0 5 329 162 127 96 67 56 55 768 0.0 5 319 138 98 78 60 75 56 780 0.0 5 339 162 88 84 60 47 57 700 0.0 5 329 136 82 60 54 39 58 591 0.0 5 259 120 89 57 40 26 59 576 0.0 5 288 110 67 39 39 33 60 529 0.0 5 256 108 55 42 47 21 61 531 0.0 5 284 108 48 31 30 30 62 501 0.0 5 254 109 63 36 16 23 63 535 0.0 5 292 99 62 29 25 28 64 499 0.0 5 279 89 56 35 26 14 65 586 0.0 5 347 101 51 39 25 23 66 520 0.0 5 336 73 43 27 20 21 67 535 0.0 5 342 81 49 30 16 17 68 497 0.0 5 312 85 40 23 26 11 69 589 0.0 5 420 84 27 18 20 20 70 537 0.0 5 369 84 31 20 24 9 71 453 0.0 5 298 61 37 23 18 16 72 471 0.0 5 336 44 37 19 22 13 73 415 0.0 5 301 47 23 20 9 15 74 436 0.0 5 311 51 30 19 17 8 75 516 0.0 5 396 47 33 19 8 13 76 461 0.0 5 330 65 25 18 12 11 77 460 0.0 5 349 50 22 24 8 7 78 366 0.0 5 271 46 24 11 9 5 79 454 0.0 5 346 48 27 19 10 4 80 412 0.0 5 315 54 20 9 9 5 81 387 0.0 5 294 45 21 12 7 8 82 330 0.0 5 242 40 16 11 11 10 83 326 0.0 5 236 47 22 10 6 5 84 398 0.0 5 302 45 18 9 12 12 85 327 0.0 5 233 49 16 7 10 12 86 332 0.0 5 245 39 25 9 10 4 87 277 0.0 5 224 21 12 8 6 6 88 368 0.0 5 312 29 12 5 4 6 89 325 0.0 5 259 23 16 11 9 7 90 277 0.0 5 216 24 14 5 10 8 91 254 0.0 5 189 30 16 7 7 5 92 309 0.0 5 249 27 18 6 5 4 93 236 0.0 5 189 20 17 2 3 5 94 227 0.0 5 176 20 11 7 6 7 95 290 0.0 5 233 31 14 2 6 4 96 282 0.0 5 217 35 11 4 8 7 97 266 0.0 5 186 36 23 6 8 7 98 186 0.0 5 145 16 8 7 6 4 99 307 0.0 5 258 25 8 8 3 5 100 208 0.0 5 154 26 8 8 7 5 101 325 0.0 5 265 24 15 11 6 4 102 323 0.0 5 267 25 8 11 7 5 103 274 0.0 5 229 19 12 4 3 7 104 254 0.0 5 192 21 15 6 12 8 105 328 0.0 5 273 22 14 9 6 4 106 233 0.0 5 188 17 5 10 10 3 107 265 0.0 5 213 30 5 6 6 5 108 266 0.0 5 215 19 11 6 10 5 109 379 0.0 5 258 48 43 10 9 11 110 364 0.0 5 293 32 8 17 9 5 111 304 0.0 5 230 28 14 14 8 10 112 729 0.0 5 604 41 29 22 14 19 113 886 0.0 5 740 71 30 17 14 14 114 3020 0.0 5 2760 135 47 39 25 14 115 557972 0.0 5 557092 671 103 58 25 23 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/Hawes/analyses/trimgalore-2/zr3644_8_R2_val_2_val_2.fq.gz ============================================= 42918508 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_8_R1_val_1_val_1_trimmed.fq.gz and zr3644_8_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_8_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_8_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_8_R1_val_1_val_1_trimmed.fq.gz and zr3644_8_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_8_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_8_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 42918508 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 581663 (1.36%) >>> Now running FastQC on the validated data zr3644_8_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_8_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_8_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_8_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_8_R1_val_1_val_1_trimmed.fq.gz and zr3644_8_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_9_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_9_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/Hawes/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 zr3644_9_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/Hawes/analyses/trimgalore-2/zr3644_9_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_9_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1267.87 s (26 µs/read; 2.31 M reads/minute). === Summary === Total reads processed: 48,723,657 Reads with adapters: 5,495,904 (11.3%) Reads written (passing filters): 48,723,657 (100.0%) Total basepairs processed: 5,033,175,847 bp Quality-trimmed: 1,723,200 bp (0.0%) Total written (filtered): 4,938,658,194 bp (98.1%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5495904 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: 26.9% C: 4.6% G: 0.0% T: 68.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3134508 12180914.2 0 3134508 2 892961 3045228.6 0 892961 3 192992 761307.1 0 192992 4 54577 190326.8 0 54577 5 16809 47581.7 0 16809 6 5066 11895.4 0 5066 7 2304 2973.9 0 2304 8 1580 743.5 0 1580 9 1522 185.9 0 1522 10 3088 46.5 1 1427 1661 11 2759 11.6 1 1333 1426 12 2375 2.9 1 1222 1153 13 2208 0.7 1 1080 1128 14 1970 0.2 1 1015 955 15 1568 0.0 1 729 839 16 1378 0.0 1 722 656 17 1205 0.0 1 630 575 18 940 0.0 1 580 360 19 899 0.0 1 518 381 20 1335 0.0 2 518 301 516 21 1228 0.0 2 497 308 423 22 1160 0.0 2 508 266 386 23 1075 0.0 2 489 260 326 24 1035 0.0 2 447 266 322 25 957 0.0 2 439 256 262 26 836 0.0 2 377 192 267 27 806 0.0 2 360 215 231 28 736 0.0 2 376 211 149 29 702 0.0 2 338 225 139 30 929 0.0 3 340 184 176 229 31 878 0.0 3 311 185 126 256 32 831 0.0 3 309 192 132 198 33 743 0.0 3 283 148 124 188 34 820 0.0 3 299 194 117 210 35 778 0.0 3 292 188 127 171 36 672 0.0 3 268 128 111 165 37 672 0.0 3 258 148 117 149 38 628 0.0 3 254 143 115 116 39 610 0.0 3 275 131 103 101 40 743 0.0 4 245 151 98 74 175 41 749 0.0 4 267 143 96 116 127 42 723 0.0 4 235 151 104 92 141 43 685 0.0 4 205 145 89 84 162 44 677 0.0 4 215 122 91 92 157 45 666 0.0 4 216 140 109 74 127 46 676 0.0 4 222 138 92 107 117 47 690 0.0 4 259 150 93 85 103 48 746 0.0 4 293 170 101 91 91 49 1558 0.0 4 666 355 221 185 131 50 1801 0.0 5 826 319 217 171 125 143 51 1385 0.0 5 715 264 154 115 83 54 52 1331 0.0 5 770 232 121 91 60 57 53 1059 0.0 5 648 186 97 60 38 30 54 1222 0.0 5 771 213 100 62 48 28 55 1374 0.0 5 963 193 106 60 30 22 56 1480 0.0 5 1049 219 84 67 39 22 57 1374 0.0 5 1034 169 75 47 33 16 58 1550 0.0 5 1185 170 98 51 26 20 59 1860 0.0 5 1489 183 88 45 34 21 60 1276 0.0 5 900 239 70 37 17 13 61 1340 0.0 5 1025 189 64 27 20 15 62 1537 0.0 5 1216 183 77 33 16 12 63 1703 0.0 5 1418 167 61 29 19 9 64 2600 0.0 5 2291 189 64 19 21 16 65 1560 0.0 5 1235 181 62 35 27 20 66 1898 0.0 5 1550 213 69 38 18 10 67 2080 0.0 5 1782 195 60 20 13 10 68 2772 0.0 5 2416 238 67 24 15 12 69 3689 0.0 5 3357 210 68 27 14 13 70 6439 0.0 5 6062 255 73 27 10 12 71 13230 0.0 5 12740 360 81 29 15 5 72 49277 0.0 5 48653 500 71 32 16 5 73 110423 0.0 5 109672 590 106 25 21 9 74 578072 0.0 5 576285 1565 171 31 10 10 75 51191 0.0 5 50812 264 68 29 11 7 76 29762 0.0 5 29506 178 42 21 7 8 77 116649 0.0 5 116229 336 58 21 0 5 78 17605 0.0 5 17426 128 27 12 11 1 79 72726 0.0 5 72470 198 39 7 9 3 80 20121 0.0 5 19957 97 35 15 9 8 81 11628 0.0 5 11500 76 21 8 13 10 82 23137 0.0 5 22998 86 30 14 4 5 83 3931 0.0 5 3799 86 18 15 3 10 84 5112 0.0 5 4973 92 20 13 8 6 85 2238 0.0 5 2131 60 21 14 7 5 86 299 0.0 5 209 41 26 12 8 3 87 232 0.0 5 152 34 20 15 8 3 88 236 0.0 5 166 31 11 9 11 8 89 194 0.0 5 124 25 23 8 9 5 90 207 0.0 5 149 25 14 10 5 4 91 207 0.0 5 154 19 8 11 10 5 92 169 0.0 5 117 20 13 9 6 4 93 169 0.0 5 118 26 11 6 3 5 94 158 0.0 5 97 25 10 13 7 6 95 146 0.0 5 94 24 12 5 5 6 96 150 0.0 5 99 23 7 9 9 3 97 132 0.0 5 83 18 14 7 5 5 98 107 0.0 5 77 12 2 8 5 3 99 99 0.0 5 64 11 11 4 6 3 100 102 0.0 5 67 9 11 3 7 5 101 97 0.0 5 62 11 9 5 8 2 102 92 0.0 5 56 11 7 7 7 4 103 59 0.0 5 43 8 2 3 2 1 104 54 0.0 5 40 8 3 0 1 2 105 36 0.0 5 27 3 1 1 3 1 106 48 0.0 5 31 5 4 4 2 2 107 40 0.0 5 30 3 2 3 1 1 108 40 0.0 5 25 5 4 2 1 3 109 33 0.0 5 18 5 6 0 1 3 110 25 0.0 5 14 2 4 3 1 1 111 23 0.0 5 19 1 1 0 0 2 112 23 0.0 5 17 1 1 0 2 2 113 18 0.0 5 11 1 1 1 1 3 114 15 0.0 5 12 2 0 1 115 209 0.0 5 198 6 0 2 2 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_9_R1_val_1_val_1.fq.gz ============================================= 48723657 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_9_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_9_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/Hawes/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 zr3644_9_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/Hawes/analyses/trimgalore-2/zr3644_9_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_9_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1283.62 s (26 µs/read; 2.28 M reads/minute). === Summary === Total reads processed: 48,723,657 Reads with adapters: 5,209,964 (10.7%) Reads written (passing filters): 48,723,657 (100.0%) Total basepairs processed: 5,030,415,232 bp Quality-trimmed: 2,391,524 bp (0.0%) Total written (filtered): 4,889,604,657 bp (97.2%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5209964 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: 13.6% C: 5.7% G: 0.0% T: 80.7% 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 2942525 12180914.2 0 2942525 2 814990 3045228.6 0 814990 3 179942 761307.1 0 179942 4 50935 190326.8 0 50935 5 15523 47581.7 0 15523 6 4388 11895.4 0 4388 7 1613 2973.9 0 1613 8 901 743.5 0 901 9 748 185.9 0 748 10 2608 46.5 1 716 1892 11 2093 11.6 1 627 1466 12 1743 2.9 1 557 1186 13 1568 0.7 1 505 1063 14 1343 0.2 1 486 857 15 1181 0.0 1 405 776 16 984 0.0 1 349 635 17 755 0.0 1 271 484 18 564 0.0 1 275 289 19 528 0.0 1 258 270 20 1252 0.0 2 306 281 665 21 1160 0.0 2 311 223 626 22 1047 0.0 2 285 240 522 23 1017 0.0 2 289 207 521 24 881 0.0 2 276 214 391 25 830 0.0 2 271 187 372 26 727 0.0 2 230 169 328 27 598 0.0 2 245 131 222 28 528 0.0 2 240 128 160 29 487 0.0 2 218 123 146 30 868 0.0 3 190 126 156 396 31 832 0.0 3 217 111 129 375 32 793 0.0 3 197 112 127 357 33 762 0.0 3 211 114 112 325 34 679 0.0 3 167 98 136 278 35 642 0.0 3 174 92 119 257 36 584 0.0 3 163 106 102 213 37 535 0.0 3 182 91 86 176 38 501 0.0 3 157 110 96 138 39 483 0.0 3 167 93 81 142 40 746 0.0 4 157 70 86 112 321 41 728 0.0 4 165 82 89 121 271 42 636 0.0 4 143 89 72 99 233 43 629 0.0 4 152 59 86 80 252 44 603 0.0 4 148 75 80 81 219 45 617 0.0 4 137 89 88 106 197 46 557 0.0 4 146 81 55 109 166 47 524 0.0 4 155 95 80 66 128 48 665 0.0 4 206 143 107 109 100 49 1741 0.0 4 543 364 304 276 254 50 1822 0.0 5 480 329 312 257 254 190 51 1410 0.0 5 478 288 193 170 146 135 52 1316 0.0 5 473 270 186 158 123 106 53 1172 0.0 5 499 223 147 118 115 70 54 1043 0.0 5 430 186 151 106 101 69 55 951 0.0 5 404 211 115 93 68 60 56 985 0.0 5 486 196 113 80 62 48 57 926 0.0 5 492 156 96 74 58 50 58 798 0.0 5 379 149 104 76 44 46 59 746 0.0 5 407 134 75 65 39 26 60 823 0.0 5 427 144 108 65 38 41 61 703 0.0 5 364 141 74 54 40 30 62 720 0.0 5 425 131 67 42 28 27 63 724 0.0 5 451 114 60 53 23 23 64 734 0.0 5 445 132 75 41 20 21 65 829 0.0 5 555 121 68 38 22 25 66 715 0.0 5 453 115 60 37 25 25 67 812 0.0 5 551 113 66 37 29 16 68 762 0.0 5 507 110 56 32 27 30 69 877 0.0 5 639 112 60 31 23 12 70 853 0.0 5 656 88 42 26 29 12 71 652 0.0 5 458 90 52 20 13 19 72 680 0.0 5 493 89 50 19 15 14 73 650 0.0 5 473 89 32 27 19 10 74 617 0.0 5 472 61 37 20 17 10 75 749 0.0 5 616 70 26 16 9 12 76 689 0.0 5 523 69 34 31 15 17 77 690 0.0 5 560 57 33 21 13 6 78 521 0.0 5 403 45 28 13 18 14 79 668 0.0 5 541 67 26 17 8 9 80 545 0.0 5 415 65 24 10 17 14 81 535 0.0 5 429 49 26 15 9 7 82 500 0.0 5 381 57 21 21 11 9 83 464 0.0 5 372 34 23 18 9 8 84 524 0.0 5 429 46 20 13 10 6 85 476 0.0 5 375 52 27 6 9 7 86 510 0.0 5 409 46 28 10 9 8 87 435 0.0 5 351 41 14 17 8 4 88 535 0.0 5 423 52 27 13 7 13 89 475 0.0 5 387 49 17 7 7 8 90 432 0.0 5 371 30 14 7 3 7 91 390 0.0 5 308 38 11 14 13 6 92 466 0.0 5 401 36 10 9 4 6 93 376 0.0 5 304 30 17 5 15 5 94 300 0.0 5 232 30 23 9 3 3 95 396 0.0 5 329 26 14 12 7 8 96 383 0.0 5 298 51 14 9 5 6 97 433 0.0 5 327 51 16 16 12 11 98 318 0.0 5 251 28 22 6 6 5 99 484 0.0 5 410 37 12 10 10 5 100 283 0.0 5 206 37 15 11 7 7 101 464 0.0 5 403 20 16 13 6 6 102 445 0.0 5 361 45 14 15 6 4 103 401 0.0 5 335 29 15 7 7 8 104 330 0.0 5 271 23 12 10 10 4 105 464 0.0 5 406 30 8 7 9 4 106 383 0.0 5 310 28 14 9 18 4 107 384 0.0 5 310 38 10 9 9 8 108 369 0.0 5 306 23 11 14 7 8 109 627 0.0 5 444 64 82 16 12 9 110 549 0.0 5 443 53 21 16 8 8 111 419 0.0 5 308 53 29 9 10 10 112 1077 0.0 5 932 59 29 20 17 20 113 1293 0.0 5 1079 102 55 17 22 18 114 4493 0.0 5 4133 197 55 52 32 24 115 1115785 0.0 5 1114524 961 163 74 35 28 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/Hawes/analyses/trimgalore-2/zr3644_9_R2_val_2_val_2.fq.gz ============================================= 48723657 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_9_R1_val_1_val_1_trimmed.fq.gz and zr3644_9_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_9_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_9_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_9_R1_val_1_val_1_trimmed.fq.gz and zr3644_9_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_9_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_9_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 48723657 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1149992 (2.36%) >>> Now running FastQC on the validated data zr3644_9_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_9_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_9_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_9_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_9_R1_val_1_val_1_trimmed.fq.gz and zr3644_9_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_10_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_10_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/Hawes/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 zr3644_10_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/Hawes/analyses/trimgalore-2/zr3644_10_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_10_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1404.33 s (27 µs/read; 2.25 M reads/minute). === Summary === Total reads processed: 52,562,481 Reads with adapters: 5,380,701 (10.2%) Reads written (passing filters): 52,562,481 (100.0%) Total basepairs processed: 5,537,936,665 bp Quality-trimmed: 1,931,281 bp (0.0%) Total written (filtered): 5,479,477,567 bp (98.9%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5380701 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: 20.8% C: 4.8% G: 0.0% T: 74.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3426678 13140620.2 0 3426678 2 960542 3285155.1 0 960542 3 205913 821288.8 0 205913 4 57186 205322.2 0 57186 5 17032 51330.5 0 17032 6 5247 12832.6 0 5247 7 2267 3208.2 0 2267 8 1655 802.0 0 1655 9 1515 200.5 0 1515 10 3090 50.1 1 1418 1672 11 2773 12.5 1 1323 1450 12 2506 3.1 1 1211 1295 13 2182 0.8 1 1091 1091 14 1929 0.2 1 980 949 15 1705 0.0 1 857 848 16 1448 0.0 1 753 695 17 1226 0.0 1 630 596 18 973 0.0 1 585 388 19 878 0.0 1 531 347 20 1306 0.0 2 527 329 450 21 1314 0.0 2 531 344 439 22 1251 0.0 2 562 304 385 23 1170 0.0 2 542 272 356 24 1120 0.0 2 518 285 317 25 988 0.0 2 412 277 299 26 910 0.0 2 433 217 260 27 834 0.0 2 406 205 223 28 744 0.0 2 372 204 168 29 768 0.0 2 404 210 154 30 967 0.0 3 341 222 155 249 31 887 0.0 3 335 201 150 201 32 826 0.0 3 339 193 126 168 33 714 0.0 3 284 157 113 160 34 819 0.0 3 290 193 147 189 35 738 0.0 3 269 185 124 160 36 685 0.0 3 274 147 125 139 37 668 0.0 3 269 169 94 136 38 623 0.0 3 265 136 117 105 39 587 0.0 3 237 151 99 100 40 739 0.0 4 268 138 115 93 125 41 735 0.0 4 248 162 110 90 125 42 742 0.0 4 273 154 93 85 137 43 692 0.0 4 241 124 89 100 138 44 682 0.0 4 237 138 97 91 119 45 657 0.0 4 206 129 96 99 127 46 664 0.0 4 227 152 97 96 92 47 634 0.0 4 248 132 94 75 85 48 712 0.0 4 290 160 106 94 62 49 1417 0.0 4 592 290 241 164 130 50 1545 0.0 5 661 312 168 149 141 114 51 1143 0.0 5 636 215 112 82 58 40 52 1079 0.0 5 627 183 98 76 48 47 53 862 0.0 5 539 146 60 57 33 27 54 942 0.0 5 582 171 77 54 32 26 55 1078 0.0 5 700 186 91 56 31 14 56 1174 0.0 5 841 167 78 43 30 15 57 1056 0.0 5 761 149 73 35 23 15 58 1103 0.0 5 813 140 64 44 21 21 59 1251 0.0 5 950 151 70 33 33 14 60 970 0.0 5 699 146 50 39 23 13 61 1042 0.0 5 776 143 57 29 29 8 62 1183 0.0 5 899 169 52 31 20 12 63 1304 0.0 5 1083 114 47 27 21 12 64 1597 0.0 5 1361 133 47 28 14 14 65 1108 0.0 5 854 138 69 23 12 12 66 1265 0.0 5 1029 135 52 26 11 12 67 1535 0.0 5 1294 143 41 24 18 15 68 2080 0.0 5 1789 178 62 30 13 8 69 2739 0.0 5 2441 198 64 21 6 9 70 4875 0.0 5 4603 182 44 27 12 7 71 10457 0.0 5 10115 250 53 24 10 5 72 31398 0.0 5 30987 310 61 25 10 5 73 88324 0.0 5 87787 434 68 15 9 11 74 293554 0.0 5 292588 825 113 17 7 4 75 25862 0.0 5 25617 164 46 17 8 10 76 20993 0.0 5 20792 139 34 10 10 8 77 59954 0.0 5 59679 184 41 25 16 9 78 11603 0.0 5 11469 72 35 14 11 2 79 36429 0.0 5 36260 117 21 13 11 7 80 10669 0.0 5 10517 93 33 14 5 7 81 7287 0.0 5 7168 78 16 14 8 3 82 12542 0.0 5 12399 94 25 13 7 4 83 5113 0.0 5 4977 82 26 9 11 8 84 8188 0.0 5 8040 103 19 10 11 5 85 1932 0.0 5 1830 49 24 9 14 6 86 341 0.0 5 264 36 20 9 8 4 87 227 0.0 5 162 35 12 10 3 5 88 197 0.0 5 134 28 12 11 8 4 89 183 0.0 5 127 22 15 6 6 7 90 207 0.0 5 136 30 16 14 4 7 91 172 0.0 5 116 28 14 7 4 3 92 157 0.0 5 111 17 15 10 3 1 93 153 0.0 5 109 15 10 7 8 4 94 139 0.0 5 105 14 13 2 3 2 95 152 0.0 5 94 23 17 7 5 6 96 129 0.0 5 89 15 11 8 1 5 97 94 0.0 5 62 15 7 3 6 1 98 110 0.0 5 76 13 7 6 4 4 99 92 0.0 5 60 14 6 6 3 3 100 84 0.0 5 50 9 10 6 5 4 101 94 0.0 5 65 7 6 9 4 3 102 82 0.0 5 48 10 7 10 5 2 103 67 0.0 5 41 13 6 4 2 1 104 56 0.0 5 37 5 2 6 3 3 105 45 0.0 5 32 3 5 0 2 3 106 53 0.0 5 37 3 5 4 3 1 107 39 0.0 5 25 3 5 2 1 3 108 27 0.0 5 18 4 0 2 2 1 109 17 0.0 5 10 2 0 3 1 1 110 20 0.0 5 13 2 2 1 1 1 111 16 0.0 5 13 0 1 0 1 1 112 16 0.0 5 11 2 0 0 2 1 113 12 0.0 5 10 0 0 1 0 1 114 12 0.0 5 9 1 0 2 115 134 0.0 5 133 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_10_R1_val_1_val_1.fq.gz ============================================= 52562481 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_10_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_10_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/Hawes/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 zr3644_10_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/Hawes/analyses/trimgalore-2/zr3644_10_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_10_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1442.63 s (27 µs/read; 2.19 M reads/minute). === Summary === Total reads processed: 52,562,481 Reads with adapters: 4,989,069 (9.5%) Reads written (passing filters): 52,562,481 (100.0%) Total basepairs processed: 5,534,104,698 bp Quality-trimmed: 2,667,788 bp (0.0%) Total written (filtered): 5,448,955,814 bp (98.5%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4989069 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: 13.5% C: 5.4% G: 0.0% T: 81.0% 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 3158430 13140620.2 0 3158430 2 855582 3285155.1 0 855582 3 189172 821288.8 0 189172 4 52982 205322.2 0 52982 5 15951 51330.5 0 15951 6 4513 12832.6 0 4513 7 1642 3208.2 0 1642 8 880 802.0 0 880 9 747 200.5 0 747 10 2681 50.1 1 671 2010 11 2382 12.5 1 646 1736 12 1866 3.1 1 513 1353 13 1625 0.8 1 478 1147 14 1447 0.2 1 433 1014 15 1216 0.0 1 370 846 16 991 0.0 1 352 639 17 774 0.0 1 261 513 18 553 0.0 1 260 293 19 494 0.0 1 239 255 20 1334 0.0 2 356 259 719 21 1210 0.0 2 286 257 667 22 1125 0.0 2 295 245 585 23 976 0.0 2 276 219 481 24 1003 0.0 2 283 199 521 25 837 0.0 2 263 165 409 26 811 0.0 2 269 190 352 27 668 0.0 2 241 125 302 28 507 0.0 2 219 127 161 29 515 0.0 2 225 122 168 30 890 0.0 3 221 112 150 407 31 879 0.0 3 188 104 162 425 32 836 0.0 3 177 107 170 382 33 746 0.0 3 187 111 110 338 34 679 0.0 3 159 99 128 293 35 674 0.0 3 163 115 133 263 36 654 0.0 3 178 94 125 257 37 557 0.0 3 178 92 97 190 38 521 0.0 3 182 98 98 143 39 491 0.0 3 169 108 88 126 40 748 0.0 4 154 93 79 109 313 41 736 0.0 4 176 76 80 113 291 42 677 0.0 4 129 83 82 110 273 43 662 0.0 4 127 82 69 110 274 44 617 0.0 4 134 83 71 108 221 45 583 0.0 4 147 58 70 93 215 46 634 0.0 4 182 100 70 89 193 47 570 0.0 4 184 97 81 59 149 48 590 0.0 4 165 115 96 115 99 49 1790 0.0 4 476 365 335 336 278 50 1852 0.0 5 431 348 286 300 257 230 51 1417 0.0 5 421 287 215 166 168 160 52 1228 0.0 5 411 255 181 149 127 105 53 1159 0.0 5 427 249 170 114 108 91 54 1041 0.0 5 417 204 145 115 91 69 55 903 0.0 5 406 185 114 87 63 48 56 999 0.0 5 488 174 122 80 65 70 57 852 0.0 5 429 152 97 69 59 46 58 807 0.0 5 388 152 100 70 53 44 59 735 0.0 5 398 128 76 58 38 37 60 758 0.0 5 397 129 79 76 42 35 61 702 0.0 5 349 142 82 69 31 29 62 712 0.0 5 397 125 60 58 30 42 63 737 0.0 5 441 130 66 43 35 22 64 692 0.0 5 392 142 68 37 35 18 65 729 0.0 5 466 119 58 37 23 26 66 671 0.0 5 423 106 51 41 21 29 67 788 0.0 5 500 140 61 34 26 27 68 712 0.0 5 462 118 59 37 23 13 69 780 0.0 5 558 94 54 39 22 13 70 708 0.0 5 531 88 30 23 19 17 71 547 0.0 5 397 63 30 30 10 17 72 556 0.0 5 391 84 23 30 19 9 73 509 0.0 5 374 64 29 17 8 17 74 535 0.0 5 385 71 30 19 13 17 75 647 0.0 5 501 80 26 17 11 12 76 523 0.0 5 372 69 32 19 18 13 77 541 0.0 5 417 57 31 19 12 5 78 455 0.0 5 332 55 24 18 17 9 79 502 0.0 5 377 55 28 16 14 12 80 434 0.0 5 324 45 27 13 15 10 81 457 0.0 5 358 36 23 10 16 14 82 420 0.0 5 308 55 23 12 13 9 83 402 0.0 5 304 47 25 6 10 10 84 472 0.0 5 383 47 11 12 9 10 85 393 0.0 5 294 51 20 14 7 7 86 371 0.0 5 294 38 17 8 6 8 87 339 0.0 5 258 32 22 14 7 6 88 450 0.0 5 380 32 15 11 6 6 89 387 0.0 5 307 44 13 11 5 7 90 368 0.0 5 293 34 12 7 9 13 91 337 0.0 5 248 32 16 15 18 8 92 382 0.0 5 315 36 7 12 5 7 93 289 0.0 5 231 23 21 8 4 2 94 309 0.0 5 231 37 12 14 4 11 95 330 0.0 5 256 31 10 10 11 12 96 344 0.0 5 253 33 23 16 14 5 97 325 0.0 5 243 35 22 10 11 4 98 269 0.0 5 202 28 14 10 9 6 99 360 0.0 5 288 28 16 12 7 9 100 254 0.0 5 188 28 11 10 9 8 101 385 0.0 5 325 28 14 7 4 7 102 388 0.0 5 314 39 14 10 5 6 103 335 0.0 5 273 27 12 12 9 2 104 306 0.0 5 253 18 13 9 9 4 105 415 0.0 5 353 25 17 4 8 8 106 327 0.0 5 261 28 13 11 9 5 107 356 0.0 5 291 32 16 6 8 3 108 317 0.0 5 256 24 11 14 10 2 109 492 0.0 5 342 56 59 19 9 7 110 487 0.0 5 390 45 19 14 7 12 111 415 0.0 5 312 36 25 15 16 11 112 939 0.0 5 750 81 43 24 19 22 113 1100 0.0 5 909 82 46 27 23 13 114 3568 0.0 5 3262 156 53 47 20 30 115 630302 0.0 5 629203 823 151 64 30 31 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/Hawes/analyses/trimgalore-2/zr3644_10_R2_val_2_val_2.fq.gz ============================================= 52562481 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_10_R1_val_1_val_1_trimmed.fq.gz and zr3644_10_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_10_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_10_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_10_R1_val_1_val_1_trimmed.fq.gz and zr3644_10_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_10_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_10_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 52562481 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 659769 (1.26%) >>> Now running FastQC on the validated data zr3644_10_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_10_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_10_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_10_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_10_R1_val_1_val_1_trimmed.fq.gz and zr3644_10_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_11_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_11_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/Hawes/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 zr3644_11_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/Hawes/analyses/trimgalore-2/zr3644_11_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_11_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1529.44 s (27 µs/read; 2.23 M reads/minute). === Summary === Total reads processed: 56,774,259 Reads with adapters: 5,732,334 (10.1%) Reads written (passing filters): 56,774,259 (100.0%) Total basepairs processed: 5,978,475,419 bp Quality-trimmed: 2,146,451 bp (0.0%) Total written (filtered): 5,915,242,593 bp (98.9%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5732334 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: 4.6% G: 0.0% T: 73.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3650659 14193564.8 0 3650659 2 1015310 3548391.2 0 1015310 3 218716 887097.8 0 218716 4 60337 221774.4 0 60337 5 17948 55443.6 0 17948 6 5413 13860.9 0 5413 7 2382 3465.2 0 2382 8 1645 866.3 0 1645 9 1659 216.6 0 1659 10 3270 54.1 1 1482 1788 11 2944 13.5 1 1393 1551 12 2674 3.4 1 1366 1308 13 2311 0.8 1 1158 1153 14 1970 0.2 1 1024 946 15 1733 0.1 1 857 876 16 1523 0.0 1 802 721 17 1218 0.0 1 620 598 18 1018 0.0 1 616 402 19 963 0.0 1 576 387 20 1426 0.0 2 584 313 529 21 1377 0.0 2 589 334 454 22 1283 0.0 2 569 327 387 23 1172 0.0 2 524 299 349 24 1069 0.0 2 513 266 290 25 1043 0.0 2 485 265 293 26 947 0.0 2 434 250 263 27 868 0.0 2 409 230 229 28 739 0.0 2 389 206 144 29 760 0.0 2 370 211 179 30 990 0.0 3 398 200 172 220 31 921 0.0 3 351 227 133 210 32 820 0.0 3 338 162 122 198 33 848 0.0 3 325 190 146 187 34 899 0.0 3 343 197 150 209 35 779 0.0 3 306 185 134 154 36 713 0.0 3 279 172 130 132 37 768 0.0 3 287 201 131 149 38 706 0.0 3 313 184 121 88 39 599 0.0 3 265 154 88 92 40 762 0.0 4 267 154 88 96 157 41 770 0.0 4 271 165 104 99 131 42 796 0.0 4 289 158 132 87 130 43 731 0.0 4 237 165 114 83 132 44 706 0.0 4 254 131 106 86 129 45 656 0.0 4 238 133 91 88 106 46 663 0.0 4 221 143 102 96 101 47 694 0.0 4 289 149 108 66 82 48 728 0.0 4 263 183 117 91 74 49 1409 0.0 4 609 302 202 160 136 50 1668 0.0 5 741 331 231 158 110 97 51 1284 0.0 5 693 240 136 94 69 52 52 1089 0.0 5 644 185 103 77 38 42 53 971 0.0 5 581 164 107 55 35 29 54 1028 0.0 5 630 165 97 62 48 26 55 1112 0.0 5 730 174 88 57 43 20 56 1085 0.0 5 751 166 73 40 32 23 57 1059 0.0 5 730 151 86 44 34 14 58 1168 0.0 5 879 146 65 38 27 13 59 1328 0.0 5 1042 154 71 27 25 9 60 994 0.0 5 697 177 52 34 21 13 61 1039 0.0 5 784 142 56 30 17 10 62 1106 0.0 5 845 154 52 23 22 10 63 1254 0.0 5 998 123 61 42 20 10 64 1770 0.0 5 1504 148 49 35 21 13 65 1098 0.0 5 853 129 58 22 19 17 66 1315 0.0 5 1040 159 56 42 11 7 67 1475 0.0 5 1209 173 48 21 17 7 68 1818 0.0 5 1543 175 53 21 21 5 69 2275 0.0 5 1978 197 56 24 13 7 70 3641 0.0 5 3376 171 52 17 20 5 71 7044 0.0 5 6714 227 52 34 7 10 72 30314 0.0 5 29876 333 63 25 11 6 73 51430 0.0 5 50956 370 55 25 12 12 74 368613 0.0 5 367342 1087 138 28 11 7 75 29835 0.0 5 29527 211 60 14 15 8 76 14470 0.0 5 14294 118 30 14 8 6 77 72864 0.0 5 72549 222 50 16 16 11 78 8948 0.0 5 8784 99 25 13 14 13 79 44683 0.0 5 44473 141 36 18 9 6 80 12681 0.0 5 12543 78 30 15 10 5 81 6529 0.0 5 6386 80 27 16 7 13 82 15673 0.0 5 15553 82 22 6 4 6 83 3984 0.0 5 3849 85 24 12 10 4 84 9845 0.0 5 9699 101 25 11 3 6 85 2290 0.0 5 2190 58 19 10 8 5 86 315 0.0 5 219 50 17 16 7 6 87 238 0.0 5 169 30 24 9 3 3 88 209 0.0 5 148 28 20 5 6 2 89 215 0.0 5 139 28 20 10 4 14 90 210 0.0 5 142 36 15 7 5 5 91 194 0.0 5 132 30 16 7 4 5 92 140 0.0 5 98 18 13 5 4 2 93 138 0.0 5 90 19 13 9 5 2 94 155 0.0 5 103 22 12 5 6 7 95 119 0.0 5 82 11 12 9 2 3 96 135 0.0 5 82 19 19 10 3 2 97 133 0.0 5 81 18 15 10 5 4 98 122 0.0 5 78 14 12 10 7 1 99 109 0.0 5 65 19 14 6 1 4 100 111 0.0 5 78 10 7 7 5 4 101 95 0.0 5 65 15 5 8 1 1 102 76 0.0 5 43 10 9 6 5 3 103 66 0.0 5 40 9 8 4 2 3 104 39 0.0 5 27 3 4 3 2 105 48 0.0 5 38 0 1 5 2 2 106 44 0.0 5 30 5 3 3 3 107 40 0.0 5 25 4 2 5 4 108 39 0.0 5 28 5 3 0 2 1 109 17 0.0 5 12 1 2 1 0 1 110 15 0.0 5 9 0 1 3 0 2 111 22 0.0 5 12 3 2 1 1 3 112 17 0.0 5 13 1 2 1 113 15 0.0 5 11 0 1 1 0 2 114 15 0.0 5 10 4 0 0 1 115 128 0.0 5 121 4 2 0 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_11_R1_val_1_val_1.fq.gz ============================================= 56774259 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_11_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_11_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/Hawes/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 zr3644_11_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/Hawes/analyses/trimgalore-2/zr3644_11_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_11_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1559.41 s (27 µs/read; 2.18 M reads/minute). === Summary === Total reads processed: 56,774,259 Reads with adapters: 5,376,084 (9.5%) Reads written (passing filters): 56,774,259 (100.0%) Total basepairs processed: 5,974,775,072 bp Quality-trimmed: 2,827,983 bp (0.0%) Total written (filtered): 5,883,233,315 bp (98.5%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5376084 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: 13.5% C: 5.2% G: 0.0% T: 81.3% 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 3408527 14193564.8 0 3408527 2 922948 3548391.2 0 922948 3 202718 887097.8 0 202718 4 56510 221774.4 0 56510 5 16839 55443.6 0 16839 6 4716 13860.9 0 4716 7 1608 3465.2 0 1608 8 948 866.3 0 948 9 765 216.6 0 765 10 2785 54.1 1 679 2106 11 2271 13.5 1 627 1644 12 1923 3.4 1 569 1354 13 1672 0.8 1 507 1165 14 1476 0.2 1 473 1003 15 1239 0.1 1 422 817 16 1064 0.0 1 368 696 17 799 0.0 1 291 508 18 594 0.0 1 282 312 19 573 0.0 1 298 275 20 1359 0.0 2 354 289 716 21 1234 0.0 2 345 247 642 22 1147 0.0 2 332 262 553 23 1044 0.0 2 319 206 519 24 943 0.0 2 298 173 472 25 957 0.0 2 297 195 465 26 777 0.0 2 265 174 338 27 680 0.0 2 296 136 248 28 546 0.0 2 253 130 163 29 538 0.0 2 228 153 157 30 919 0.0 3 249 125 154 391 31 865 0.0 3 227 102 146 390 32 797 0.0 3 204 122 139 332 33 773 0.0 3 220 110 107 336 34 748 0.0 3 186 128 125 309 35 709 0.0 3 208 105 131 265 36 686 0.0 3 205 100 107 274 37 555 0.0 3 174 109 82 190 38 535 0.0 3 178 116 101 140 39 503 0.0 3 180 95 100 128 40 772 0.0 4 183 93 76 134 286 41 766 0.0 4 187 97 87 90 305 42 701 0.0 4 142 86 84 113 276 43 706 0.0 4 148 97 77 123 261 44 638 0.0 4 143 91 86 108 210 45 629 0.0 4 155 94 82 96 202 46 582 0.0 4 164 85 56 102 175 47 651 0.0 4 211 106 88 75 171 48 673 0.0 4 191 145 126 104 107 49 1672 0.0 4 489 335 320 279 249 50 1904 0.0 5 501 363 306 253 269 212 51 1371 0.0 5 438 282 213 158 147 133 52 1295 0.0 5 439 292 199 136 111 118 53 1166 0.0 5 513 227 160 104 97 65 54 997 0.0 5 440 203 117 101 69 67 55 903 0.0 5 394 175 119 83 64 68 56 969 0.0 5 488 169 122 77 59 54 57 921 0.0 5 488 167 94 75 61 36 58 792 0.0 5 410 150 86 58 44 44 59 761 0.0 5 412 141 82 47 51 28 60 709 0.0 5 387 121 72 50 38 41 61 692 0.0 5 397 128 61 41 35 30 62 659 0.0 5 401 114 52 51 21 20 63 678 0.0 5 388 153 46 40 32 19 64 666 0.0 5 396 120 66 39 26 19 65 752 0.0 5 476 118 66 42 36 14 66 690 0.0 5 452 111 59 37 20 11 67 744 0.0 5 501 128 57 21 23 14 68 743 0.0 5 512 111 57 25 17 21 69 799 0.0 5 590 112 41 22 19 15 70 695 0.0 5 526 86 38 19 15 11 71 612 0.0 5 439 88 28 28 16 13 72 599 0.0 5 458 65 29 25 10 12 73 560 0.0 5 414 68 29 21 13 15 74 583 0.0 5 441 61 39 23 12 7 75 726 0.0 5 568 76 41 20 8 13 76 609 0.0 5 449 83 30 18 14 15 77 605 0.0 5 480 51 29 19 13 13 78 518 0.0 5 393 57 28 16 18 6 79 549 0.0 5 435 64 15 18 11 6 80 499 0.0 5 388 40 28 19 14 10 81 480 0.0 5 364 54 28 16 13 5 82 441 0.0 5 351 47 23 11 7 2 83 427 0.0 5 329 45 22 10 14 7 84 456 0.0 5 373 40 14 19 4 6 85 402 0.0 5 306 50 25 10 6 5 86 403 0.0 5 326 39 18 12 6 2 87 374 0.0 5 289 48 12 6 11 8 88 453 0.0 5 374 41 12 17 2 7 89 411 0.0 5 345 30 11 12 7 6 90 418 0.0 5 340 33 20 10 12 3 91 346 0.0 5 269 41 16 9 6 5 92 387 0.0 5 319 34 9 17 3 5 93 320 0.0 5 256 27 14 8 8 7 94 258 0.0 5 210 25 9 8 5 1 95 394 0.0 5 332 29 20 8 4 1 96 368 0.0 5 287 46 19 5 3 8 97 347 0.0 5 289 31 12 6 4 5 98 294 0.0 5 241 28 9 7 5 4 99 418 0.0 5 350 30 20 11 3 4 100 266 0.0 5 200 23 16 10 7 10 101 424 0.0 5 362 28 9 9 10 6 102 389 0.0 5 316 37 14 8 9 5 103 375 0.0 5 333 15 10 9 3 5 104 285 0.0 5 238 24 5 6 9 3 105 464 0.0 5 386 41 17 5 9 6 106 332 0.0 5 268 30 14 11 4 5 107 352 0.0 5 279 36 17 5 8 7 108 321 0.0 5 260 27 9 11 11 3 109 493 0.0 5 352 60 53 14 7 7 110 541 0.0 5 443 50 22 9 6 11 111 427 0.0 5 321 50 18 16 10 12 112 959 0.0 5 791 69 38 23 18 20 113 1068 0.0 5 881 86 39 29 17 16 114 3819 0.0 5 3502 164 67 35 28 23 115 679326 0.0 5 678197 871 134 68 30 26 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/Hawes/analyses/trimgalore-2/zr3644_11_R2_val_2_val_2.fq.gz ============================================= 56774259 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_11_R1_val_1_val_1_trimmed.fq.gz and zr3644_11_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_11_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_11_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_11_R1_val_1_val_1_trimmed.fq.gz and zr3644_11_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_11_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_11_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 56774259 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 710911 (1.25%) >>> Now running FastQC on the validated data zr3644_11_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_11_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_11_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_11_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_11_R1_val_1_val_1_trimmed.fq.gz and zr3644_11_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_12_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_12_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/Hawes/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 zr3644_12_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/Hawes/analyses/trimgalore-2/zr3644_12_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_12_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1268.68 s (27 µs/read; 2.25 M reads/minute). === Summary === Total reads processed: 47,649,823 Reads with adapters: 4,772,407 (10.0%) Reads written (passing filters): 47,649,823 (100.0%) Total basepairs processed: 5,027,464,006 bp Quality-trimmed: 1,642,861 bp (0.0%) Total written (filtered): 4,959,893,400 bp (98.7%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4772407 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: 4.2% G: 0.0% T: 72.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2942062 11912455.8 0 2942062 2 775633 2978113.9 0 775633 3 161258 744528.5 0 161258 4 43307 186132.1 0 43307 5 12400 46533.0 0 12400 6 3542 11633.3 0 3542 7 1646 2908.3 0 1646 8 1154 727.1 0 1154 9 1096 181.8 0 1096 10 2300 45.4 1 1027 1273 11 1858 11.4 1 860 998 12 1686 2.8 1 795 891 13 1470 0.7 1 711 759 14 1323 0.2 1 628 695 15 1126 0.0 1 577 549 16 954 0.0 1 497 457 17 750 0.0 1 386 364 18 609 0.0 1 347 262 19 593 0.0 1 380 213 20 912 0.0 2 402 222 288 21 811 0.0 2 334 211 266 22 792 0.0 2 348 210 234 23 720 0.0 2 316 200 204 24 644 0.0 2 309 155 180 25 627 0.0 2 300 166 161 26 617 0.0 2 269 171 177 27 472 0.0 2 226 134 112 28 454 0.0 2 229 123 102 29 452 0.0 2 223 135 94 30 619 0.0 3 229 138 89 163 31 607 0.0 3 227 109 114 157 32 548 0.0 3 194 126 85 143 33 538 0.0 3 203 126 73 136 34 547 0.0 3 198 129 109 111 35 445 0.0 3 168 120 67 90 36 447 0.0 3 165 107 82 93 37 438 0.0 3 177 98 83 80 38 426 0.0 3 173 101 84 68 39 404 0.0 3 166 100 75 63 40 490 0.0 4 160 106 73 64 87 41 466 0.0 4 159 95 64 66 82 42 489 0.0 4 155 117 69 63 85 43 448 0.0 4 156 87 57 59 89 44 442 0.0 4 151 98 73 56 64 45 435 0.0 4 147 87 55 50 96 46 435 0.0 4 168 101 51 53 62 47 439 0.0 4 146 101 77 55 60 48 505 0.0 4 192 127 91 56 39 49 929 0.0 4 387 220 163 89 70 50 1195 0.0 5 595 210 152 105 71 62 51 871 0.0 5 493 168 108 48 29 25 52 846 0.0 5 488 146 77 65 38 32 53 753 0.0 5 466 133 79 32 26 17 54 751 0.0 5 496 124 49 36 29 17 55 909 0.0 5 609 135 76 40 30 19 56 979 0.0 5 700 144 59 41 21 14 57 886 0.0 5 613 147 61 35 19 11 58 975 0.0 5 753 113 46 37 18 8 59 1267 0.0 5 990 148 65 29 23 12 60 836 0.0 5 580 146 59 24 18 9 61 912 0.0 5 690 128 39 26 14 15 62 983 0.0 5 745 150 50 21 11 6 63 1078 0.0 5 892 93 44 25 16 8 64 1849 0.0 5 1630 132 48 19 12 8 65 1080 0.0 5 852 137 44 28 11 8 66 1280 0.0 5 1049 137 42 28 12 12 67 1447 0.0 5 1183 141 66 25 23 9 68 1750 0.0 5 1484 186 50 14 8 8 69 2270 0.0 5 2046 140 45 18 12 9 70 3784 0.0 5 3501 201 45 14 18 5 71 7318 0.0 5 7006 223 44 21 17 7 72 32638 0.0 5 32197 348 63 16 9 5 73 52143 0.0 5 51639 395 76 19 8 6 74 428261 0.0 5 426797 1285 147 23 7 2 75 35524 0.0 5 35241 198 48 17 12 8 76 15564 0.0 5 15343 155 29 18 13 6 77 83772 0.0 5 83488 219 44 14 6 1 78 9260 0.0 5 9132 82 16 14 9 7 79 49613 0.0 5 49407 163 25 11 6 1 80 13507 0.0 5 13362 89 34 9 6 7 81 6973 0.0 5 6874 57 17 15 5 5 82 17228 0.0 5 17119 72 12 10 4 11 83 4549 0.0 5 4457 57 16 10 6 3 84 12667 0.0 5 12510 118 15 13 9 2 85 3064 0.0 5 2994 40 11 11 4 4 86 302 0.0 5 240 32 10 4 11 5 87 140 0.0 5 93 19 11 5 8 4 88 156 0.0 5 112 14 15 6 6 3 89 135 0.0 5 83 28 13 3 7 1 90 136 0.0 5 85 21 7 9 7 7 91 140 0.0 5 96 17 9 10 4 4 92 124 0.0 5 81 24 8 3 4 4 93 106 0.0 5 62 16 11 8 7 2 94 110 0.0 5 61 21 11 7 7 3 95 92 0.0 5 62 8 11 2 4 5 96 82 0.0 5 53 13 6 3 5 2 97 69 0.0 5 44 10 6 4 3 2 98 63 0.0 5 41 12 6 0 3 1 99 69 0.0 5 39 9 7 4 7 3 100 63 0.0 5 37 10 4 5 4 3 101 44 0.0 5 29 3 4 5 3 102 60 0.0 5 34 12 6 3 5 103 36 0.0 5 25 7 2 2 104 39 0.0 5 22 7 4 4 1 1 105 37 0.0 5 21 4 7 2 1 2 106 31 0.0 5 22 4 3 1 0 1 107 21 0.0 5 14 3 2 1 1 108 23 0.0 5 15 0 3 1 2 2 109 13 0.0 5 5 0 0 2 1 5 110 9 0.0 5 5 1 0 1 2 111 10 0.0 5 9 0 1 112 12 0.0 5 8 0 1 1 1 1 113 6 0.0 5 4 0 0 1 0 1 114 12 0.0 5 7 0 2 0 2 1 115 120 0.0 5 119 0 0 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_12_R1_val_1_val_1.fq.gz ============================================= 47649823 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_12_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_12_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/Hawes/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 zr3644_12_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/Hawes/analyses/trimgalore-2/zr3644_12_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_12_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1302.43 s (27 µs/read; 2.20 M reads/minute). === Summary === Total reads processed: 47,649,823 Reads with adapters: 4,531,436 (9.5%) Reads written (passing filters): 47,649,823 (100.0%) Total basepairs processed: 5,024,099,499 bp Quality-trimmed: 2,327,079 bp (0.0%) Total written (filtered): 4,923,989,958 bp (98.0%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4531436 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: 12.3% C: 5.0% G: 0.0% T: 82.6% 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 2773134 11912455.8 0 2773134 2 708218 2978113.9 0 708218 3 151674 744528.5 0 151674 4 40802 186132.1 0 40802 5 11526 46533.0 0 11526 6 3351 11633.3 0 3351 7 1133 2908.3 0 1133 8 679 727.1 0 679 9 583 181.8 0 583 10 2036 45.4 1 492 1544 11 1604 11.4 1 428 1176 12 1364 2.8 1 383 981 13 1153 0.7 1 338 815 14 968 0.2 1 289 679 15 860 0.0 1 295 565 16 693 0.0 1 241 452 17 540 0.0 1 184 356 18 383 0.0 1 189 194 19 355 0.0 1 165 190 20 918 0.0 2 215 183 520 21 884 0.0 2 261 176 447 22 843 0.0 2 236 185 422 23 744 0.0 2 216 142 386 24 661 0.0 2 189 147 325 25 669 0.0 2 221 154 294 26 574 0.0 2 190 133 251 27 411 0.0 2 156 79 176 28 411 0.0 2 177 93 141 29 367 0.0 2 143 97 127 30 665 0.0 3 154 88 96 327 31 668 0.0 3 159 85 120 304 32 637 0.0 3 169 81 115 272 33 586 0.0 3 147 87 103 249 34 515 0.0 3 132 70 94 219 35 441 0.0 3 114 74 75 178 36 490 0.0 3 149 74 80 187 37 424 0.0 3 148 77 63 136 38 374 0.0 3 152 75 58 89 39 354 0.0 3 140 73 54 87 40 562 0.0 4 125 63 73 69 232 41 557 0.0 4 133 71 57 86 210 42 535 0.0 4 126 62 69 82 196 43 518 0.0 4 120 61 57 90 190 44 479 0.0 4 101 64 56 78 180 45 456 0.0 4 128 62 50 66 150 46 449 0.0 4 138 53 51 76 131 47 443 0.0 4 122 74 66 71 110 48 480 0.0 4 143 93 96 73 75 49 1376 0.0 4 395 309 258 227 187 50 1449 0.0 5 373 296 242 202 178 158 51 1160 0.0 5 364 225 203 140 113 115 52 1117 0.0 5 412 213 165 122 106 99 53 973 0.0 5 382 204 123 114 76 74 54 876 0.0 5 349 182 117 98 69 61 55 757 0.0 5 327 168 95 68 56 43 56 829 0.0 5 415 164 93 63 59 35 57 790 0.0 5 384 163 92 64 50 37 58 605 0.0 5 283 124 65 58 40 35 59 604 0.0 5 340 108 60 54 26 16 60 596 0.0 5 319 109 62 52 32 22 61 568 0.0 5 293 115 70 43 20 27 62 601 0.0 5 341 100 61 28 41 30 63 614 0.0 5 360 95 62 45 28 24 64 577 0.0 5 352 98 51 37 23 16 65 630 0.0 5 401 108 44 33 29 15 66 594 0.0 5 375 96 45 33 29 16 67 663 0.0 5 434 97 66 33 19 14 68 644 0.0 5 447 100 42 28 13 14 69 730 0.0 5 562 89 26 21 19 13 70 647 0.0 5 489 74 41 25 12 6 71 518 0.0 5 388 62 23 18 17 10 72 460 0.0 5 344 54 21 17 14 10 73 516 0.0 5 374 68 30 21 15 8 74 553 0.0 5 431 51 33 16 14 8 75 614 0.0 5 478 70 27 17 10 12 76 499 0.0 5 380 63 23 15 13 5 77 546 0.0 5 440 57 20 15 8 6 78 428 0.0 5 337 47 16 15 9 4 79 510 0.0 5 405 48 23 14 12 8 80 411 0.0 5 306 54 26 9 9 7 81 442 0.0 5 339 54 23 9 9 8 82 378 0.0 5 294 49 13 10 7 5 83 343 0.0 5 270 36 19 6 10 2 84 418 0.0 5 334 32 20 16 11 5 85 379 0.0 5 311 40 14 10 2 2 86 391 0.0 5 309 44 16 14 7 1 87 370 0.0 5 305 35 11 10 6 3 88 466 0.0 5 397 43 9 5 7 5 89 381 0.0 5 319 28 16 5 8 5 90 360 0.0 5 301 28 13 7 3 8 91 294 0.0 5 238 30 9 11 1 5 92 353 0.0 5 308 23 8 3 6 5 93 278 0.0 5 224 22 19 7 3 3 94 265 0.0 5 221 15 10 11 4 4 95 334 0.0 5 279 31 6 8 5 5 96 366 0.0 5 283 44 19 8 6 6 97 318 0.0 5 256 32 13 5 8 4 98 222 0.0 5 166 24 6 10 9 7 99 371 0.0 5 315 21 17 7 7 4 100 255 0.0 5 206 29 7 6 4 3 101 446 0.0 5 388 27 12 9 3 7 102 387 0.0 5 327 32 11 4 8 5 103 356 0.0 5 305 22 12 9 3 5 104 258 0.0 5 211 18 13 7 7 2 105 410 0.0 5 362 28 10 3 4 3 106 313 0.0 5 261 33 12 2 2 3 107 357 0.0 5 276 42 17 4 11 7 108 322 0.0 5 271 26 16 3 3 3 109 481 0.0 5 343 67 52 9 8 2 110 495 0.0 5 394 53 23 9 10 6 111 412 0.0 5 315 34 19 17 14 13 112 866 0.0 5 703 81 28 23 17 14 113 1121 0.0 5 929 90 38 25 21 18 114 3908 0.0 5 3627 153 48 32 31 17 115 774694 0.0 5 773586 856 142 50 28 32 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/Hawes/analyses/trimgalore-2/zr3644_12_R2_val_2_val_2.fq.gz ============================================= 47649823 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_12_R1_val_1_val_1_trimmed.fq.gz and zr3644_12_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_12_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_12_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_12_R1_val_1_val_1_trimmed.fq.gz and zr3644_12_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_12_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_12_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 47649823 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 800252 (1.68%) >>> Now running FastQC on the validated data zr3644_12_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_12_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_12_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_12_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_12_R1_val_1_val_1_trimmed.fq.gz and zr3644_12_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_13_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_13_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/Hawes/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 zr3644_13_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/Hawes/analyses/trimgalore-2/zr3644_13_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_13_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1455.43 s (27 µs/read; 2.22 M reads/minute). === Summary === Total reads processed: 53,883,255 Reads with adapters: 5,317,560 (9.9%) Reads written (passing filters): 53,883,255 (100.0%) Total basepairs processed: 5,724,812,088 bp Quality-trimmed: 2,019,136 bp (0.0%) Total written (filtered): 5,672,570,928 bp (99.1%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5317560 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: 19.4% C: 4.6% G: 0.0% T: 76.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3464646 13470813.8 0 3464646 2 949824 3367703.4 0 949824 3 202256 841925.9 0 202256 4 55563 210481.5 0 55563 5 16106 52620.4 0 16106 6 5073 13155.1 0 5073 7 2241 3288.8 0 2241 8 1539 822.2 0 1539 9 1388 205.5 0 1388 10 2981 51.4 1 1359 1622 11 2582 12.8 1 1229 1353 12 2352 3.2 1 1135 1217 13 2153 0.8 1 1060 1093 14 1865 0.2 1 947 918 15 1599 0.1 1 819 780 16 1386 0.0 1 701 685 17 1138 0.0 1 613 525 18 897 0.0 1 541 356 19 828 0.0 1 507 321 20 1344 0.0 2 515 354 475 21 1250 0.0 2 516 298 436 22 1135 0.0 2 479 298 358 23 1128 0.0 2 489 284 355 24 937 0.0 2 411 252 274 25 924 0.0 2 431 248 245 26 872 0.0 2 383 236 253 27 736 0.0 2 352 188 196 28 673 0.0 2 329 214 130 29 662 0.0 2 307 198 157 30 874 0.0 3 305 206 142 221 31 858 0.0 3 317 178 149 214 32 780 0.0 3 299 176 109 196 33 782 0.0 3 288 176 135 183 34 782 0.0 3 284 181 130 187 35 732 0.0 3 285 171 121 155 36 658 0.0 3 276 133 123 126 37 626 0.0 3 260 140 102 124 38 591 0.0 3 270 152 87 82 39 528 0.0 3 237 107 87 97 40 664 0.0 4 231 126 88 86 133 41 720 0.0 4 256 136 91 100 137 42 704 0.0 4 214 145 100 98 147 43 685 0.0 4 205 143 116 94 127 44 562 0.0 4 178 106 89 77 112 45 541 0.0 4 166 136 77 65 97 46 610 0.0 4 201 140 88 76 105 47 670 0.0 4 259 153 76 93 89 48 664 0.0 4 246 165 109 83 61 49 1343 0.0 4 568 281 195 179 120 50 1393 0.0 5 635 267 173 122 104 92 51 1019 0.0 5 554 193 121 72 39 40 52 1037 0.0 5 590 173 113 62 55 44 53 804 0.0 5 478 130 80 54 41 21 54 883 0.0 5 540 157 76 48 35 27 55 976 0.0 5 647 157 70 48 29 25 56 1082 0.0 5 756 162 67 50 31 16 57 1110 0.0 5 789 165 71 44 27 14 58 1101 0.0 5 775 158 87 45 25 11 59 1027 0.0 5 752 150 64 32 21 8 60 862 0.0 5 600 144 57 35 17 9 61 960 0.0 5 713 137 45 36 18 11 62 1172 0.0 5 912 155 53 25 18 9 63 1280 0.0 5 1055 126 48 25 12 14 64 1298 0.0 5 1031 147 63 29 20 8 65 1076 0.0 5 849 129 51 21 18 8 66 1255 0.0 5 1022 130 47 37 11 8 67 1606 0.0 5 1363 152 42 25 14 10 68 2044 0.0 5 1803 140 42 29 23 7 69 3043 0.0 5 2767 188 52 18 9 9 70 5740 0.0 5 5470 184 42 25 15 4 71 13199 0.0 5 12865 234 64 22 7 7 72 34112 0.0 5 33698 312 63 21 13 5 73 114186 0.0 5 113539 538 61 19 22 7 74 214039 0.0 5 213350 596 67 16 7 3 75 23798 0.0 5 23558 167 48 14 7 4 76 24804 0.0 5 24601 151 28 11 7 6 77 44060 0.0 5 43851 161 23 12 6 7 78 14210 0.0 5 14077 84 29 9 7 4 79 28749 0.0 5 28594 97 26 14 11 7 80 9118 0.0 5 9007 66 15 18 4 8 81 7707 0.0 5 7574 87 20 14 7 5 82 7897 0.0 5 7784 66 24 6 9 8 83 3919 0.0 5 3793 89 15 10 9 3 84 3237 0.0 5 3121 67 26 11 7 5 85 582 0.0 5 510 35 14 8 4 11 86 236 0.0 5 161 33 19 9 8 6 87 188 0.0 5 131 26 14 5 8 4 88 169 0.0 5 122 20 8 6 7 6 89 178 0.0 5 109 25 24 7 9 4 90 189 0.0 5 132 28 13 9 5 2 91 177 0.0 5 118 29 14 5 6 5 92 146 0.0 5 100 19 10 5 7 5 93 130 0.0 5 86 19 8 8 4 5 94 129 0.0 5 84 18 11 9 5 2 95 109 0.0 5 71 10 8 13 2 5 96 110 0.0 5 68 16 9 9 5 3 97 108 0.0 5 65 23 8 4 6 2 98 90 0.0 5 62 12 4 4 6 2 99 95 0.0 5 50 26 6 9 4 100 79 0.0 5 50 11 5 4 5 4 101 70 0.0 5 41 15 6 4 3 1 102 82 0.0 5 53 7 12 6 3 1 103 47 0.0 5 33 7 3 1 2 1 104 53 0.0 5 35 3 6 3 2 4 105 44 0.0 5 26 7 3 4 2 2 106 36 0.0 5 24 2 1 4 3 2 107 37 0.0 5 26 4 2 3 2 108 27 0.0 5 18 1 0 4 0 4 109 20 0.0 5 10 6 0 0 3 1 110 21 0.0 5 17 0 2 1 0 1 111 15 0.0 5 12 2 0 1 112 15 0.0 5 11 3 0 1 113 8 0.0 5 3 0 3 2 114 8 0.0 5 4 1 1 0 0 2 115 107 0.0 5 102 4 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_13_R1_val_1_val_1.fq.gz ============================================= 53883255 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_13_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_13_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/Hawes/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 zr3644_13_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/Hawes/analyses/trimgalore-2/zr3644_13_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_13_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1500.86 s (28 µs/read; 2.15 M reads/minute). === Summary === Total reads processed: 53,883,255 Reads with adapters: 4,945,898 (9.2%) Reads written (passing filters): 53,883,255 (100.0%) Total basepairs processed: 5,721,640,887 bp Quality-trimmed: 2,829,016 bp (0.0%) Total written (filtered): 5,645,679,455 bp (98.7%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4945898 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: 13.4% C: 5.2% G: 0.0% T: 81.4% 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 3210896 13470813.8 0 3210896 2 849626 3367703.4 0 849626 3 186144 841925.9 0 186144 4 51710 210481.5 0 51710 5 15418 52620.4 0 15418 6 4215 13155.1 0 4215 7 1567 3288.8 0 1567 8 849 822.2 0 849 9 741 205.5 0 741 10 2761 51.4 1 723 2038 11 2284 12.8 1 597 1687 12 1818 3.2 1 535 1283 13 1626 0.8 1 528 1098 14 1299 0.2 1 395 904 15 1137 0.1 1 351 786 16 1008 0.0 1 345 663 17 783 0.0 1 277 506 18 531 0.0 1 275 256 19 499 0.0 1 213 286 20 1279 0.0 2 321 242 716 21 1190 0.0 2 316 248 626 22 1071 0.0 2 291 231 549 23 982 0.0 2 274 222 486 24 817 0.0 2 259 190 368 25 796 0.0 2 242 149 405 26 718 0.0 2 228 175 315 27 630 0.0 2 254 122 254 28 501 0.0 2 233 116 152 29 464 0.0 2 190 114 160 30 885 0.0 3 211 120 148 406 31 852 0.0 3 182 115 143 412 32 727 0.0 3 182 79 134 332 33 735 0.0 3 184 115 115 321 34 668 0.0 3 152 97 122 297 35 626 0.0 3 167 82 140 237 36 594 0.0 3 193 82 93 226 37 552 0.0 3 187 76 78 211 38 471 0.0 3 174 80 89 128 39 426 0.0 3 135 75 87 129 40 677 0.0 4 142 77 68 113 277 41 708 0.0 4 168 98 74 107 261 42 683 0.0 4 159 75 71 111 267 43 635 0.0 4 146 79 88 107 215 44 616 0.0 4 133 73 90 88 232 45 575 0.0 4 136 66 86 87 200 46 559 0.0 4 141 84 71 83 180 47 554 0.0 4 185 82 77 73 137 48 563 0.0 4 187 114 107 78 77 49 1463 0.0 4 428 300 270 225 240 50 1588 0.0 5 367 297 253 242 221 208 51 1233 0.0 5 405 238 181 145 136 128 52 1171 0.0 5 393 223 175 148 133 99 53 1069 0.0 5 431 188 142 133 93 82 54 895 0.0 5 351 194 122 90 77 61 55 799 0.0 5 364 148 112 78 52 45 56 834 0.0 5 401 164 107 58 55 49 57 723 0.0 5 328 133 97 83 45 37 58 660 0.0 5 325 118 72 62 44 39 59 660 0.0 5 346 116 74 57 37 30 60 684 0.0 5 357 133 81 44 39 30 61 584 0.0 5 324 107 59 31 37 26 62 590 0.0 5 325 116 54 36 29 30 63 601 0.0 5 326 106 60 40 36 33 64 589 0.0 5 339 94 61 44 31 20 65 627 0.0 5 387 103 51 39 27 20 66 608 0.0 5 364 97 58 47 26 16 67 592 0.0 5 366 109 48 36 15 18 68 604 0.0 5 390 91 49 41 10 23 69 654 0.0 5 491 84 29 23 17 10 70 632 0.0 5 453 75 44 23 23 14 71 560 0.0 5 392 80 29 24 17 18 72 477 0.0 5 330 63 39 21 15 9 73 452 0.0 5 316 59 33 16 13 15 74 504 0.0 5 381 50 32 16 16 9 75 601 0.0 5 445 72 39 22 14 9 76 471 0.0 5 334 64 34 21 11 7 77 476 0.0 5 375 59 20 9 9 4 78 430 0.0 5 303 41 31 24 19 12 79 452 0.0 5 327 61 24 14 12 14 80 400 0.0 5 299 43 19 17 12 10 81 392 0.0 5 303 45 20 16 4 4 82 365 0.0 5 290 36 15 11 10 3 83 311 0.0 5 240 30 18 13 7 3 84 367 0.0 5 302 31 13 9 7 5 85 316 0.0 5 255 22 11 12 7 9 86 357 0.0 5 294 34 9 0 15 5 87 297 0.0 5 236 27 16 8 6 4 88 404 0.0 5 329 28 17 13 8 9 89 337 0.0 5 275 25 14 13 4 6 90 308 0.0 5 262 20 9 5 8 4 91 301 0.0 5 228 38 13 8 7 7 92 329 0.0 5 271 28 8 12 3 7 93 252 0.0 5 192 29 9 13 4 5 94 263 0.0 5 206 26 13 7 5 6 95 309 0.0 5 259 19 9 8 9 5 96 293 0.0 5 224 28 19 10 7 5 97 299 0.0 5 247 22 9 4 11 6 98 236 0.0 5 191 23 12 3 4 3 99 325 0.0 5 267 30 9 14 3 2 100 235 0.0 5 190 21 12 7 4 1 101 360 0.0 5 305 26 12 11 3 3 102 335 0.0 5 277 30 7 8 6 7 103 291 0.0 5 240 13 12 13 6 7 104 231 0.0 5 188 18 16 2 4 3 105 345 0.0 5 287 19 13 12 6 8 106 256 0.0 5 215 19 7 5 6 4 107 277 0.0 5 221 21 8 10 10 7 108 281 0.0 5 215 24 13 11 8 10 109 396 0.0 5 301 31 39 11 8 6 110 447 0.0 5 339 42 21 25 12 8 111 378 0.0 5 282 30 24 14 10 18 112 804 0.0 5 675 48 26 23 15 17 113 947 0.0 5 782 78 26 21 25 15 114 3166 0.0 5 2896 127 51 35 29 28 115 552939 0.0 5 552099 624 114 48 30 24 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/Hawes/analyses/trimgalore-2/zr3644_13_R2_val_2_val_2.fq.gz ============================================= 53883255 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_13_R1_val_1_val_1_trimmed.fq.gz and zr3644_13_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_13_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_13_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_13_R1_val_1_val_1_trimmed.fq.gz and zr3644_13_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_13_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_13_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 53883255 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 579819 (1.08%) >>> Now running FastQC on the validated data zr3644_13_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_13_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_13_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_13_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_13_R1_val_1_val_1_trimmed.fq.gz and zr3644_13_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_14_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_14_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/Hawes/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 zr3644_14_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/Hawes/analyses/trimgalore-2/zr3644_14_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 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/Hawes/analyses/trimgalore-2/zr3644_14_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1086.89 s (29 µs/read; 2.03 M reads/minute). === Summary === Total reads processed: 36,852,584 Reads with adapters: 3,871,772 (10.5%) Reads written (passing filters): 36,852,584 (100.0%) Total basepairs processed: 3,887,759,431 bp Quality-trimmed: 2,061,809 bp (0.1%) Total written (filtered): 3,842,513,410 bp (98.8%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 3871772 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: 21.3% C: 5.2% G: 0.0% T: 73.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2455597 9213146.0 0 2455597 2 673791 2303286.5 0 673791 3 145479 575821.6 0 145479 4 40319 143955.4 0 40319 5 12550 35988.9 0 12550 6 3628 8997.2 0 3628 7 1559 2249.3 0 1559 8 948 562.3 0 948 9 916 140.6 0 916 10 2182 35.1 1 875 1307 11 1850 8.8 1 786 1064 12 1589 2.2 1 713 876 13 1381 0.5 1 659 722 14 1260 0.1 1 594 666 15 1070 0.0 1 472 598 16 913 0.0 1 416 497 17 716 0.0 1 322 394 18 598 0.0 1 320 278 19 505 0.0 1 280 225 20 891 0.0 2 310 218 363 21 792 0.0 2 278 197 317 22 771 0.0 2 300 175 296 23 714 0.0 2 261 184 269 24 644 0.0 2 235 178 231 25 607 0.0 2 240 161 206 26 565 0.0 2 220 161 184 27 467 0.0 2 199 117 151 28 398 0.0 2 186 120 92 29 408 0.0 2 171 139 98 30 584 0.0 3 171 138 91 184 31 567 0.0 3 178 117 115 157 32 509 0.0 3 148 115 97 149 33 470 0.0 3 145 99 88 138 34 519 0.0 3 169 112 93 145 35 469 0.0 3 158 108 85 118 36 462 0.0 3 143 102 104 113 37 407 0.0 3 161 102 50 94 38 355 0.0 3 128 104 56 67 39 347 0.0 3 110 83 73 81 40 477 0.0 4 136 95 82 48 116 41 426 0.0 4 136 68 63 64 95 42 506 0.0 4 132 104 86 75 109 43 424 0.0 4 120 80 59 65 100 44 401 0.0 4 94 92 69 56 90 45 387 0.0 4 106 79 64 60 78 46 421 0.0 4 131 94 60 55 81 47 418 0.0 4 143 91 58 52 74 48 420 0.0 4 151 91 72 60 46 49 920 0.0 4 336 213 167 108 96 50 1084 0.0 5 435 205 154 120 94 76 51 843 0.0 5 418 183 104 60 50 28 52 779 0.0 5 406 158 88 58 44 25 53 650 0.0 5 330 113 85 56 36 30 54 738 0.0 5 426 135 74 45 34 24 55 775 0.0 5 454 150 80 40 37 14 56 924 0.0 5 561 176 83 56 32 16 57 798 0.0 5 532 130 63 35 22 16 58 796 0.0 5 561 112 48 31 27 17 59 980 0.0 5 737 118 56 31 18 20 60 768 0.0 5 491 146 47 40 25 19 61 758 0.0 5 482 148 56 37 17 18 62 856 0.0 5 611 135 45 33 16 16 63 979 0.0 5 743 126 48 24 24 14 64 1397 0.0 5 1166 113 54 29 20 15 65 913 0.0 5 664 136 56 37 9 11 66 1078 0.0 5 837 125 63 19 22 12 67 1215 0.0 5 946 151 54 32 17 15 68 1521 0.0 5 1269 135 67 24 12 14 69 2000 0.0 5 1712 185 52 24 20 7 70 3499 0.0 5 3214 182 50 25 11 17 71 6991 0.0 5 6635 247 65 21 18 5 72 24321 0.0 5 23765 412 88 32 16 8 73 52686 0.0 5 52024 531 81 30 14 6 74 230585 0.0 5 229130 1204 194 37 13 7 75 26665 0.0 5 26383 180 43 31 14 14 76 13332 0.0 5 13133 117 39 23 10 10 77 53517 0.0 5 53275 178 33 17 9 5 78 7638 0.0 5 7506 79 23 15 9 6 79 34661 0.0 5 34507 112 15 12 8 7 80 9896 0.0 5 9789 44 26 17 12 8 81 5417 0.0 5 5328 40 18 16 7 8 82 11210 0.0 5 11123 57 10 3 12 5 83 2406 0.0 5 2311 47 17 19 10 2 84 4172 0.0 5 4066 56 17 14 15 4 85 836 0.0 5 765 22 18 15 8 8 86 124 0.0 5 72 21 7 14 8 2 87 110 0.0 5 55 24 9 8 9 5 88 112 0.0 5 60 18 16 8 8 2 89 89 0.0 5 45 12 14 8 6 4 90 89 0.0 5 50 14 3 11 6 5 91 86 0.0 5 56 10 6 2 6 6 92 85 0.0 5 45 13 13 6 5 3 93 78 0.0 5 41 14 9 9 3 2 94 59 0.0 5 33 11 8 4 1 2 95 65 0.0 5 37 7 5 7 6 3 96 59 0.0 5 27 8 5 5 9 5 97 53 0.0 5 32 9 3 3 4 2 98 58 0.0 5 28 8 10 7 3 2 99 50 0.0 5 28 10 2 4 2 4 100 40 0.0 5 17 6 10 3 1 3 101 43 0.0 5 19 10 3 6 1 4 102 30 0.0 5 19 6 1 0 3 1 103 27 0.0 5 15 1 5 1 5 104 24 0.0 5 15 3 4 1 1 105 30 0.0 5 17 4 2 1 5 1 106 16 0.0 5 8 2 1 2 2 1 107 19 0.0 5 11 2 3 1 1 1 108 8 0.0 5 4 2 1 0 0 1 109 9 0.0 5 7 2 110 8 0.0 5 5 0 1 1 0 1 111 9 0.0 5 4 2 3 112 8 0.0 5 6 1 0 1 113 6 0.0 5 6 114 5 0.0 5 4 1 115 92 0.0 5 90 1 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_14_R1_val_1_val_1.fq.gz ============================================= 36852584 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_14_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_14_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/Hawes/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 zr3644_14_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/Hawes/analyses/trimgalore-2/zr3644_14_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 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/Hawes/analyses/trimgalore-2/zr3644_14_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 996.88 s (27 µs/read; 2.22 M reads/minute). === Summary === Total reads processed: 36,852,584 Reads with adapters: 3,529,798 (9.6%) Reads written (passing filters): 36,852,584 (100.0%) Total basepairs processed: 3,889,651,677 bp Quality-trimmed: 1,591,963 bp (0.0%) Total written (filtered): 3,824,820,009 bp (98.3%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 3529798 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: 13.2% C: 5.6% G: 0.0% T: 81.2% 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 2218945 9213146.0 0 2218945 2 592978 2303286.5 0 592978 3 127853 575821.6 0 127853 4 35272 143955.4 0 35272 5 10241 35988.9 0 10241 6 2754 8997.2 0 2754 7 967 2249.3 0 967 8 528 562.3 0 528 9 471 140.6 0 471 10 1492 35.1 1 422 1070 11 1246 8.8 1 388 858 12 1016 2.2 1 360 656 13 923 0.5 1 299 624 14 826 0.1 1 282 544 15 714 0.0 1 230 484 16 600 0.0 1 198 402 17 479 0.0 1 176 303 18 345 0.0 1 167 178 19 324 0.0 1 166 158 20 789 0.0 2 227 174 388 21 706 0.0 2 221 175 310 22 699 0.0 2 221 156 322 23 624 0.0 2 186 136 302 24 529 0.0 2 167 125 237 25 534 0.0 2 162 140 232 26 433 0.0 2 149 109 175 27 407 0.0 2 172 95 140 28 311 0.0 2 145 69 97 29 336 0.0 2 161 75 100 30 534 0.0 3 138 89 85 222 31 540 0.0 3 162 81 73 224 32 535 0.0 3 129 80 110 216 33 462 0.0 3 123 71 79 189 34 449 0.0 3 125 69 79 176 35 425 0.0 3 120 70 84 151 36 405 0.0 3 126 79 75 125 37 311 0.0 3 97 64 57 93 38 323 0.0 3 104 68 67 84 39 289 0.0 3 96 60 64 69 40 394 0.0 4 98 45 49 62 140 41 482 0.0 4 115 77 57 66 167 42 453 0.0 4 104 60 57 74 158 43 409 0.0 4 105 64 41 68 131 44 394 0.0 4 111 49 53 60 121 45 401 0.0 4 105 59 45 65 127 46 377 0.0 4 106 49 40 66 116 47 382 0.0 4 113 74 50 58 87 48 405 0.0 4 131 76 69 67 62 49 950 0.0 4 296 189 170 171 124 50 1049 0.0 5 288 195 161 144 142 119 51 797 0.0 5 282 171 122 84 61 77 52 709 0.0 5 298 138 92 61 56 64 53 660 0.0 5 280 123 89 73 49 46 54 586 0.0 5 287 98 71 56 35 39 55 513 0.0 5 243 121 56 37 29 27 56 529 0.0 5 298 99 51 26 33 22 57 461 0.0 5 265 76 43 40 24 13 58 439 0.0 5 222 90 48 35 24 20 59 422 0.0 5 237 75 41 25 25 19 60 409 0.0 5 220 78 40 31 26 14 61 370 0.0 5 214 67 42 18 16 13 62 368 0.0 5 221 66 37 15 15 14 63 416 0.0 5 261 74 37 13 22 9 64 395 0.0 5 227 84 36 18 18 12 65 407 0.0 5 266 66 34 15 13 13 66 334 0.0 5 210 54 25 23 15 7 67 430 0.0 5 309 58 26 17 13 7 68 394 0.0 5 271 56 30 16 12 9 69 447 0.0 5 341 47 23 15 12 9 70 409 0.0 5 316 43 12 19 7 12 71 348 0.0 5 255 44 23 12 11 3 72 338 0.0 5 252 38 26 9 9 4 73 351 0.0 5 272 40 15 7 10 7 74 384 0.0 5 297 46 11 11 13 6 75 439 0.0 5 347 46 20 10 7 9 76 341 0.0 5 266 44 13 6 8 4 77 406 0.0 5 325 33 27 12 5 4 78 287 0.0 5 224 34 11 9 5 4 79 313 0.0 5 256 27 12 7 4 7 80 288 0.0 5 226 33 11 8 5 5 81 261 0.0 5 218 19 9 6 5 4 82 244 0.0 5 183 32 15 6 3 5 83 251 0.0 5 189 27 14 8 10 3 84 257 0.0 5 212 21 12 3 5 4 85 267 0.0 5 219 19 12 9 4 4 86 277 0.0 5 237 24 7 3 5 1 87 230 0.0 5 180 22 9 10 4 5 88 278 0.0 5 246 18 5 2 5 2 89 241 0.0 5 202 24 6 4 3 2 90 231 0.0 5 188 20 8 8 2 5 91 211 0.0 5 164 25 10 8 2 2 92 241 0.0 5 197 24 5 8 5 2 93 190 0.0 5 153 19 8 4 4 2 94 167 0.0 5 125 20 7 8 4 3 95 205 0.0 5 163 15 13 4 7 3 96 200 0.0 5 160 16 13 5 2 4 97 169 0.0 5 130 25 8 4 2 98 145 0.0 5 109 17 6 5 6 2 99 235 0.0 5 203 18 5 2 2 5 100 133 0.0 5 100 18 7 3 1 4 101 262 0.0 5 229 15 7 3 5 3 102 239 0.0 5 210 14 9 2 3 1 103 200 0.0 5 178 6 7 1 5 3 104 163 0.0 5 132 9 6 8 4 4 105 275 0.0 5 236 16 8 7 5 3 106 189 0.0 5 151 22 5 7 4 107 215 0.0 5 181 21 5 5 2 1 108 174 0.0 5 144 7 3 5 7 8 109 294 0.0 5 202 39 31 13 7 2 110 314 0.0 5 243 27 14 8 10 12 111 264 0.0 5 177 30 14 15 12 16 112 587 0.0 5 478 40 18 15 20 16 113 660 0.0 5 525 55 30 25 8 17 114 2094 0.0 5 1890 91 42 35 22 14 115 493134 0.0 5 492360 586 95 41 26 26 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/Hawes/analyses/trimgalore-2/zr3644_14_R2_val_2_val_2.fq.gz ============================================= 36852584 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_14_R1_val_1_val_1_trimmed.fq.gz and zr3644_14_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_14_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_14_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_14_R1_val_1_val_1_trimmed.fq.gz and zr3644_14_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_14_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_14_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 36852584 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 511723 (1.39%) >>> Now running FastQC on the validated data zr3644_14_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_14_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_14_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_14_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_14_R1_val_1_val_1_trimmed.fq.gz and zr3644_14_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_15_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_15_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/Hawes/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 zr3644_15_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/Hawes/analyses/trimgalore-2/zr3644_15_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_15_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1671.13 s (28 µs/read; 2.12 M reads/minute). === Summary === Total reads processed: 59,105,662 Reads with adapters: 5,883,911 (10.0%) Reads written (passing filters): 59,105,662 (100.0%) Total basepairs processed: 6,252,033,716 bp Quality-trimmed: 2,264,103 bp (0.0%) Total written (filtered): 6,191,737,029 bp (99.0%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5883911 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: 20.3% C: 4.9% G: 0.0% T: 74.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3812155 14776415.5 0 3812155 2 1044369 3694103.9 0 1044369 3 222397 923526.0 0 222397 4 61237 230881.5 0 61237 5 18057 57720.4 0 18057 6 5294 14430.1 0 5294 7 2438 3607.5 0 2438 8 1661 901.9 0 1661 9 1569 225.5 0 1569 10 3463 56.4 1 1564 1899 11 2881 14.1 1 1384 1497 12 2539 3.5 1 1260 1279 13 2363 0.9 1 1201 1162 14 2061 0.2 1 1088 973 15 1766 0.1 1 887 879 16 1547 0.0 1 781 766 17 1362 0.0 1 669 693 18 1013 0.0 1 612 401 19 933 0.0 1 563 370 20 1441 0.0 2 579 367 495 21 1383 0.0 2 591 366 426 22 1236 0.0 2 542 342 352 23 1247 0.0 2 534 356 357 24 1106 0.0 2 527 273 306 25 1063 0.0 2 502 257 304 26 922 0.0 2 424 265 233 27 875 0.0 2 411 220 244 28 814 0.0 2 391 231 192 29 728 0.0 2 348 214 166 30 1019 0.0 3 357 237 182 243 31 995 0.0 3 364 226 170 235 32 897 0.0 3 354 182 139 222 33 807 0.0 3 320 178 136 173 34 855 0.0 3 345 183 142 185 35 826 0.0 3 325 171 136 194 36 801 0.0 3 307 183 137 174 37 714 0.0 3 276 153 128 157 38 733 0.0 3 311 169 122 131 39 668 0.0 3 302 143 120 103 40 757 0.0 4 270 166 87 102 132 41 771 0.0 4 235 153 119 103 161 42 831 0.0 4 272 165 139 115 140 43 734 0.0 4 248 143 119 89 135 44 730 0.0 4 252 145 96 97 140 45 721 0.0 4 256 141 111 92 121 46 765 0.0 4 270 163 127 102 103 47 730 0.0 4 279 158 123 70 100 48 792 0.0 4 320 179 131 97 65 49 1431 0.0 4 592 331 208 174 126 50 1669 0.0 5 729 318 245 159 121 97 51 1207 0.0 5 652 226 132 62 69 66 52 1146 0.0 5 689 194 97 70 52 44 53 1013 0.0 5 603 177 99 60 48 26 54 951 0.0 5 614 148 83 43 31 32 55 1077 0.0 5 712 180 81 48 39 17 56 1166 0.0 5 828 167 86 36 33 16 57 1118 0.0 5 800 172 64 39 23 20 58 1181 0.0 5 908 146 63 26 23 15 59 1184 0.0 5 904 147 55 49 17 12 60 980 0.0 5 710 157 54 34 13 12 61 1075 0.0 5 815 144 59 32 12 13 62 1150 0.0 5 899 151 39 34 16 11 63 1224 0.0 5 992 133 52 22 17 8 64 1685 0.0 5 1402 148 68 30 21 16 65 1090 0.0 5 853 139 49 21 18 10 66 1314 0.0 5 1054 146 66 28 11 9 67 1600 0.0 5 1315 175 53 29 18 10 68 1861 0.0 5 1563 181 60 27 15 15 69 2524 0.0 5 2214 198 60 26 19 7 70 4233 0.0 5 3912 213 55 30 13 10 71 8657 0.0 5 8338 215 56 31 8 9 72 29963 0.0 5 29491 348 81 19 13 11 73 68623 0.0 5 68087 435 58 21 17 5 74 312605 0.0 5 311500 944 128 20 9 4 75 28762 0.0 5 28484 199 42 23 6 8 76 18318 0.0 5 18125 134 34 8 13 4 77 60633 0.0 5 60372 203 31 15 4 8 78 10890 0.0 5 10717 95 35 19 10 14 79 39979 0.0 5 39756 162 33 13 9 6 80 11462 0.0 5 11332 82 23 13 8 4 81 7299 0.0 5 7168 92 17 9 8 5 82 12697 0.0 5 12561 83 20 12 14 7 83 7183 0.0 5 7042 84 26 17 9 5 84 13948 0.0 5 13805 95 27 10 8 3 85 2643 0.0 5 2546 55 21 14 5 2 86 367 0.0 5 287 32 21 13 12 2 87 265 0.0 5 188 37 20 5 7 8 88 210 0.0 5 136 44 15 6 6 3 89 210 0.0 5 144 33 15 8 7 3 90 211 0.0 5 137 28 22 16 7 1 91 195 0.0 5 134 25 15 8 7 6 92 166 0.0 5 109 24 11 8 8 6 93 161 0.0 5 108 19 13 13 4 4 94 150 0.0 5 102 18 19 5 5 1 95 129 0.0 5 91 18 8 5 5 2 96 110 0.0 5 69 17 10 4 6 4 97 128 0.0 5 88 16 10 5 5 4 98 103 0.0 5 70 14 8 6 3 2 99 102 0.0 5 66 17 7 5 5 2 100 101 0.0 5 69 12 9 6 4 1 101 87 0.0 5 54 10 8 7 2 6 102 81 0.0 5 52 8 9 5 3 4 103 79 0.0 5 49 9 9 7 3 2 104 45 0.0 5 29 5 3 1 4 3 105 44 0.0 5 25 4 6 2 4 3 106 42 0.0 5 28 2 4 4 3 1 107 28 0.0 5 16 5 2 1 4 108 32 0.0 5 18 1 3 5 2 3 109 24 0.0 5 19 1 2 0 0 2 110 32 0.0 5 22 4 1 2 1 2 111 23 0.0 5 17 0 2 1 1 2 112 13 0.0 5 10 1 0 0 1 1 113 11 0.0 5 6 1 1 1 1 1 114 14 0.0 5 11 2 0 1 115 141 0.0 5 136 3 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_15_R1_val_1_val_1.fq.gz ============================================= 59105662 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_15_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_15_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/Hawes/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 zr3644_15_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/Hawes/analyses/trimgalore-2/zr3644_15_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_15_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1804.13 s (31 µs/read; 1.97 M reads/minute). === Summary === Total reads processed: 59,105,662 Reads with adapters: 5,526,578 (9.4%) Reads written (passing filters): 59,105,662 (100.0%) Total basepairs processed: 6,250,583,827 bp Quality-trimmed: 2,830,102 bp (0.0%) Total written (filtered): 6,163,466,021 bp (98.6%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5526578 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: 13.5% C: 5.5% G: 0.0% T: 80.9% 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 3560457 14776415.5 0 3560457 2 954715 3694103.9 0 954715 3 208723 923526.0 0 208723 4 57094 230881.5 0 57094 5 16659 57720.4 0 16659 6 4698 14430.1 0 4698 7 1755 3607.5 0 1755 8 1018 901.9 0 1018 9 783 225.5 0 783 10 2887 56.4 1 787 2100 11 2441 14.1 1 680 1761 12 1928 3.5 1 558 1370 13 1757 0.9 1 515 1242 14 1419 0.2 1 424 995 15 1305 0.1 1 413 892 16 1121 0.0 1 392 729 17 842 0.0 1 281 561 18 591 0.0 1 283 308 19 537 0.0 1 262 275 20 1434 0.0 2 361 282 791 21 1275 0.0 2 338 251 686 22 1226 0.0 2 338 232 656 23 1088 0.0 2 301 248 539 24 976 0.0 2 296 222 458 25 927 0.0 2 277 198 452 26 801 0.0 2 265 194 342 27 651 0.0 2 234 141 276 28 550 0.0 2 236 126 188 29 528 0.0 2 214 132 182 30 958 0.0 3 220 138 163 437 31 946 0.0 3 218 133 154 441 32 822 0.0 3 181 108 153 380 33 813 0.0 3 204 103 128 378 34 782 0.0 3 170 108 144 360 35 776 0.0 3 210 114 151 301 36 702 0.0 3 172 107 134 289 37 556 0.0 3 184 90 90 192 38 590 0.0 3 213 113 104 160 39 476 0.0 3 161 106 90 119 40 761 0.0 4 167 94 83 116 301 41 806 0.0 4 189 100 94 147 276 42 702 0.0 4 141 86 87 110 278 43 688 0.0 4 162 88 68 119 251 44 660 0.0 4 147 85 80 118 230 45 653 0.0 4 163 74 76 114 226 46 609 0.0 4 160 65 73 113 198 47 634 0.0 4 186 94 95 86 173 48 685 0.0 4 216 139 124 113 93 49 1775 0.0 4 507 402 308 313 245 50 2018 0.0 5 480 374 325 308 283 248 51 1501 0.0 5 436 333 213 211 161 147 52 1307 0.0 5 445 267 199 146 125 125 53 1187 0.0 5 472 237 158 111 124 85 54 1005 0.0 5 426 191 134 103 76 75 55 943 0.0 5 426 178 128 80 70 61 56 1008 0.0 5 496 194 118 77 71 52 57 885 0.0 5 454 157 98 71 51 54 58 828 0.0 5 400 189 93 63 41 42 59 747 0.0 5 385 150 76 56 49 31 60 718 0.0 5 373 118 83 68 38 38 61 703 0.0 5 378 125 80 58 38 24 62 652 0.0 5 374 108 77 41 33 19 63 720 0.0 5 418 129 65 47 35 26 64 673 0.0 5 402 107 59 34 44 27 65 730 0.0 5 455 109 65 36 35 30 66 675 0.0 5 445 99 44 41 27 19 67 723 0.0 5 472 104 63 33 28 23 68 733 0.0 5 507 95 47 41 20 23 69 745 0.0 5 564 85 45 15 28 8 70 673 0.0 5 505 83 32 21 12 20 71 562 0.0 5 401 76 26 27 23 9 72 566 0.0 5 418 65 31 27 17 8 73 505 0.0 5 366 57 39 16 12 15 74 554 0.0 5 407 61 29 18 30 9 75 647 0.0 5 501 77 27 16 13 13 76 564 0.0 5 428 73 28 13 9 13 77 593 0.0 5 451 82 27 19 7 7 78 450 0.0 5 336 57 25 17 7 8 79 534 0.0 5 413 57 26 16 12 10 80 488 0.0 5 355 60 43 14 5 11 81 421 0.0 5 320 51 17 10 15 8 82 391 0.0 5 301 49 18 9 7 7 83 357 0.0 5 285 35 14 10 6 7 84 424 0.0 5 336 40 22 10 12 4 85 382 0.0 5 291 40 19 20 8 4 86 429 0.0 5 349 34 25 10 8 3 87 346 0.0 5 273 37 14 13 4 5 88 440 0.0 5 380 27 14 6 7 6 89 383 0.0 5 309 34 15 8 12 5 90 316 0.0 5 268 26 11 6 3 2 91 298 0.0 5 230 28 14 9 11 6 92 346 0.0 5 267 40 16 11 5 7 93 272 0.0 5 218 24 7 8 10 5 94 256 0.0 5 201 31 8 9 6 1 95 322 0.0 5 246 32 23 11 5 5 96 327 0.0 5 246 43 16 8 5 9 97 292 0.0 5 225 28 20 12 3 4 98 254 0.0 5 193 28 13 7 7 6 99 345 0.0 5 291 23 9 8 8 6 100 227 0.0 5 173 17 15 13 6 3 101 356 0.0 5 299 23 14 6 5 9 102 345 0.0 5 271 35 14 9 13 3 103 292 0.0 5 244 19 13 6 4 6 104 233 0.0 5 186 11 11 8 10 7 105 365 0.0 5 308 27 8 8 7 7 106 284 0.0 5 231 18 12 10 7 6 107 295 0.0 5 233 29 17 6 6 4 108 295 0.0 5 238 21 10 7 9 10 109 473 0.0 5 338 51 50 19 10 5 110 462 0.0 5 356 44 18 18 15 11 111 447 0.0 5 345 35 17 21 13 16 112 900 0.0 5 744 62 33 24 23 14 113 1072 0.0 5 868 81 48 31 27 17 114 3298 0.0 5 3009 128 66 44 27 24 115 640416 0.0 5 639454 709 111 60 40 42 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/Hawes/analyses/trimgalore-2/zr3644_15_R2_val_2_val_2.fq.gz ============================================= 59105662 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_15_R1_val_1_val_1_trimmed.fq.gz and zr3644_15_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_15_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_15_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_15_R1_val_1_val_1_trimmed.fq.gz and zr3644_15_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_15_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_15_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 59105662 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 670185 (1.13%) >>> Now running FastQC on the validated data zr3644_15_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_15_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_15_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_15_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_15_R1_val_1_val_1_trimmed.fq.gz and zr3644_15_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_16_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_16_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/Hawes/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 zr3644_16_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/Hawes/analyses/trimgalore-2/zr3644_16_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_16_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1491.97 s (29 µs/read; 2.07 M reads/minute). === Summary === Total reads processed: 51,584,355 Reads with adapters: 5,791,162 (11.2%) Reads written (passing filters): 51,584,355 (100.0%) Total basepairs processed: 5,364,699,213 bp Quality-trimmed: 2,314,216 bp (0.0%) Total written (filtered): 5,265,968,045 bp (98.2%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5791162 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: 26.1% C: 4.7% G: 0.0% T: 69.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3339201 12896088.8 0 3339201 2 934050 3224022.2 0 934050 3 200373 806005.5 0 200373 4 56161 201501.4 0 56161 5 16521 50375.3 0 16521 6 4889 12593.8 0 4889 7 1939 3148.5 0 1939 8 1329 787.1 0 1329 9 1217 196.8 0 1217 10 2870 49.2 1 1185 1685 11 2488 12.3 1 1125 1363 12 2200 3.1 1 1018 1182 13 2003 0.8 1 950 1053 14 1602 0.2 1 753 849 15 1408 0.0 1 656 752 16 1220 0.0 1 593 627 17 1018 0.0 1 509 509 18 745 0.0 1 425 320 19 792 0.0 1 479 313 20 1213 0.0 2 451 282 480 21 1109 0.0 2 431 222 456 22 1047 0.0 2 413 238 396 23 962 0.0 2 390 227 345 24 935 0.0 2 389 240 306 25 837 0.0 2 347 215 275 26 738 0.0 2 297 223 218 27 630 0.0 2 264 167 199 28 604 0.0 2 280 186 138 29 561 0.0 2 275 160 126 30 786 0.0 3 262 152 126 246 31 726 0.0 3 249 161 126 190 32 707 0.0 3 231 137 140 199 33 646 0.0 3 205 139 120 182 34 669 0.0 3 239 144 117 169 35 663 0.0 3 245 156 102 160 36 603 0.0 3 220 122 118 143 37 632 0.0 3 230 117 123 162 38 607 0.0 3 273 152 96 86 39 564 0.0 3 219 131 104 110 40 643 0.0 4 191 127 82 81 162 41 695 0.0 4 195 148 115 83 154 42 666 0.0 4 200 123 90 92 161 43 614 0.0 4 184 132 93 80 125 44 582 0.0 4 168 125 82 88 119 45 569 0.0 4 173 104 94 78 120 46 601 0.0 4 210 122 85 73 111 47 603 0.0 4 203 132 90 81 97 48 626 0.0 4 236 144 98 76 72 49 1500 0.0 4 614 341 238 183 124 50 1777 0.0 5 815 343 245 147 142 85 51 1402 0.0 5 766 252 133 108 81 62 52 1238 0.0 5 663 238 140 85 64 48 53 1163 0.0 5 664 215 100 95 49 40 54 1284 0.0 5 801 218 119 69 44 33 55 1432 0.0 5 959 223 111 68 40 31 56 1601 0.0 5 1118 209 134 65 55 20 57 1458 0.0 5 1020 220 110 55 33 20 58 1640 0.0 5 1270 193 76 54 28 19 59 1823 0.0 5 1449 211 88 35 26 14 60 1335 0.0 5 915 239 74 52 40 15 61 1435 0.0 5 1075 203 72 40 25 20 62 1655 0.0 5 1238 238 92 46 26 15 63 1847 0.0 5 1516 198 68 28 22 15 64 2690 0.0 5 2344 187 76 38 31 14 65 1622 0.0 5 1283 188 80 34 22 15 66 2026 0.0 5 1655 218 72 43 22 16 67 2409 0.0 5 2001 252 89 37 19 11 68 3135 0.0 5 2745 261 66 40 15 8 69 4234 0.0 5 3770 320 83 34 16 11 70 7590 0.0 5 7098 338 86 33 18 17 71 16083 0.0 5 15504 411 108 42 12 6 72 53732 0.0 5 52893 658 108 42 16 15 73 139036 0.0 5 138020 861 104 26 18 7 74 572038 0.0 5 569783 1946 252 36 13 8 75 49724 0.0 5 49305 312 63 25 14 5 76 33969 0.0 5 33663 223 42 19 11 11 77 119841 0.0 5 119390 347 67 22 10 5 78 19594 0.0 5 19410 115 40 14 10 5 79 77113 0.0 5 76829 216 38 16 9 5 80 20850 0.0 5 20671 113 37 18 6 5 81 12559 0.0 5 12435 67 24 17 10 6 82 23604 0.0 5 23455 106 22 10 7 4 83 4020 0.0 5 3882 82 22 18 8 8 84 6309 0.0 5 6138 107 22 18 11 13 85 872 0.0 5 781 48 14 14 10 5 86 203 0.0 5 123 38 20 9 9 4 87 173 0.0 5 110 28 18 8 5 4 88 180 0.0 5 113 28 13 6 14 6 89 163 0.0 5 100 27 14 4 9 9 90 177 0.0 5 111 25 13 15 9 4 91 175 0.0 5 98 35 20 5 12 5 92 127 0.0 5 94 19 4 6 2 2 93 126 0.0 5 70 22 10 14 6 4 94 117 0.0 5 66 29 13 4 1 4 95 128 0.0 5 71 24 11 10 6 6 96 116 0.0 5 64 24 13 7 4 4 97 109 0.0 5 59 19 9 9 10 3 98 90 0.0 5 46 17 12 3 8 4 99 77 0.0 5 42 15 7 4 6 3 100 86 0.0 5 44 12 16 8 5 1 101 62 0.0 5 41 6 4 6 3 2 102 55 0.0 5 33 10 4 2 4 2 103 56 0.0 5 28 7 4 8 3 6 104 41 0.0 5 23 8 5 2 0 3 105 42 0.0 5 25 3 4 5 1 4 106 32 0.0 5 17 4 3 1 5 2 107 29 0.0 5 21 3 2 3 108 24 0.0 5 10 4 5 3 1 1 109 20 0.0 5 13 3 1 2 0 1 110 17 0.0 5 13 0 2 0 2 111 15 0.0 5 6 3 1 2 0 3 112 9 0.0 5 5 1 0 1 1 1 113 11 0.0 5 5 0 3 3 114 14 0.0 5 9 1 2 1 0 1 115 184 0.0 5 175 4 3 1 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_16_R1_val_1_val_1.fq.gz ============================================= 51584355 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_16_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_16_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/Hawes/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 zr3644_16_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/Hawes/analyses/trimgalore-2/zr3644_16_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_16_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1479.73 s (29 µs/read; 2.09 M reads/minute). === Summary === Total reads processed: 51,584,355 Reads with adapters: 5,425,476 (10.5%) Reads written (passing filters): 51,584,355 (100.0%) Total basepairs processed: 5,363,477,485 bp Quality-trimmed: 2,579,071 bp (0.0%) Total written (filtered): 5,216,889,470 bp (97.3%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5425476 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: 13.3% C: 5.4% G: 0.0% T: 81.2% 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 3091558 12896088.8 0 3091558 2 838171 3224022.2 0 838171 3 182943 806005.5 0 182943 4 50638 201501.4 0 50638 5 14790 50375.3 0 14790 6 4152 12593.8 0 4152 7 1406 3148.5 0 1406 8 793 787.1 0 793 9 647 196.8 0 647 10 2295 49.2 1 610 1685 11 1941 12.3 1 557 1384 12 1512 3.1 1 455 1057 13 1286 0.8 1 409 877 14 1175 0.2 1 398 777 15 1039 0.0 1 341 698 16 824 0.0 1 278 546 17 694 0.0 1 254 440 18 494 0.0 1 235 259 19 466 0.0 1 222 244 20 1097 0.0 2 298 206 593 21 1007 0.0 2 285 209 513 22 1002 0.0 2 293 200 509 23 903 0.0 2 246 172 485 24 799 0.0 2 243 164 392 25 758 0.0 2 243 169 346 26 602 0.0 2 205 122 275 27 565 0.0 2 238 119 208 28 456 0.0 2 189 109 158 29 390 0.0 2 161 102 127 30 716 0.0 3 169 85 125 337 31 796 0.0 3 217 114 127 338 32 642 0.0 3 162 104 120 256 33 644 0.0 3 164 97 96 287 34 576 0.0 3 146 94 89 247 35 579 0.0 3 181 101 87 210 36 558 0.0 3 186 96 92 184 37 502 0.0 3 171 91 64 176 38 430 0.0 3 142 86 81 121 39 435 0.0 3 155 77 95 108 40 646 0.0 4 161 79 63 113 230 41 660 0.0 4 167 78 76 105 234 42 622 0.0 4 134 75 75 104 234 43 604 0.0 4 133 81 92 101 197 44 584 0.0 4 137 80 76 85 206 45 547 0.0 4 121 67 65 103 191 46 508 0.0 4 133 71 72 74 158 47 484 0.0 4 167 94 62 52 109 48 537 0.0 4 167 95 106 89 80 49 1509 0.0 4 466 326 259 245 213 50 1590 0.0 5 400 311 246 247 202 184 51 1218 0.0 5 393 249 172 142 133 129 52 1110 0.0 5 420 224 166 126 109 65 53 1002 0.0 5 396 196 138 121 77 74 54 860 0.0 5 359 167 133 90 50 61 55 795 0.0 5 373 159 89 73 52 49 56 893 0.0 5 460 170 88 73 55 47 57 801 0.0 5 400 153 79 71 54 44 58 701 0.0 5 357 141 73 54 39 37 59 657 0.0 5 356 118 68 51 41 23 60 632 0.0 5 350 132 54 40 33 23 61 606 0.0 5 343 111 68 35 24 25 62 567 0.0 5 320 110 58 32 24 23 63 654 0.0 5 395 121 57 35 28 18 64 626 0.0 5 353 117 66 36 32 22 65 705 0.0 5 442 113 67 37 19 27 66 610 0.0 5 387 96 48 32 31 16 67 671 0.0 5 457 93 58 26 25 12 68 657 0.0 5 452 90 53 31 19 12 69 822 0.0 5 643 83 41 22 21 12 70 712 0.0 5 541 83 39 18 14 17 71 566 0.0 5 409 76 39 20 14 8 72 589 0.0 5 437 79 28 24 7 14 73 567 0.0 5 424 75 30 15 13 10 74 633 0.0 5 502 69 30 9 10 13 75 739 0.0 5 609 57 35 20 8 10 76 641 0.0 5 497 62 32 22 17 11 77 676 0.0 5 526 71 36 15 16 12 78 460 0.0 5 356 53 20 13 10 8 79 592 0.0 5 484 50 17 17 13 11 80 499 0.0 5 382 58 30 5 13 11 81 477 0.0 5 377 45 29 14 8 4 82 423 0.0 5 330 46 18 18 5 6 83 389 0.0 5 294 49 13 13 11 9 84 444 0.0 5 373 31 9 13 7 11 85 410 0.0 5 302 67 15 8 12 6 86 481 0.0 5 394 40 19 7 8 13 87 401 0.0 5 326 36 14 12 7 6 88 526 0.0 5 444 36 18 15 8 5 89 446 0.0 5 381 34 7 6 14 4 90 426 0.0 5 372 26 8 8 5 7 91 364 0.0 5 274 43 22 9 10 6 92 445 0.0 5 379 32 16 7 8 3 93 306 0.0 5 252 20 14 11 6 3 94 290 0.0 5 236 25 12 6 8 3 95 377 0.0 5 317 27 10 9 6 8 96 397 0.0 5 302 55 16 12 6 6 97 407 0.0 5 327 42 15 7 8 8 98 264 0.0 5 200 28 10 12 9 5 99 427 0.0 5 376 23 13 5 7 3 100 261 0.0 5 210 26 4 10 5 6 101 583 0.0 5 512 35 16 10 7 3 102 478 0.0 5 404 37 19 5 9 4 103 422 0.0 5 370 25 8 13 0 6 104 317 0.0 5 260 24 9 10 9 5 105 472 0.0 5 424 27 10 4 4 3 106 353 0.0 5 288 31 12 9 7 6 107 365 0.0 5 308 24 11 6 11 5 108 359 0.0 5 301 22 15 11 3 7 109 631 0.0 5 434 74 89 10 14 10 110 639 0.0 5 502 66 31 18 17 5 111 414 0.0 5 318 46 21 12 10 7 112 1072 0.0 5 923 67 28 24 16 14 113 1257 0.0 5 1098 81 30 26 11 11 114 4488 0.0 5 4163 191 49 27 39 19 115 1165832 0.0 5 1164581 991 149 43 27 41 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/Hawes/analyses/trimgalore-2/zr3644_16_R2_val_2_val_2.fq.gz ============================================= 51584355 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_16_R1_val_1_val_1_trimmed.fq.gz and zr3644_16_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_16_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_16_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_16_R1_val_1_val_1_trimmed.fq.gz and zr3644_16_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_16_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_16_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 51584355 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1197753 (2.32%) >>> Now running FastQC on the validated data zr3644_16_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_16_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_16_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_16_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_16_R1_val_1_val_1_trimmed.fq.gz and zr3644_16_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_17_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_17_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/Hawes/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 zr3644_17_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/Hawes/analyses/trimgalore-2/zr3644_17_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_17_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1573.31 s (27 µs/read; 2.22 M reads/minute). === Summary === Total reads processed: 58,274,646 Reads with adapters: 5,997,555 (10.3%) Reads written (passing filters): 58,274,646 (100.0%) Total basepairs processed: 6,121,665,955 bp Quality-trimmed: 2,079,557 bp (0.0%) Total written (filtered): 6,049,045,099 bp (98.8%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5997555 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: 21.2% C: 4.6% G: 0.0% T: 74.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3749779 14568661.5 0 3749779 2 1048622 3642165.4 0 1048622 3 225102 910541.3 0 225102 4 62944 227635.3 0 62944 5 17496 56908.8 0 17496 6 5356 14227.2 0 5356 7 2312 3556.8 0 2312 8 1562 889.2 0 1562 9 1410 222.3 0 1410 10 3100 55.6 1 1346 1754 11 2518 13.9 1 1199 1319 12 2259 3.5 1 1145 1114 13 2037 0.9 1 1018 1019 14 1798 0.2 1 870 928 15 1485 0.1 1 738 747 16 1398 0.0 1 733 665 17 1123 0.0 1 572 551 18 873 0.0 1 521 352 19 827 0.0 1 498 329 20 1331 0.0 2 526 329 476 21 1186 0.0 2 498 300 388 22 1095 0.0 2 458 305 332 23 1049 0.0 2 445 264 340 24 985 0.0 2 447 276 262 25 826 0.0 2 372 227 227 26 744 0.0 2 374 188 182 27 686 0.0 2 322 182 182 28 692 0.0 2 372 181 139 29 636 0.0 2 296 182 158 30 809 0.0 3 302 182 113 212 31 848 0.0 3 319 183 140 206 32 773 0.0 3 303 159 132 179 33 724 0.0 3 285 156 112 171 34 754 0.0 3 289 188 130 147 35 667 0.0 3 244 155 124 144 36 600 0.0 3 225 154 83 138 37 660 0.0 3 285 151 93 131 38 589 0.0 3 256 140 108 85 39 532 0.0 3 239 116 91 86 40 642 0.0 4 212 136 89 83 122 41 677 0.0 4 207 143 103 97 127 42 690 0.0 4 219 146 104 81 140 43 631 0.0 4 194 113 104 90 130 44 587 0.0 4 180 114 80 86 127 45 562 0.0 4 196 95 83 75 113 46 588 0.0 4 220 124 71 81 92 47 600 0.0 4 237 131 84 59 89 48 614 0.0 4 245 138 93 73 65 49 1320 0.0 4 561 303 206 142 108 50 1549 0.0 5 727 300 177 141 112 92 51 1185 0.0 5 660 220 124 77 57 47 52 1089 0.0 5 647 220 103 60 41 18 53 996 0.0 5 617 170 77 70 33 29 54 973 0.0 5 613 170 77 62 29 22 55 1168 0.0 5 817 184 64 48 32 23 56 1292 0.0 5 972 167 80 47 17 9 57 1248 0.0 5 898 196 87 34 19 14 58 1365 0.0 5 1066 151 74 39 19 16 59 1321 0.0 5 1047 134 75 38 17 10 60 1081 0.0 5 787 170 55 34 24 11 61 1232 0.0 5 937 164 68 41 18 4 62 1526 0.0 5 1209 187 68 35 17 10 63 1791 0.0 5 1528 160 52 17 22 12 64 1895 0.0 5 1622 170 49 26 17 11 65 1523 0.0 5 1240 156 69 22 20 16 66 1829 0.0 5 1527 211 50 17 17 7 67 2350 0.0 5 1998 219 77 34 15 7 68 3170 0.0 5 2839 235 48 29 9 10 69 4673 0.0 5 4305 250 67 30 13 8 70 9104 0.0 5 8746 248 62 17 17 14 71 20773 0.0 5 20362 312 55 24 14 6 72 52712 0.0 5 52122 467 73 28 15 7 73 196754 0.0 5 195824 801 93 23 6 7 74 277918 0.0 5 276998 763 122 17 13 5 75 28719 0.0 5 28451 192 46 21 7 2 76 41046 0.0 5 40797 180 37 17 7 8 77 61535 0.0 5 61255 215 40 16 5 4 78 22596 0.0 5 22421 129 26 9 8 3 79 40730 0.0 5 40551 134 25 11 6 3 80 12792 0.0 5 12667 77 23 14 7 4 81 11000 0.0 5 10882 68 27 12 7 4 82 12213 0.0 5 12098 69 20 14 5 7 83 8267 0.0 5 8145 78 22 14 8 84 8850 0.0 5 8730 80 19 8 9 4 85 1403 0.0 5 1336 38 15 7 5 2 86 267 0.0 5 203 30 19 8 2 5 87 212 0.0 5 149 28 20 7 3 5 88 187 0.0 5 124 29 18 7 5 4 89 180 0.0 5 138 21 8 7 4 2 90 173 0.0 5 121 19 14 5 9 5 91 151 0.0 5 106 21 7 7 9 1 92 146 0.0 5 90 25 20 3 5 3 93 144 0.0 5 88 17 19 11 7 2 94 135 0.0 5 90 18 12 4 5 6 95 119 0.0 5 80 19 8 4 5 3 96 112 0.0 5 71 16 9 4 9 3 97 105 0.0 5 69 14 6 9 5 2 98 95 0.0 5 57 16 11 7 1 3 99 74 0.0 5 47 12 2 7 4 2 100 92 0.0 5 51 12 13 13 1 2 101 73 0.0 5 46 8 7 4 7 1 102 65 0.0 5 43 6 9 5 0 2 103 38 0.0 5 15 9 2 6 0 6 104 53 0.0 5 36 7 4 3 2 1 105 36 0.0 5 23 7 3 1 2 106 33 0.0 5 17 3 3 6 1 3 107 32 0.0 5 20 2 1 3 3 3 108 27 0.0 5 19 2 1 2 2 1 109 14 0.0 5 10 0 1 1 0 2 110 23 0.0 5 13 2 0 6 1 1 111 22 0.0 5 10 2 3 2 0 5 112 11 0.0 5 10 0 1 113 6 0.0 5 4 1 0 0 1 114 6 0.0 5 6 115 158 0.0 5 154 2 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_17_R1_val_1_val_1.fq.gz ============================================= 58274646 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_17_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_17_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/Hawes/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 zr3644_17_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/Hawes/analyses/trimgalore-2/zr3644_17_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_17_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1579.06 s (27 µs/read; 2.21 M reads/minute). === Summary === Total reads processed: 58,274,646 Reads with adapters: 5,699,368 (9.8%) Reads written (passing filters): 58,274,646 (100.0%) Total basepairs processed: 6,118,928,609 bp Quality-trimmed: 2,771,814 bp (0.0%) Total written (filtered): 6,011,821,590 bp (98.2%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5699368 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: 13.5% C: 5.2% G: 0.0% T: 81.3% 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 3542427 14568661.5 0 3542427 2 968038 3642165.4 0 968038 3 212784 910541.3 0 212784 4 59469 227635.3 0 59469 5 16969 56908.8 0 16969 6 4783 14227.2 0 4783 7 1617 3556.8 0 1617 8 811 889.2 0 811 9 754 222.3 0 754 10 2676 55.6 1 635 2041 11 2254 13.9 1 598 1656 12 1701 3.5 1 540 1161 13 1579 0.9 1 468 1111 14 1321 0.2 1 424 897 15 1143 0.1 1 385 758 16 1000 0.0 1 329 671 17 736 0.0 1 258 478 18 513 0.0 1 250 263 19 514 0.0 1 254 260 20 1245 0.0 2 307 250 688 21 1193 0.0 2 326 243 624 22 1047 0.0 2 268 190 589 23 941 0.0 2 274 196 471 24 873 0.0 2 250 183 440 25 797 0.0 2 252 163 382 26 687 0.0 2 234 170 283 27 616 0.0 2 223 136 257 28 508 0.0 2 221 119 168 29 449 0.0 2 189 112 148 30 882 0.0 3 183 119 144 436 31 878 0.0 3 188 141 158 391 32 747 0.0 3 182 106 128 331 33 684 0.0 3 172 82 107 323 34 640 0.0 3 141 100 117 282 35 647 0.0 3 175 102 109 261 36 606 0.0 3 166 101 97 242 37 505 0.0 3 177 90 75 163 38 460 0.0 3 169 84 84 123 39 448 0.0 3 179 75 84 110 40 724 0.0 4 147 84 68 107 318 41 757 0.0 4 181 94 69 104 309 42 676 0.0 4 145 85 83 100 263 43 618 0.0 4 137 93 61 90 237 44 586 0.0 4 128 68 74 95 221 45 553 0.0 4 127 74 66 94 192 46 561 0.0 4 150 88 67 88 168 47 572 0.0 4 183 85 74 63 167 48 593 0.0 4 173 120 107 94 99 49 1724 0.0 4 497 359 310 289 269 50 1703 0.0 5 423 306 288 253 230 203 51 1330 0.0 5 421 256 201 168 139 145 52 1248 0.0 5 437 217 202 147 131 114 53 1155 0.0 5 458 247 150 116 100 84 54 987 0.0 5 417 166 139 106 81 78 55 907 0.0 5 407 177 114 85 60 64 56 979 0.0 5 447 203 124 97 58 50 57 851 0.0 5 425 182 94 71 38 41 58 819 0.0 5 410 168 82 58 56 45 59 706 0.0 5 366 148 85 48 27 32 60 683 0.0 5 380 119 79 44 34 27 61 691 0.0 5 367 132 68 45 43 36 62 643 0.0 5 384 101 58 47 28 25 63 703 0.0 5 407 125 71 42 34 24 64 690 0.0 5 411 118 69 37 25 30 65 783 0.0 5 507 121 63 48 21 23 66 651 0.0 5 412 102 61 40 21 15 67 755 0.0 5 499 122 56 40 23 15 68 759 0.0 5 517 112 46 41 27 16 69 805 0.0 5 605 101 43 26 18 12 70 765 0.0 5 580 84 41 18 20 22 71 624 0.0 5 452 81 42 20 20 9 72 647 0.0 5 499 75 28 16 19 10 73 565 0.0 5 421 74 25 22 12 11 74 585 0.0 5 454 70 26 12 12 11 75 727 0.0 5 579 78 24 23 12 11 76 607 0.0 5 465 72 34 20 6 10 77 623 0.0 5 501 68 26 10 10 8 78 497 0.0 5 377 59 27 15 13 6 79 599 0.0 5 500 50 18 15 8 8 80 458 0.0 5 349 53 24 16 9 7 81 466 0.0 5 349 48 23 18 14 14 82 434 0.0 5 355 39 17 9 9 5 83 420 0.0 5 318 50 20 17 10 5 84 463 0.0 5 376 40 17 14 11 5 85 377 0.0 5 298 36 9 17 7 10 86 448 0.0 5 357 37 17 18 10 9 87 361 0.0 5 284 42 13 10 5 7 88 475 0.0 5 405 28 17 10 8 7 89 408 0.0 5 344 33 12 8 5 6 90 403 0.0 5 335 35 15 8 5 5 91 360 0.0 5 284 39 17 6 5 9 92 408 0.0 5 343 27 17 9 7 5 93 340 0.0 5 269 28 19 12 8 4 94 312 0.0 5 261 25 7 8 4 7 95 359 0.0 5 314 21 12 6 3 3 96 394 0.0 5 294 50 19 9 14 8 97 330 0.0 5 251 41 11 13 9 5 98 243 0.0 5 185 30 12 3 8 5 99 402 0.0 5 346 26 9 8 5 8 100 285 0.0 5 218 34 12 14 4 3 101 442 0.0 5 397 23 5 8 5 4 102 436 0.0 5 376 37 7 9 5 2 103 403 0.0 5 349 20 14 8 8 4 104 299 0.0 5 240 27 14 7 7 4 105 482 0.0 5 421 36 12 5 6 2 106 344 0.0 5 279 26 18 5 10 6 107 368 0.0 5 313 29 9 6 5 6 108 374 0.0 5 309 29 13 8 9 6 109 530 0.0 5 385 53 69 10 7 6 110 548 0.0 5 443 65 11 11 9 9 111 451 0.0 5 339 52 21 8 18 13 112 1044 0.0 5 872 62 38 24 23 25 113 1260 0.0 5 1059 91 35 38 19 18 114 4207 0.0 5 3862 178 80 33 22 32 115 812641 0.0 5 811466 898 150 63 38 26 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/Hawes/analyses/trimgalore-2/zr3644_17_R2_val_2_val_2.fq.gz ============================================= 58274646 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_17_R1_val_1_val_1_trimmed.fq.gz and zr3644_17_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_17_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_17_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_17_R1_val_1_val_1_trimmed.fq.gz and zr3644_17_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_17_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_17_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 58274646 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 844903 (1.45%) >>> Now running FastQC on the validated data zr3644_17_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_17_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_17_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_17_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_17_R1_val_1_val_1_trimmed.fq.gz and zr3644_17_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_18_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_18_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/Hawes/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 zr3644_18_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/Hawes/analyses/trimgalore-2/zr3644_18_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_18_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1377.71 s (27 µs/read; 2.25 M reads/minute). === Summary === Total reads processed: 51,684,377 Reads with adapters: 5,334,346 (10.3%) Reads written (passing filters): 51,684,377 (100.0%) Total basepairs processed: 5,432,148,452 bp Quality-trimmed: 1,909,821 bp (0.0%) Total written (filtered): 5,367,881,890 bp (98.8%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5334346 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: 22.2% C: 4.6% G: 0.0% T: 73.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3345375 12921094.2 0 3345375 2 933536 3230273.6 0 933536 3 200779 807568.4 0 200779 4 55040 201892.1 0 55040 5 16114 50473.0 0 16114 6 4504 12618.3 0 4504 7 1903 3154.6 0 1903 8 1342 788.6 0 1342 9 1218 197.2 0 1218 10 2627 49.3 1 1175 1452 11 2319 12.3 1 1125 1194 12 1991 3.1 1 967 1024 13 1717 0.8 1 850 867 14 1602 0.2 1 811 791 15 1408 0.0 1 703 705 16 1226 0.0 1 623 603 17 920 0.0 1 480 440 18 710 0.0 1 441 269 19 718 0.0 1 447 271 20 1124 0.0 2 462 269 393 21 980 0.0 2 404 242 334 22 900 0.0 2 395 240 265 23 849 0.0 2 365 204 280 24 832 0.0 2 385 215 232 25 768 0.0 2 344 216 208 26 656 0.0 2 298 178 180 27 625 0.0 2 305 152 168 28 519 0.0 2 298 119 102 29 508 0.0 2 238 165 105 30 746 0.0 3 272 163 130 181 31 672 0.0 3 234 157 125 156 32 649 0.0 3 233 147 111 158 33 626 0.0 3 240 131 98 157 34 616 0.0 3 212 151 114 139 35 581 0.0 3 231 141 84 125 36 542 0.0 3 205 129 78 130 37 566 0.0 3 224 139 86 117 38 459 0.0 3 198 108 80 73 39 457 0.0 3 187 115 77 78 40 518 0.0 4 181 92 75 65 105 41 551 0.0 4 184 105 105 73 84 42 589 0.0 4 200 110 87 87 105 43 534 0.0 4 161 123 77 75 98 44 513 0.0 4 158 103 85 81 86 45 449 0.0 4 136 88 76 63 86 46 507 0.0 4 158 102 82 85 80 47 462 0.0 4 164 120 65 49 64 48 539 0.0 4 210 134 76 61 58 49 1093 0.0 4 480 242 160 125 86 50 1334 0.0 5 642 240 151 121 99 81 51 974 0.0 5 561 169 103 71 46 24 52 911 0.0 5 504 182 92 52 46 35 53 804 0.0 5 479 150 70 50 31 24 54 871 0.0 5 578 123 86 39 29 16 55 995 0.0 5 690 141 77 39 25 23 56 1013 0.0 5 743 130 60 36 30 14 57 1031 0.0 5 756 132 64 48 19 12 58 1006 0.0 5 746 127 62 35 19 17 59 1207 0.0 5 966 123 41 36 22 19 60 839 0.0 5 608 133 56 16 17 9 61 917 0.0 5 688 142 47 24 12 4 62 1090 0.0 5 833 149 55 26 19 8 63 1184 0.0 5 966 126 42 28 13 9 64 1656 0.0 5 1434 128 50 27 12 5 65 1092 0.0 5 897 118 40 21 12 4 66 1279 0.0 5 1061 126 44 23 16 9 67 1467 0.0 5 1232 157 44 15 13 6 68 1843 0.0 5 1594 153 50 25 12 9 69 2456 0.0 5 2223 160 30 23 11 9 70 4223 0.0 5 3961 165 54 23 13 7 71 8564 0.0 5 8223 234 62 24 13 8 72 29806 0.0 5 29345 344 63 28 17 9 73 76462 0.0 5 75973 391 58 19 13 8 74 359374 0.0 5 358189 1039 104 14 20 8 75 29685 0.0 5 29416 193 46 20 8 2 76 20280 0.0 5 20066 160 29 11 8 6 77 71266 0.0 5 70992 213 32 18 6 5 78 11491 0.0 5 11355 89 27 8 6 6 79 44041 0.0 5 43846 137 28 14 9 7 80 12371 0.0 5 12247 78 20 14 8 4 81 7464 0.0 5 7333 78 28 9 11 5 82 14982 0.0 5 14848 86 22 9 10 7 83 6437 0.0 5 6322 77 19 12 5 2 84 13890 0.0 5 13727 126 20 13 2 2 85 3071 0.0 5 2979 53 18 11 5 5 86 355 0.0 5 294 29 13 11 4 4 87 196 0.0 5 134 25 13 11 11 2 88 144 0.0 5 92 23 15 7 4 3 89 156 0.0 5 100 22 12 11 8 3 90 162 0.0 5 103 29 15 8 4 3 91 150 0.0 5 97 30 9 6 5 3 92 102 0.0 5 64 17 7 9 4 1 93 128 0.0 5 81 20 14 7 5 1 94 112 0.0 5 81 15 7 5 3 1 95 122 0.0 5 73 17 6 15 6 5 96 103 0.0 5 68 12 13 6 1 3 97 89 0.0 5 58 10 11 3 4 3 98 86 0.0 5 60 11 7 5 1 2 99 52 0.0 5 32 6 4 6 3 1 100 74 0.0 5 52 8 4 7 1 2 101 63 0.0 5 38 10 8 3 1 3 102 54 0.0 5 34 9 6 2 2 1 103 43 0.0 5 29 4 2 4 0 4 104 30 0.0 5 17 6 1 2 4 105 25 0.0 5 12 6 2 2 1 2 106 26 0.0 5 16 3 2 3 2 107 18 0.0 5 11 2 4 0 0 1 108 22 0.0 5 15 0 4 1 0 2 109 17 0.0 5 10 1 0 3 0 3 110 23 0.0 5 13 4 0 2 2 2 111 14 0.0 5 10 0 3 0 1 112 13 0.0 5 10 1 0 0 1 1 113 1 0.0 5 1 114 11 0.0 5 8 0 3 115 100 0.0 5 100 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_18_R1_val_1_val_1.fq.gz ============================================= 51684377 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_18_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_18_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/Hawes/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 zr3644_18_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/Hawes/analyses/trimgalore-2/zr3644_18_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_18_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1399.55 s (27 µs/read; 2.22 M reads/minute). === Summary === Total reads processed: 51,684,377 Reads with adapters: 4,995,894 (9.7%) Reads written (passing filters): 51,684,377 (100.0%) Total basepairs processed: 5,429,561,606 bp Quality-trimmed: 2,494,613 bp (0.0%) Total written (filtered): 5,335,514,446 bp (98.3%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4995894 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: 13.5% C: 5.3% G: 0.0% T: 81.2% 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 3112300 12921094.2 0 3112300 2 842208 3230273.6 0 842208 3 185819 807568.4 0 185819 4 50994 201892.1 0 50994 5 14295 50473.0 0 14295 6 4008 12618.3 0 4008 7 1353 3154.6 0 1353 8 746 788.6 0 746 9 657 197.2 0 657 10 2382 49.3 1 617 1765 11 1903 12.3 1 505 1398 12 1518 3.1 1 453 1065 13 1338 0.8 1 407 931 14 1193 0.2 1 373 820 15 989 0.0 1 337 652 16 869 0.0 1 310 559 17 648 0.0 1 237 411 18 444 0.0 1 226 218 19 462 0.0 1 237 225 20 1074 0.0 2 285 219 570 21 1013 0.0 2 272 219 522 22 998 0.0 2 288 214 496 23 868 0.0 2 250 169 449 24 808 0.0 2 261 163 384 25 722 0.0 2 243 161 318 26 666 0.0 2 217 149 300 27 541 0.0 2 214 94 233 28 463 0.0 2 221 101 141 29 467 0.0 2 197 134 136 30 824 0.0 3 217 124 117 366 31 766 0.0 3 194 116 144 312 32 655 0.0 3 157 92 120 286 33 695 0.0 3 184 103 131 277 34 642 0.0 3 147 101 97 297 35 608 0.0 3 149 107 110 242 36 539 0.0 3 161 76 99 203 37 490 0.0 3 162 83 77 168 38 436 0.0 3 139 104 90 103 39 415 0.0 3 159 79 81 96 40 678 0.0 4 145 90 84 99 260 41 684 0.0 4 149 71 79 102 283 42 631 0.0 4 158 69 73 102 229 43 611 0.0 4 139 79 82 100 211 44 578 0.0 4 125 73 82 87 211 45 540 0.0 4 138 54 68 86 194 46 523 0.0 4 156 70 59 73 165 47 519 0.0 4 175 90 64 67 123 48 555 0.0 4 172 109 95 91 88 49 1460 0.0 4 444 305 256 230 225 50 1575 0.0 5 383 288 272 249 198 185 51 1192 0.0 5 402 246 167 151 120 106 52 1114 0.0 5 416 219 148 127 109 95 53 1020 0.0 5 395 207 146 118 88 66 54 914 0.0 5 402 171 116 95 67 63 55 812 0.0 5 377 168 93 81 52 41 56 865 0.0 5 450 180 82 69 54 30 57 773 0.0 5 400 143 94 59 45 32 58 698 0.0 5 347 142 81 55 44 29 59 681 0.0 5 353 135 70 55 37 31 60 627 0.0 5 350 120 67 34 31 25 61 618 0.0 5 339 124 62 39 33 21 62 594 0.0 5 329 100 76 35 37 17 63 641 0.0 5 377 118 58 45 20 23 64 626 0.0 5 379 119 64 28 23 13 65 648 0.0 5 446 94 45 22 21 20 66 585 0.0 5 369 101 48 37 22 8 67 654 0.0 5 441 97 58 22 26 10 68 682 0.0 5 472 104 41 29 17 19 69 748 0.0 5 567 104 36 19 15 7 70 705 0.0 5 550 77 29 20 15 14 71 535 0.0 5 403 60 26 22 11 13 72 509 0.0 5 383 70 24 11 14 7 73 515 0.0 5 400 63 18 21 9 4 74 505 0.0 5 404 49 17 19 8 8 75 576 0.0 5 460 67 17 20 6 6 76 489 0.0 5 376 56 27 7 12 11 77 559 0.0 5 480 44 19 10 5 1 78 453 0.0 5 360 49 19 10 10 5 79 498 0.0 5 406 48 18 11 9 6 80 460 0.0 5 369 49 18 11 5 8 81 409 0.0 5 331 42 12 11 8 5 82 382 0.0 5 310 36 18 8 5 5 83 364 0.0 5 293 37 17 6 7 4 84 400 0.0 5 332 32 11 13 8 4 85 351 0.0 5 284 38 11 8 5 5 86 423 0.0 5 355 46 9 5 2 6 87 357 0.0 5 291 40 10 8 4 4 88 396 0.0 5 343 33 14 2 4 89 332 0.0 5 289 21 8 8 3 3 90 365 0.0 5 306 27 16 7 6 3 91 294 0.0 5 235 29 16 8 2 4 92 380 0.0 5 317 28 12 10 5 8 93 283 0.0 5 226 26 12 7 8 4 94 305 0.0 5 252 27 10 5 6 5 95 318 0.0 5 265 33 7 4 4 5 96 327 0.0 5 259 36 17 10 3 2 97 353 0.0 5 283 36 10 12 8 4 98 252 0.0 5 214 13 7 9 2 7 99 375 0.0 5 335 18 8 9 3 2 100 228 0.0 5 178 31 4 4 5 6 101 405 0.0 5 366 21 8 3 2 5 102 425 0.0 5 364 30 17 4 5 5 103 347 0.0 5 303 24 7 4 8 1 104 268 0.0 5 230 15 11 5 5 2 105 380 0.0 5 332 35 4 3 3 3 106 280 0.0 5 233 20 13 6 5 3 107 338 0.0 5 267 44 12 6 5 4 108 340 0.0 5 279 32 12 4 9 4 109 500 0.0 5 356 69 47 13 6 9 110 503 0.0 5 419 42 18 9 7 8 111 419 0.0 5 319 40 17 23 9 11 112 929 0.0 5 779 66 37 16 15 16 113 1099 0.0 5 901 100 43 15 23 17 114 3813 0.0 5 3539 147 61 29 21 16 115 712488 0.0 5 711428 826 134 58 25 17 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/Hawes/analyses/trimgalore-2/zr3644_18_R2_val_2_val_2.fq.gz ============================================= 51684377 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_18_R1_val_1_val_1_trimmed.fq.gz and zr3644_18_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_18_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_18_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_18_R1_val_1_val_1_trimmed.fq.gz and zr3644_18_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_18_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_18_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 51684377 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 740954 (1.43%) >>> Now running FastQC on the validated data zr3644_18_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_18_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_18_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_18_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_18_R1_val_1_val_1_trimmed.fq.gz and zr3644_18_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_19_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_19_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/Hawes/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 zr3644_19_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/Hawes/analyses/trimgalore-2/zr3644_19_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_19_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1340.27 s (27 µs/read; 2.21 M reads/minute). === Summary === Total reads processed: 49,333,920 Reads with adapters: 5,033,638 (10.2%) Reads written (passing filters): 49,333,920 (100.0%) Total basepairs processed: 5,196,153,986 bp Quality-trimmed: 1,917,305 bp (0.0%) Total written (filtered): 5,136,156,029 bp (98.8%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5033638 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: 21.7% C: 4.6% G: 0.0% T: 73.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3170491 12333480.0 0 3170491 2 875860 3083370.0 0 875860 3 187018 770842.5 0 187018 4 51346 192710.6 0 51346 5 14915 48177.7 0 14915 6 4467 12044.4 0 4467 7 1971 3011.1 0 1971 8 1368 752.8 0 1368 9 1258 188.2 0 1258 10 2627 47.0 1 1190 1437 11 2366 11.8 1 1070 1296 12 2053 2.9 1 982 1071 13 1919 0.7 1 958 961 14 1647 0.2 1 812 835 15 1435 0.0 1 708 727 16 1228 0.0 1 617 611 17 979 0.0 1 498 481 18 853 0.0 1 502 351 19 781 0.0 1 475 306 20 1153 0.0 2 456 274 423 21 1153 0.0 2 450 282 421 22 1018 0.0 2 426 250 342 23 989 0.0 2 381 274 334 24 861 0.0 2 344 248 269 25 809 0.0 2 381 205 223 26 802 0.0 2 350 217 235 27 661 0.0 2 309 166 186 28 614 0.0 2 300 186 128 29 551 0.0 2 255 159 137 30 805 0.0 3 270 203 122 210 31 743 0.0 3 252 168 124 199 32 683 0.0 3 229 151 108 195 33 687 0.0 3 256 146 124 161 34 672 0.0 3 252 149 121 150 35 607 0.0 3 208 158 100 141 36 666 0.0 3 244 148 106 168 37 619 0.0 3 257 117 109 136 38 571 0.0 3 222 133 119 97 39 517 0.0 3 223 125 85 84 40 583 0.0 4 186 118 74 87 118 41 673 0.0 4 200 132 109 106 126 42 654 0.0 4 195 139 103 87 130 43 543 0.0 4 177 118 74 71 103 44 546 0.0 4 167 100 100 82 97 45 581 0.0 4 182 107 85 97 110 46 547 0.0 4 162 121 84 78 102 47 542 0.0 4 201 115 91 57 78 48 592 0.0 4 228 133 96 84 51 49 1243 0.0 4 500 283 201 148 111 50 1440 0.0 5 667 257 156 143 121 96 51 1060 0.0 5 579 188 117 82 53 41 52 1001 0.0 5 575 180 97 56 51 42 53 915 0.0 5 538 148 100 59 43 27 54 919 0.0 5 566 170 71 53 33 26 55 982 0.0 5 637 156 86 45 40 18 56 1084 0.0 5 723 179 78 45 35 24 57 988 0.0 5 693 153 58 37 29 18 58 1070 0.0 5 787 143 69 44 18 9 59 1174 0.0 5 899 135 64 38 19 19 60 945 0.0 5 664 148 74 29 15 15 61 1028 0.0 5 739 171 62 24 17 15 62 1118 0.0 5 881 137 50 23 16 11 63 1284 0.0 5 1014 148 58 37 13 14 64 1680 0.0 5 1454 138 45 23 13 7 65 1116 0.0 5 884 138 48 24 13 9 66 1341 0.0 5 1089 144 55 30 11 12 67 1540 0.0 5 1291 156 53 17 12 11 68 2039 0.0 5 1761 171 40 32 23 12 69 2750 0.0 5 2449 182 68 24 19 8 70 4637 0.0 5 4329 214 48 21 14 11 71 9624 0.0 5 9302 221 58 25 8 10 72 30578 0.0 5 30104 355 75 21 12 11 73 85105 0.0 5 84509 476 72 25 15 8 74 314541 0.0 5 313442 943 115 25 10 6 75 26169 0.0 5 25916 176 49 17 8 3 76 21254 0.0 5 21047 140 27 18 12 10 77 63401 0.0 5 63127 205 42 19 6 2 78 11969 0.0 5 11829 81 26 17 11 5 79 39549 0.0 5 39361 142 27 14 2 3 80 11087 0.0 5 10967 69 28 15 5 3 81 7375 0.0 5 7268 62 23 11 8 3 82 12964 0.0 5 12838 80 24 6 10 6 83 6512 0.0 5 6379 86 23 8 10 6 84 12350 0.0 5 12205 96 16 14 10 9 85 2340 0.0 5 2256 51 12 8 11 2 86 248 0.0 5 186 25 15 16 6 87 184 0.0 5 110 31 22 6 11 4 88 151 0.0 5 101 27 12 5 2 4 89 144 0.0 5 96 29 10 4 5 90 147 0.0 5 106 21 8 6 3 3 91 147 0.0 5 104 16 7 7 10 3 92 144 0.0 5 89 23 9 15 6 2 93 124 0.0 5 78 24 11 5 5 1 94 111 0.0 5 69 14 12 11 4 1 95 116 0.0 5 77 14 10 5 5 5 96 99 0.0 5 55 16 11 7 9 1 97 96 0.0 5 67 17 3 5 4 98 93 0.0 5 61 10 7 10 3 2 99 78 0.0 5 46 13 3 7 5 4 100 70 0.0 5 48 9 3 5 3 2 101 58 0.0 5 35 8 5 4 5 1 102 46 0.0 5 31 6 3 5 1 103 54 0.0 5 34 6 3 7 1 3 104 41 0.0 5 24 4 2 5 3 3 105 32 0.0 5 16 5 3 2 5 1 106 32 0.0 5 26 0 1 2 3 107 26 0.0 5 15 1 3 1 2 4 108 22 0.0 5 13 3 0 2 3 1 109 19 0.0 5 13 2 0 2 1 1 110 21 0.0 5 16 0 1 0 1 3 111 10 0.0 5 9 0 0 0 0 1 112 10 0.0 5 8 0 0 1 0 1 113 9 0.0 5 5 2 0 0 2 114 6 0.0 5 4 1 0 1 115 104 0.0 5 102 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_19_R1_val_1_val_1.fq.gz ============================================= 49333920 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_19_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_19_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/Hawes/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 zr3644_19_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/Hawes/analyses/trimgalore-2/zr3644_19_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_19_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1352.54 s (27 µs/read; 2.19 M reads/minute). === Summary === Total reads processed: 49,333,920 Reads with adapters: 4,796,171 (9.7%) Reads written (passing filters): 49,333,920 (100.0%) Total basepairs processed: 5,192,834,966 bp Quality-trimmed: 2,511,560 bp (0.0%) Total written (filtered): 5,104,568,897 bp (98.3%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4796171 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: 13.5% C: 5.1% G: 0.0% T: 81.4% 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 3000773 12333480.0 0 3000773 2 811870 3083370.0 0 811870 3 178102 770842.5 0 178102 4 48802 192710.6 0 48802 5 14686 48177.7 0 14686 6 4033 12044.4 0 4033 7 1537 3011.1 0 1537 8 750 752.8 0 750 9 655 188.2 0 655 10 2475 47.0 1 620 1855 11 2078 11.8 1 532 1546 12 1725 2.9 1 507 1218 13 1524 0.7 1 463 1061 14 1234 0.2 1 416 818 15 1118 0.0 1 314 804 16 860 0.0 1 270 590 17 668 0.0 1 226 442 18 449 0.0 1 194 255 19 423 0.0 1 178 245 20 1159 0.0 2 247 239 673 21 1098 0.0 2 274 222 602 22 982 0.0 2 239 215 528 23 904 0.0 2 209 212 483 24 802 0.0 2 212 168 422 25 760 0.0 2 215 160 385 26 615 0.0 2 179 149 287 27 514 0.0 2 200 94 220 28 452 0.0 2 201 112 139 29 435 0.0 2 181 111 143 30 757 0.0 3 155 90 129 383 31 792 0.0 3 199 100 139 354 32 649 0.0 3 138 97 115 299 33 632 0.0 3 133 85 126 288 34 648 0.0 3 132 99 113 304 35 595 0.0 3 147 102 91 255 36 537 0.0 3 130 90 100 217 37 445 0.0 3 148 69 68 160 38 420 0.0 3 137 90 72 121 39 403 0.0 3 130 86 78 109 40 659 0.0 4 134 68 74 117 266 41 657 0.0 4 136 73 63 112 273 42 576 0.0 4 112 52 87 79 246 43 584 0.0 4 112 75 75 89 233 44 545 0.0 4 111 63 73 91 207 45 529 0.0 4 132 65 53 93 186 46 487 0.0 4 112 65 53 74 183 47 476 0.0 4 120 70 68 75 143 48 501 0.0 4 153 96 93 81 78 49 1471 0.0 4 408 322 265 238 238 50 1596 0.0 5 383 307 271 249 198 188 51 1218 0.0 5 373 212 192 161 152 128 52 1137 0.0 5 375 236 164 148 129 85 53 1037 0.0 5 421 181 143 138 78 76 54 889 0.0 5 345 174 121 106 75 68 55 822 0.0 5 378 149 94 81 62 58 56 832 0.0 5 389 163 99 74 62 45 57 790 0.0 5 363 153 107 64 54 49 58 698 0.0 5 313 145 84 67 52 37 59 689 0.0 5 358 135 83 54 30 29 60 646 0.0 5 310 133 74 51 40 38 61 610 0.0 5 286 124 81 46 34 39 62 582 0.0 5 330 88 71 42 25 26 63 622 0.0 5 339 117 71 44 33 18 64 622 0.0 5 356 112 63 40 34 17 65 622 0.0 5 376 108 51 42 31 14 66 561 0.0 5 334 109 36 35 24 23 67 682 0.0 5 424 104 70 34 23 27 68 639 0.0 5 443 81 42 21 33 19 69 661 0.0 5 492 83 37 25 12 12 70 634 0.0 5 468 71 46 17 21 11 71 467 0.0 5 323 59 31 24 18 12 72 507 0.0 5 349 70 32 27 16 13 73 461 0.0 5 338 53 29 22 14 5 74 447 0.0 5 331 58 23 22 7 6 75 568 0.0 5 432 75 18 10 17 16 76 484 0.0 5 358 66 18 14 14 14 77 516 0.0 5 400 49 28 24 6 9 78 393 0.0 5 299 45 22 7 10 10 79 466 0.0 5 355 51 24 18 12 6 80 389 0.0 5 274 43 25 23 14 10 81 400 0.0 5 297 51 20 13 12 7 82 354 0.0 5 253 52 22 9 12 6 83 358 0.0 5 268 26 17 17 19 11 84 377 0.0 5 285 39 23 14 9 7 85 344 0.0 5 259 32 20 10 16 7 86 361 0.0 5 296 27 18 7 4 9 87 308 0.0 5 249 23 17 13 4 2 88 401 0.0 5 326 27 23 10 9 6 89 335 0.0 5 264 36 17 10 5 3 90 355 0.0 5 284 40 11 8 9 3 91 295 0.0 5 233 33 10 5 8 6 92 345 0.0 5 269 28 16 13 9 10 93 250 0.0 5 185 23 10 13 14 5 94 240 0.0 5 180 21 15 10 9 5 95 270 0.0 5 207 35 13 7 5 3 96 300 0.0 5 229 39 17 1 9 5 97 309 0.0 5 217 45 15 12 13 7 98 230 0.0 5 170 25 12 11 6 6 99 335 0.0 5 284 28 12 5 4 2 100 205 0.0 5 167 22 5 6 2 3 101 342 0.0 5 292 17 11 9 8 5 102 295 0.0 5 240 24 13 5 6 7 103 267 0.0 5 219 20 11 4 8 5 104 258 0.0 5 197 23 11 13 6 8 105 336 0.0 5 276 21 16 12 5 6 106 239 0.0 5 177 30 12 10 3 7 107 285 0.0 5 239 22 9 8 4 3 108 280 0.0 5 222 24 15 6 4 9 109 439 0.0 5 298 55 58 13 7 8 110 416 0.0 5 327 48 17 11 7 6 111 366 0.0 5 278 35 18 6 20 9 112 773 0.0 5 663 41 24 17 13 15 113 944 0.0 5 784 78 36 15 16 15 114 3194 0.0 5 2939 126 51 36 26 16 115 666232 0.0 5 665346 644 122 52 42 26 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/Hawes/analyses/trimgalore-2/zr3644_19_R2_val_2_val_2.fq.gz ============================================= 49333920 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_19_R1_val_1_val_1_trimmed.fq.gz and zr3644_19_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_19_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_19_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_19_R1_val_1_val_1_trimmed.fq.gz and zr3644_19_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_19_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_19_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 49333920 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 692353 (1.40%) >>> Now running FastQC on the validated data zr3644_19_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_19_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_19_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_19_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_19_R1_val_1_val_1_trimmed.fq.gz and zr3644_19_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_20_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_20_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/Hawes/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 zr3644_20_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/Hawes/analyses/trimgalore-2/zr3644_20_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_20_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1764.72 s (33 µs/read; 1.84 M reads/minute). === Summary === Total reads processed: 54,059,234 Reads with adapters: 5,748,185 (10.6%) Reads written (passing filters): 54,059,234 (100.0%) Total basepairs processed: 5,733,128,604 bp Quality-trimmed: 4,382,457 bp (0.1%) Total written (filtered): 5,671,566,936 bp (98.9%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5748185 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: 20.0% C: 5.3% G: 0.0% T: 74.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3707873 13514808.5 0 3707873 2 1020721 3378702.1 0 1020721 3 224478 844675.5 0 224478 4 62495 211168.9 0 62495 5 19367 52792.2 0 19367 6 5991 13198.1 0 5991 7 2433 3299.5 0 2433 8 1513 824.9 0 1513 9 1289 206.2 0 1289 10 3424 51.6 1 1195 2229 11 2748 12.9 1 1021 1727 12 2421 3.2 1 987 1434 13 2160 0.8 1 924 1236 14 1787 0.2 1 770 1017 15 1533 0.1 1 662 871 16 1357 0.0 1 607 750 17 1053 0.0 1 452 601 18 812 0.0 1 405 407 19 745 0.0 1 390 355 20 1298 0.0 2 349 334 615 21 1185 0.0 2 360 313 512 22 1094 0.0 2 337 299 458 23 999 0.0 2 334 260 405 24 889 0.0 2 292 246 351 25 856 0.0 2 272 243 341 26 753 0.0 2 256 199 298 27 645 0.0 2 232 192 221 28 557 0.0 2 233 183 141 29 531 0.0 2 211 165 155 30 847 0.0 3 221 189 155 282 31 753 0.0 3 191 170 152 240 32 750 0.0 3 203 169 142 236 33 685 0.0 3 194 151 131 209 34 635 0.0 3 169 154 117 195 35 646 0.0 3 173 169 129 175 36 640 0.0 3 201 144 115 180 37 532 0.0 3 164 131 101 136 38 476 0.0 3 142 118 103 113 39 486 0.0 3 149 137 93 107 40 610 0.0 4 147 111 101 92 159 41 631 0.0 4 139 130 111 92 159 42 613 0.0 4 133 99 98 111 172 43 538 0.0 4 124 103 99 75 137 44 551 0.0 4 131 109 88 69 154 45 538 0.0 4 136 95 86 84 137 46 572 0.0 4 153 117 103 79 120 47 538 0.0 4 141 125 116 68 88 48 536 0.0 4 149 113 110 84 80 49 1335 0.0 4 460 313 232 187 143 50 1599 0.0 5 668 309 192 161 148 121 51 1267 0.0 5 640 240 156 98 74 59 52 1135 0.0 5 572 211 135 101 65 51 53 1064 0.0 5 545 208 122 87 53 49 54 1215 0.0 5 691 232 115 76 59 42 55 1243 0.0 5 684 230 133 98 57 41 56 1267 0.0 5 767 245 126 62 45 22 57 1148 0.0 5 701 220 111 53 43 20 58 1151 0.0 5 746 179 99 58 35 34 59 1494 0.0 5 1086 205 92 55 29 27 60 1192 0.0 5 754 240 87 58 34 19 61 1122 0.0 5 741 190 83 56 27 25 62 1289 0.0 5 844 233 95 58 38 21 63 1319 0.0 5 979 175 72 46 23 24 64 2044 0.0 5 1700 189 73 38 21 23 65 1405 0.0 5 1065 178 79 37 27 19 66 1674 0.0 5 1313 182 78 52 37 12 67 2002 0.0 5 1576 243 82 56 25 20 68 2477 0.0 5 2088 223 93 39 22 12 69 3223 0.0 5 2737 306 91 52 25 12 70 5570 0.0 5 5089 301 96 53 15 16 71 10688 0.0 5 10041 437 125 46 22 17 72 34347 0.0 5 33284 768 188 59 23 25 73 67843 0.0 5 66575 961 213 61 23 10 74 275869 0.0 5 273142 2193 400 89 24 21 75 39846 0.0 5 39323 378 83 27 23 12 76 15945 0.0 5 15701 147 47 28 12 10 77 78006 0.0 5 77618 289 42 25 17 15 78 8696 0.0 5 8531 74 38 25 11 17 79 49399 0.0 5 49190 131 35 21 12 10 80 13492 0.0 5 13327 81 38 18 13 15 81 6339 0.0 5 6205 59 24 28 16 7 82 15991 0.0 5 15867 57 34 20 9 4 83 2282 0.0 5 2170 52 22 13 12 13 84 4882 0.0 5 4746 78 23 16 14 5 85 943 0.0 5 849 38 26 15 10 5 86 158 0.0 5 74 27 21 12 16 8 87 147 0.0 5 67 33 15 17 11 4 88 122 0.0 5 59 22 17 14 4 6 89 112 0.0 5 40 25 19 13 6 9 90 112 0.0 5 54 11 14 17 9 7 91 107 0.0 5 51 20 10 11 12 3 92 84 0.0 5 38 8 16 5 9 8 93 101 0.0 5 50 15 12 7 9 8 94 91 0.0 5 44 14 8 13 6 6 95 61 0.0 5 30 10 6 5 4 6 96 62 0.0 5 27 12 7 8 3 5 97 63 0.0 5 31 10 7 6 4 5 98 65 0.0 5 26 14 9 7 4 5 99 53 0.0 5 15 14 6 8 7 3 100 64 0.0 5 21 10 8 14 4 7 101 54 0.0 5 16 9 11 10 4 4 102 44 0.0 5 21 5 4 10 2 2 103 35 0.0 5 16 4 4 4 3 4 104 26 0.0 5 9 3 4 4 3 3 105 25 0.0 5 10 5 4 3 1 2 106 25 0.0 5 8 3 3 0 7 4 107 14 0.0 5 5 2 5 1 1 108 21 0.0 5 11 2 1 3 0 4 109 12 0.0 5 9 0 2 0 1 110 10 0.0 5 5 0 2 1 0 2 111 7 0.0 5 6 0 0 1 112 4 0.0 5 2 2 113 7 0.0 5 3 2 0 1 1 114 13 0.0 5 9 1 2 1 115 99 0.0 5 92 4 1 2 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_20_R1_val_1_val_1.fq.gz ============================================= 54059234 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_20_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_20_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/Hawes/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 zr3644_20_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/Hawes/analyses/trimgalore-2/zr3644_20_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_20_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1465.57 s (27 µs/read; 2.21 M reads/minute). === Summary === Total reads processed: 54,059,234 Reads with adapters: 5,197,879 (9.6%) Reads written (passing filters): 54,059,234 (100.0%) Total basepairs processed: 5,740,716,711 bp Quality-trimmed: 2,246,683 bp (0.0%) Total written (filtered): 5,655,145,410 bp (98.5%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5197879 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: 13.1% C: 4.8% G: 0.0% T: 82.1% 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 3334060 13514808.5 0 3334060 2 894690 3378702.1 0 894690 3 191344 844675.5 0 191344 4 51912 211168.9 0 51912 5 14211 52792.2 0 14211 6 3833 13198.1 0 3833 7 1270 3299.5 0 1270 8 719 824.9 0 719 9 678 206.2 0 678 10 2108 51.6 1 644 1464 11 1746 12.9 1 525 1221 12 1452 3.2 1 487 965 13 1312 0.8 1 460 852 14 1124 0.2 1 405 719 15 992 0.1 1 343 649 16 827 0.0 1 318 509 17 665 0.0 1 247 418 18 480 0.0 1 208 272 19 461 0.0 1 224 237 20 1063 0.0 2 278 223 562 21 962 0.0 2 289 202 471 22 900 0.0 2 278 180 442 23 789 0.0 2 249 176 364 24 749 0.0 2 271 171 307 25 736 0.0 2 251 163 322 26 627 0.0 2 233 155 239 27 512 0.0 2 190 114 208 28 473 0.0 2 203 118 152 29 469 0.0 2 209 113 147 30 702 0.0 3 225 93 113 271 31 715 0.0 3 190 106 128 291 32 617 0.0 3 179 93 115 230 33 607 0.0 3 197 95 93 222 34 597 0.0 3 172 96 109 220 35 572 0.0 3 161 108 104 199 36 547 0.0 3 177 84 99 187 37 450 0.0 3 155 70 88 137 38 417 0.0 3 183 79 67 88 39 442 0.0 3 167 92 87 96 40 593 0.0 4 150 79 82 93 189 41 627 0.0 4 204 83 83 79 178 42 534 0.0 4 128 82 67 77 180 43 572 0.0 4 142 96 83 84 167 44 473 0.0 4 126 67 63 86 131 45 515 0.0 4 138 67 61 92 157 46 527 0.0 4 163 79 78 74 133 47 502 0.0 4 160 92 75 48 127 48 582 0.0 4 195 118 95 93 81 49 1223 0.0 4 409 258 221 175 160 50 1359 0.0 5 336 246 228 209 186 154 51 962 0.0 5 343 202 143 97 90 87 52 845 0.0 5 359 144 101 97 71 73 53 858 0.0 5 363 184 92 95 79 45 54 761 0.0 5 368 154 87 61 50 41 55 632 0.0 5 301 137 75 49 39 31 56 701 0.0 5 378 130 77 46 35 35 57 581 0.0 5 332 102 60 30 36 21 58 571 0.0 5 312 105 56 48 27 23 59 518 0.0 5 289 93 53 40 25 18 60 551 0.0 5 308 119 50 40 20 14 61 479 0.0 5 280 73 47 31 22 26 62 505 0.0 5 323 77 54 17 25 9 63 492 0.0 5 319 68 34 39 15 17 64 503 0.0 5 315 87 53 16 19 13 65 519 0.0 5 349 80 39 24 15 12 66 486 0.0 5 338 64 38 19 18 9 67 542 0.0 5 363 78 35 39 17 10 68 466 0.0 5 324 65 38 12 11 16 69 535 0.0 5 402 65 31 16 13 8 70 484 0.0 5 359 62 23 18 15 7 71 424 0.0 5 304 51 24 17 16 12 72 408 0.0 5 287 64 25 18 7 7 73 433 0.0 5 319 43 33 19 11 8 74 423 0.0 5 323 41 33 13 8 5 75 473 0.0 5 377 50 22 7 10 7 76 399 0.0 5 298 48 23 14 11 5 77 457 0.0 5 353 58 12 9 15 10 78 348 0.0 5 253 39 22 18 10 6 79 440 0.0 5 349 49 15 6 12 9 80 351 0.0 5 281 38 16 7 7 2 81 345 0.0 5 273 35 11 10 8 8 82 312 0.0 5 249 32 16 8 5 2 83 311 0.0 5 246 39 10 6 5 5 84 358 0.0 5 286 34 14 9 7 8 85 300 0.0 5 241 31 15 2 4 7 86 323 0.0 5 253 30 13 13 4 10 87 260 0.0 5 216 22 13 2 6 1 88 372 0.0 5 327 13 13 10 6 3 89 281 0.0 5 230 21 8 9 12 1 90 261 0.0 5 211 26 14 4 3 3 91 226 0.0 5 180 28 5 7 3 3 92 326 0.0 5 259 33 16 10 6 2 93 187 0.0 5 149 16 7 9 1 5 94 218 0.0 5 170 17 17 8 4 2 95 287 0.0 5 238 23 9 6 6 5 96 278 0.0 5 211 37 14 6 2 8 97 257 0.0 5 203 34 8 4 6 2 98 185 0.0 5 152 10 6 6 6 5 99 338 0.0 5 283 29 8 8 3 7 100 183 0.0 5 129 27 9 6 8 4 101 337 0.0 5 285 26 10 7 4 5 102 311 0.0 5 257 31 10 2 7 4 103 268 0.0 5 235 16 9 1 6 1 104 232 0.0 5 194 16 7 6 4 5 105 326 0.0 5 271 27 7 8 5 8 106 239 0.0 5 191 17 12 9 5 5 107 252 0.0 5 198 18 13 11 7 5 108 253 0.0 5 190 15 18 8 12 10 109 413 0.0 5 281 50 47 14 11 10 110 422 0.0 5 331 47 20 16 6 2 111 326 0.0 5 237 39 14 18 10 8 112 779 0.0 5 644 37 30 20 23 25 113 922 0.0 5 733 72 39 32 23 23 114 2802 0.0 5 2524 128 47 28 49 26 115 643905 0.0 5 642895 744 135 62 36 33 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/Hawes/analyses/trimgalore-2/zr3644_20_R2_val_2_val_2.fq.gz ============================================= 54059234 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_20_R1_val_1_val_1_trimmed.fq.gz and zr3644_20_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_20_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_20_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_20_R1_val_1_val_1_trimmed.fq.gz and zr3644_20_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_20_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_20_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 54059234 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 669163 (1.24%) >>> Now running FastQC on the validated data zr3644_20_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_20_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_20_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_20_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_20_R1_val_1_val_1_trimmed.fq.gz and zr3644_20_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_21_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_21_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/Hawes/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 zr3644_21_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/Hawes/analyses/trimgalore-2/zr3644_21_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_21_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1448.55 s (28 µs/read; 2.12 M reads/minute). === Summary === Total reads processed: 51,084,771 Reads with adapters: 5,204,728 (10.2%) Reads written (passing filters): 51,084,771 (100.0%) Total basepairs processed: 5,409,366,714 bp Quality-trimmed: 2,493,851 bp (0.0%) Total written (filtered): 5,352,841,996 bp (99.0%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5204728 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: 20.7% C: 4.8% G: 0.0% T: 74.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3337481 12771192.8 0 3337481 2 914875 3192798.2 0 914875 3 197650 798199.5 0 197650 4 55714 199549.9 0 55714 5 16579 49887.5 0 16579 6 5088 12471.9 0 5088 7 2369 3118.0 0 2369 8 1608 779.5 0 1608 9 1497 194.9 0 1497 10 3191 48.7 1 1380 1811 11 2861 12.2 1 1308 1553 12 2465 3.0 1 1218 1247 13 2314 0.8 1 1141 1173 14 1966 0.2 1 966 1000 15 1784 0.0 1 877 907 16 1548 0.0 1 737 811 17 1217 0.0 1 608 609 18 1057 0.0 1 612 445 19 971 0.0 1 593 378 20 1457 0.0 2 591 333 533 21 1360 0.0 2 530 364 466 22 1222 0.0 2 517 304 401 23 1112 0.0 2 421 296 395 24 1062 0.0 2 457 278 327 25 995 0.0 2 407 297 291 26 868 0.0 2 394 220 254 27 846 0.0 2 408 209 229 28 765 0.0 2 385 209 171 29 703 0.0 2 342 217 144 30 925 0.0 3 330 212 140 243 31 925 0.0 3 317 220 171 217 32 828 0.0 3 286 179 149 214 33 882 0.0 3 331 204 128 219 34 852 0.0 3 305 210 140 197 35 767 0.0 3 272 202 124 169 36 709 0.0 3 273 170 129 137 37 641 0.0 3 226 165 113 137 38 652 0.0 3 262 157 121 112 39 567 0.0 3 234 149 109 75 40 756 0.0 4 252 151 110 109 134 41 757 0.0 4 262 154 108 96 137 42 780 0.0 4 255 151 110 99 165 43 677 0.0 4 232 133 98 80 134 44 694 0.0 4 215 133 98 91 157 45 688 0.0 4 219 138 106 97 128 46 669 0.0 4 215 155 107 82 110 47 682 0.0 4 244 139 119 85 95 48 734 0.0 4 318 150 123 73 70 49 1385 0.0 4 580 298 222 155 130 50 1555 0.0 5 664 330 198 157 119 87 51 1156 0.0 5 572 241 138 89 63 53 52 1111 0.0 5 598 213 126 74 55 45 53 989 0.0 5 544 172 109 73 57 34 54 1029 0.0 5 647 173 101 50 33 25 55 1122 0.0 5 685 211 96 55 45 30 56 1175 0.0 5 800 196 84 39 37 19 57 1098 0.0 5 720 178 96 58 27 19 58 1109 0.0 5 778 153 90 47 29 12 59 1262 0.0 5 929 165 80 49 23 16 60 1034 0.0 5 689 186 71 48 26 14 61 1095 0.0 5 783 193 44 35 18 22 62 1177 0.0 5 860 170 77 40 22 8 63 1259 0.0 5 994 142 63 27 22 11 64 1666 0.0 5 1397 138 68 37 16 10 65 1141 0.0 5 870 136 53 41 25 16 66 1270 0.0 5 978 157 66 34 20 15 67 1602 0.0 5 1273 193 62 41 19 14 68 1844 0.0 5 1540 172 64 37 20 11 69 2411 0.0 5 2101 195 64 26 12 13 70 4004 0.0 5 3669 214 62 33 13 13 71 7997 0.0 5 7605 257 66 30 24 15 72 25991 0.0 5 25493 359 86 25 14 14 73 69069 0.0 5 68474 461 84 30 13 7 74 287273 0.0 5 286101 1005 122 27 11 7 75 27985 0.0 5 27710 193 48 14 15 5 76 17778 0.0 5 17551 150 38 28 7 4 77 61241 0.0 5 60924 218 51 29 8 11 78 10322 0.0 5 10158 102 31 15 12 4 79 38607 0.0 5 38403 129 33 22 15 5 80 11359 0.0 5 11189 107 26 20 10 7 81 6811 0.0 5 6667 85 24 15 17 3 82 12867 0.0 5 12718 76 33 19 16 5 83 4658 0.0 5 4524 86 19 11 9 9 84 9134 0.0 5 8976 92 30 20 10 6 85 2202 0.0 5 2102 54 21 13 8 4 86 335 0.0 5 224 52 29 17 9 4 87 244 0.0 5 163 37 20 12 8 4 88 194 0.0 5 126 30 17 9 4 8 89 212 0.0 5 128 36 18 15 7 8 90 208 0.0 5 123 31 25 14 8 7 91 189 0.0 5 115 27 18 14 10 5 92 167 0.0 5 94 32 19 6 8 8 93 153 0.0 5 86 26 19 7 9 6 94 152 0.0 5 101 24 14 5 4 4 95 135 0.0 5 83 26 11 4 7 4 96 115 0.0 5 78 19 7 3 3 5 97 111 0.0 5 64 14 12 7 7 7 98 86 0.0 5 52 13 8 5 5 3 99 99 0.0 5 59 12 11 8 7 2 100 101 0.0 5 56 14 10 12 4 5 101 84 0.0 5 42 16 12 6 5 3 102 69 0.0 5 40 8 6 3 7 5 103 66 0.0 5 33 9 11 10 2 1 104 49 0.0 5 26 6 5 6 3 3 105 44 0.0 5 29 6 3 1 3 2 106 45 0.0 5 21 9 2 4 3 6 107 30 0.0 5 21 2 0 4 1 2 108 31 0.0 5 18 4 3 3 0 3 109 23 0.0 5 14 3 4 0 1 1 110 19 0.0 5 11 2 1 2 3 111 19 0.0 5 10 4 1 2 1 1 112 19 0.0 5 10 5 0 1 3 113 14 0.0 5 11 0 0 1 1 1 114 14 0.0 5 12 1 1 115 103 0.0 5 99 3 0 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_21_R1_val_1_val_1.fq.gz ============================================= 51084771 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_21_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_21_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/Hawes/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 zr3644_21_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/Hawes/analyses/trimgalore-2/zr3644_21_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_21_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1393.63 s (27 µs/read; 2.20 M reads/minute). === Summary === Total reads processed: 51,084,771 Reads with adapters: 4,778,825 (9.4%) Reads written (passing filters): 51,084,771 (100.0%) Total basepairs processed: 5,409,409,673 bp Quality-trimmed: 2,498,318 bp (0.0%) Total written (filtered): 5,328,559,450 bp (98.5%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4778825 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: 13.3% C: 5.2% G: 0.0% T: 81.5% 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 3045313 12771192.8 0 3045313 2 810557 3192798.2 0 810557 3 178296 798199.5 0 178296 4 49575 199549.9 0 49575 5 14579 49887.5 0 14579 6 4179 12471.9 0 4179 7 1567 3118.0 0 1567 8 883 779.5 0 883 9 804 194.9 0 804 10 2624 48.7 1 691 1933 11 2143 12.2 1 643 1500 12 1752 3.0 1 552 1200 13 1552 0.8 1 476 1076 14 1419 0.2 1 504 915 15 1136 0.0 1 405 731 16 1008 0.0 1 376 632 17 785 0.0 1 283 502 18 541 0.0 1 252 289 19 538 0.0 1 280 258 20 1302 0.0 2 361 251 690 21 1138 0.0 2 338 253 547 22 1066 0.0 2 293 244 529 23 1005 0.0 2 312 229 464 24 945 0.0 2 298 215 432 25 847 0.0 2 271 177 399 26 733 0.0 2 251 178 304 27 602 0.0 2 229 131 242 28 533 0.0 2 252 137 144 29 495 0.0 2 207 131 157 30 855 0.0 3 225 117 145 368 31 830 0.0 3 224 103 154 349 32 736 0.0 3 194 124 130 288 33 746 0.0 3 200 112 114 320 34 674 0.0 3 165 113 147 249 35 683 0.0 3 179 109 113 282 36 621 0.0 3 215 103 102 201 37 519 0.0 3 194 82 74 169 38 512 0.0 3 188 107 99 118 39 468 0.0 3 156 99 92 121 40 713 0.0 4 171 85 76 113 268 41 739 0.0 4 189 87 93 101 269 42 629 0.0 4 148 96 88 94 203 43 660 0.0 4 156 94 69 106 235 44 591 0.0 4 127 85 84 98 197 45 592 0.0 4 151 87 68 97 189 46 582 0.0 4 189 76 64 98 155 47 590 0.0 4 186 100 84 68 152 48 622 0.0 4 190 131 96 102 103 49 1454 0.0 4 481 296 244 223 210 50 1640 0.0 5 421 338 283 200 197 201 51 1259 0.0 5 426 245 189 166 144 89 52 1127 0.0 5 434 235 154 114 90 100 53 1071 0.0 5 470 204 137 105 76 79 54 909 0.0 5 424 178 100 84 79 44 55 880 0.0 5 414 168 101 84 70 43 56 883 0.0 5 454 176 93 64 52 44 57 805 0.0 5 432 127 99 66 40 41 58 747 0.0 5 365 149 81 58 56 38 59 686 0.0 5 372 123 72 59 35 25 60 757 0.0 5 416 141 83 63 26 28 61 646 0.0 5 373 107 67 47 28 24 62 644 0.0 5 374 133 56 43 19 19 63 676 0.0 5 400 132 63 36 28 17 64 590 0.0 5 348 109 56 31 26 20 65 647 0.0 5 393 93 65 41 24 31 66 617 0.0 5 381 107 49 29 30 21 67 627 0.0 5 428 77 47 34 30 11 68 645 0.0 5 459 81 37 37 16 15 69 702 0.0 5 515 88 50 22 18 9 70 647 0.0 5 490 77 29 22 19 10 71 538 0.0 5 381 59 37 26 21 14 72 488 0.0 5 350 61 34 18 16 9 73 494 0.0 5 363 64 23 16 17 11 74 494 0.0 5 375 57 17 21 15 9 75 558 0.0 5 455 50 17 14 13 9 76 506 0.0 5 402 51 20 20 8 5 77 509 0.0 5 391 50 29 24 9 6 78 385 0.0 5 290 46 13 18 10 8 79 479 0.0 5 380 46 25 17 6 5 80 414 0.0 5 329 36 26 9 9 5 81 391 0.0 5 286 50 28 16 8 3 82 366 0.0 5 297 31 18 10 8 2 83 381 0.0 5 295 49 19 9 4 5 84 372 0.0 5 293 34 18 14 6 7 85 347 0.0 5 280 28 14 10 9 6 86 358 0.0 5 277 44 18 6 6 7 87 326 0.0 5 247 40 15 7 10 7 88 393 0.0 5 336 23 14 9 5 6 89 370 0.0 5 286 45 14 14 5 6 90 293 0.0 5 236 23 14 11 4 5 91 308 0.0 5 232 40 14 14 3 5 92 336 0.0 5 276 29 9 9 8 5 93 269 0.0 5 216 23 11 7 7 5 94 255 0.0 5 200 25 13 5 5 7 95 300 0.0 5 251 25 15 3 4 2 96 309 0.0 5 249 29 13 8 4 6 97 287 0.0 5 216 27 16 16 8 4 98 234 0.0 5 188 18 6 7 9 6 99 332 0.0 5 279 23 9 10 9 2 100 172 0.0 5 127 18 6 8 8 5 101 326 0.0 5 284 21 8 5 4 4 102 321 0.0 5 270 26 12 4 3 6 103 295 0.0 5 237 28 12 9 5 4 104 222 0.0 5 188 8 13 6 1 6 105 344 0.0 5 293 25 12 8 5 1 106 287 0.0 5 230 28 5 12 4 8 107 287 0.0 5 227 20 17 8 10 5 108 282 0.0 5 226 19 18 4 3 12 109 411 0.0 5 291 43 49 11 7 10 110 441 0.0 5 355 39 18 8 9 12 111 379 0.0 5 277 37 18 17 15 15 112 807 0.0 5 668 58 29 18 20 14 113 921 0.0 5 777 62 35 19 9 19 114 3063 0.0 5 2827 123 36 27 27 23 115 600237 0.0 5 599385 616 126 47 40 23 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/Hawes/analyses/trimgalore-2/zr3644_21_R2_val_2_val_2.fq.gz ============================================= 51084771 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_21_R1_val_1_val_1_trimmed.fq.gz and zr3644_21_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_21_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_21_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_21_R1_val_1_val_1_trimmed.fq.gz and zr3644_21_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_21_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_21_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 51084771 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 627470 (1.23%) >>> Now running FastQC on the validated data zr3644_21_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_21_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_21_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_21_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_21_R1_val_1_val_1_trimmed.fq.gz and zr3644_21_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_22_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_22_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/Hawes/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 zr3644_22_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/Hawes/analyses/trimgalore-2/zr3644_22_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_22_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1269.64 s (27 µs/read; 2.25 M reads/minute). === Summary === Total reads processed: 47,698,628 Reads with adapters: 4,908,078 (10.3%) Reads written (passing filters): 47,698,628 (100.0%) Total basepairs processed: 5,034,918,251 bp Quality-trimmed: 1,731,407 bp (0.0%) Total written (filtered): 4,975,982,532 bp (98.8%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4908078 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: 22.4% C: 4.5% G: 0.0% T: 73.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3073822 11924657.0 0 3073822 2 859148 2981164.2 0 859148 3 185185 745291.1 0 185185 4 51606 186322.8 0 51606 5 15167 46580.7 0 15167 6 4431 11645.2 0 4431 7 1956 2911.3 0 1956 8 1306 727.8 0 1306 9 1259 182.0 0 1259 10 2741 45.5 1 1232 1509 11 2314 11.4 1 1081 1233 12 2076 2.8 1 1025 1051 13 1902 0.7 1 931 971 14 1638 0.2 1 833 805 15 1368 0.0 1 733 635 16 1216 0.0 1 632 584 17 988 0.0 1 522 466 18 816 0.0 1 494 322 19 797 0.0 1 480 317 20 1191 0.0 2 487 270 434 21 1098 0.0 2 439 263 396 22 982 0.0 2 422 235 325 23 964 0.0 2 439 214 311 24 900 0.0 2 418 214 268 25 873 0.0 2 382 245 246 26 746 0.0 2 331 211 204 27 635 0.0 2 294 160 181 28 636 0.0 2 330 170 136 29 632 0.0 2 319 167 146 30 804 0.0 3 306 145 153 200 31 799 0.0 3 288 204 122 185 32 765 0.0 3 296 147 127 195 33 689 0.0 3 267 164 91 167 34 647 0.0 3 235 135 104 173 35 647 0.0 3 260 133 120 134 36 628 0.0 3 237 155 119 117 37 581 0.0 3 232 130 95 124 38 550 0.0 3 223 127 105 95 39 548 0.0 3 222 126 90 110 40 585 0.0 4 195 130 80 70 110 41 644 0.0 4 185 141 100 95 123 42 638 0.0 4 213 124 104 72 125 43 598 0.0 4 187 130 86 92 103 44 551 0.0 4 164 131 80 79 97 45 565 0.0 4 196 112 79 82 96 46 630 0.0 4 200 125 111 95 99 47 607 0.0 4 219 130 98 72 88 48 646 0.0 4 253 143 101 77 72 49 1205 0.0 4 517 274 164 125 125 50 1384 0.0 5 647 246 191 129 93 78 51 1039 0.0 5 615 169 93 71 50 41 52 960 0.0 5 566 180 95 48 37 34 53 795 0.0 5 489 129 80 42 31 24 54 852 0.0 5 542 134 71 48 31 26 55 967 0.0 5 656 140 76 46 31 18 56 1019 0.0 5 701 164 82 31 22 19 57 960 0.0 5 700 132 58 34 22 14 58 1075 0.0 5 807 140 57 32 28 11 59 1204 0.0 5 990 107 61 18 18 10 60 825 0.0 5 595 129 47 37 11 6 61 915 0.0 5 699 108 53 32 14 9 62 1009 0.0 5 793 111 53 20 21 11 63 1071 0.0 5 866 109 50 26 13 7 64 1692 0.0 5 1456 122 56 25 22 11 65 1051 0.0 5 834 128 41 28 14 6 66 1193 0.0 5 952 142 56 18 16 9 67 1360 0.0 5 1134 136 48 18 15 9 68 1695 0.0 5 1436 162 57 15 12 13 69 2221 0.0 5 1967 154 51 22 19 8 70 3537 0.0 5 3297 154 50 13 13 10 71 6630 0.0 5 6298 223 68 26 10 5 72 25246 0.0 5 24858 298 46 22 9 13 73 52023 0.0 5 51602 336 48 18 10 9 74 344108 0.0 5 342981 981 101 32 12 1 75 32573 0.0 5 32299 195 43 19 9 8 76 15262 0.0 5 15077 120 34 19 7 5 77 69295 0.0 5 69036 204 33 11 6 5 78 9395 0.0 5 9258 85 28 9 11 4 79 43554 0.0 5 43355 143 31 14 8 3 80 12598 0.0 5 12493 68 18 8 8 3 81 6446 0.0 5 6339 68 15 13 5 6 82 14426 0.0 5 14293 86 27 8 8 4 83 4129 0.0 5 4023 66 20 9 7 4 84 9381 0.0 5 9252 92 15 11 7 4 85 1974 0.0 5 1886 47 24 8 6 3 86 235 0.0 5 177 31 11 6 5 5 87 161 0.0 5 106 24 11 6 9 5 88 167 0.0 5 111 30 13 2 4 7 89 164 0.0 5 115 22 15 6 4 2 90 166 0.0 5 115 29 8 5 4 5 91 159 0.0 5 103 31 10 5 8 2 92 119 0.0 5 93 15 8 1 1 1 93 136 0.0 5 93 19 13 6 1 4 94 117 0.0 5 86 12 6 5 4 4 95 122 0.0 5 77 23 6 7 7 2 96 88 0.0 5 57 11 12 4 1 3 97 93 0.0 5 64 10 9 4 2 4 98 91 0.0 5 53 12 8 5 7 6 99 65 0.0 5 35 12 9 2 5 2 100 72 0.0 5 43 6 6 4 7 6 101 84 0.0 5 56 5 14 4 2 3 102 65 0.0 5 37 14 8 2 1 3 103 54 0.0 5 30 15 7 0 0 2 104 36 0.0 5 23 5 2 2 4 105 39 0.0 5 29 3 2 4 1 106 35 0.0 5 23 4 4 0 3 1 107 34 0.0 5 20 6 2 1 1 4 108 21 0.0 5 16 1 1 1 0 2 109 19 0.0 5 12 1 1 0 3 2 110 14 0.0 5 12 2 111 8 0.0 5 6 2 112 10 0.0 5 5 2 1 1 0 1 113 4 0.0 5 4 114 10 0.0 5 6 1 1 1 0 1 115 106 0.0 5 105 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_22_R1_val_1_val_1.fq.gz ============================================= 47698628 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_22_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_22_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/Hawes/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 zr3644_22_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/Hawes/analyses/trimgalore-2/zr3644_22_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_22_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1298.27 s (27 µs/read; 2.20 M reads/minute). === Summary === Total reads processed: 47,698,628 Reads with adapters: 4,666,293 (9.8%) Reads written (passing filters): 47,698,628 (100.0%) Total basepairs processed: 5,031,539,124 bp Quality-trimmed: 2,384,978 bp (0.0%) Total written (filtered): 4,944,898,456 bp (98.3%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4666293 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: 13.5% C: 5.2% G: 0.0% T: 81.3% 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 2903365 11924657.0 0 2903365 2 793195 2981164.2 0 793195 3 174737 745291.1 0 174737 4 48260 186322.8 0 48260 5 14516 46580.7 0 14516 6 4100 11645.2 0 4100 7 1589 2911.3 0 1589 8 809 727.8 0 809 9 739 182.0 0 739 10 2591 45.5 1 732 1859 11 2122 11.4 1 624 1498 12 1661 2.8 1 580 1081 13 1517 0.7 1 498 1019 14 1264 0.2 1 463 801 15 1168 0.0 1 427 741 16 925 0.0 1 369 556 17 797 0.0 1 315 482 18 565 0.0 1 288 277 19 549 0.0 1 274 275 20 1133 0.0 2 342 221 570 21 1107 0.0 2 315 251 541 22 1009 0.0 2 303 204 502 23 939 0.0 2 311 195 433 24 883 0.0 2 284 191 408 25 819 0.0 2 277 189 353 26 718 0.0 2 226 182 310 27 571 0.0 2 209 124 238 28 529 0.0 2 244 128 157 29 466 0.0 2 200 108 158 30 824 0.0 3 243 121 147 313 31 810 0.0 3 208 117 138 347 32 723 0.0 3 184 99 132 308 33 633 0.0 3 176 94 96 267 34 631 0.0 3 180 99 102 250 35 588 0.0 3 170 103 115 200 36 589 0.0 3 209 89 109 182 37 496 0.0 3 188 94 74 140 38 485 0.0 3 160 100 97 128 39 454 0.0 3 166 100 82 106 40 728 0.0 4 171 88 89 106 274 41 673 0.0 4 198 98 75 86 216 42 647 0.0 4 140 95 75 109 228 43 646 0.0 4 164 87 94 95 206 44 616 0.0 4 145 100 72 87 212 45 552 0.0 4 134 80 79 81 178 46 550 0.0 4 162 79 68 84 157 47 560 0.0 4 159 118 74 79 130 48 605 0.0 4 221 120 102 73 89 49 1471 0.0 4 446 320 259 240 206 50 1654 0.0 5 433 317 279 233 208 184 51 1184 0.0 5 401 236 169 142 120 116 52 1066 0.0 5 446 184 140 115 87 94 53 1010 0.0 5 456 160 138 108 81 67 54 879 0.0 5 404 164 110 89 57 55 55 836 0.0 5 444 136 105 63 45 43 56 816 0.0 5 437 135 96 58 53 37 57 823 0.0 5 412 150 94 83 53 31 58 722 0.0 5 391 111 84 63 46 27 59 751 0.0 5 432 135 66 53 33 32 60 687 0.0 5 367 124 84 45 40 27 61 649 0.0 5 358 142 49 41 35 24 62 615 0.0 5 341 105 67 48 28 26 63 708 0.0 5 437 126 63 34 28 20 64 606 0.0 5 377 106 50 32 23 18 65 708 0.0 5 472 103 50 37 26 20 66 638 0.0 5 412 110 48 24 28 16 67 679 0.0 5 452 103 58 33 19 14 68 677 0.0 5 478 100 49 22 15 13 69 716 0.0 5 549 82 39 18 14 14 70 669 0.0 5 494 85 37 22 16 15 71 535 0.0 5 396 69 32 14 10 14 72 514 0.0 5 382 59 43 14 9 7 73 519 0.0 5 385 79 29 10 12 4 74 574 0.0 5 429 59 44 15 15 12 75 543 0.0 5 432 59 25 13 7 7 76 498 0.0 5 398 49 13 15 14 9 77 517 0.0 5 398 71 19 14 11 4 78 415 0.0 5 311 49 25 13 10 7 79 499 0.0 5 399 48 17 16 7 12 80 410 0.0 5 327 44 13 15 8 3 81 420 0.0 5 337 34 14 19 9 7 82 354 0.0 5 277 41 16 12 6 2 83 367 0.0 5 272 45 16 20 9 5 84 373 0.0 5 287 34 22 15 8 7 85 384 0.0 5 303 40 14 16 8 3 86 399 0.0 5 327 41 13 10 6 2 87 348 0.0 5 270 39 13 11 8 7 88 373 0.0 5 309 29 16 8 9 2 89 364 0.0 5 297 26 18 9 6 8 90 293 0.0 5 236 22 18 10 2 5 91 295 0.0 5 241 28 12 5 5 4 92 365 0.0 5 304 31 16 5 7 2 93 259 0.0 5 207 20 13 4 6 9 94 228 0.0 5 182 24 9 4 3 6 95 296 0.0 5 249 24 10 5 2 6 96 287 0.0 5 217 38 14 7 7 4 97 261 0.0 5 202 34 7 8 4 6 98 232 0.0 5 182 17 15 6 3 9 99 289 0.0 5 248 22 6 5 6 2 100 219 0.0 5 172 22 12 5 2 6 101 304 0.0 5 262 26 8 2 2 4 102 288 0.0 5 244 23 5 6 4 6 103 279 0.0 5 233 23 12 5 4 2 104 200 0.0 5 170 12 6 6 3 3 105 295 0.0 5 251 25 7 6 3 3 106 248 0.0 5 204 26 5 5 5 3 107 247 0.0 5 215 18 7 3 0 4 108 220 0.0 5 178 19 9 5 7 2 109 400 0.0 5 306 46 33 8 7 110 372 0.0 5 279 38 17 14 12 12 111 294 0.0 5 223 31 10 10 9 11 112 752 0.0 5 649 41 25 12 13 12 113 848 0.0 5 717 50 36 14 12 19 114 2850 0.0 5 2636 102 52 21 17 22 115 654249 0.0 5 653504 583 90 35 17 20 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/Hawes/analyses/trimgalore-2/zr3644_22_R2_val_2_val_2.fq.gz ============================================= 47698628 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_22_R1_val_1_val_1_trimmed.fq.gz and zr3644_22_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_22_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_22_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_22_R1_val_1_val_1_trimmed.fq.gz and zr3644_22_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_22_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_22_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 47698628 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 678982 (1.42%) >>> Now running FastQC on the validated data zr3644_22_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_22_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_22_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_22_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_22_R1_val_1_val_1_trimmed.fq.gz and zr3644_22_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_23_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_23_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/Hawes/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 zr3644_23_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/Hawes/analyses/trimgalore-2/zr3644_23_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_23_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1072.18 s (26 µs/read; 2.27 M reads/minute). === Summary === Total reads processed: 40,515,907 Reads with adapters: 4,185,637 (10.3%) Reads written (passing filters): 40,515,907 (100.0%) Total basepairs processed: 4,254,719,433 bp Quality-trimmed: 1,474,777 bp (0.0%) Total written (filtered): 4,202,048,819 bp (98.8%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4185637 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: 21.9% C: 4.5% G: 0.0% T: 73.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2601762 10128976.8 0 2601762 2 724803 2532244.2 0 724803 3 154809 633061.0 0 154809 4 42564 158265.3 0 42564 5 12239 39566.3 0 12239 6 3583 9891.6 0 3583 7 1649 2472.9 0 1649 8 1019 618.2 0 1019 9 1004 154.6 0 1004 10 2147 38.6 1 1017 1130 11 1853 9.7 1 892 961 12 1678 2.4 1 830 848 13 1517 0.6 1 771 746 14 1282 0.2 1 636 646 15 1181 0.0 1 570 611 16 1022 0.0 1 501 521 17 805 0.0 1 422 383 18 663 0.0 1 390 273 19 623 0.0 1 386 237 20 929 0.0 2 362 228 339 21 830 0.0 2 330 218 282 22 768 0.0 2 333 183 252 23 703 0.0 2 328 155 220 24 702 0.0 2 329 189 184 25 667 0.0 2 297 172 198 26 567 0.0 2 241 166 160 27 524 0.0 2 251 139 134 28 434 0.0 2 209 122 103 29 469 0.0 2 235 130 104 30 613 0.0 3 208 133 117 155 31 583 0.0 3 219 122 105 137 32 579 0.0 3 192 157 102 128 33 526 0.0 3 207 113 86 120 34 532 0.0 3 200 117 97 118 35 492 0.0 3 159 140 106 87 36 459 0.0 3 184 110 71 94 37 471 0.0 3 204 107 69 91 38 400 0.0 3 184 90 62 64 39 367 0.0 3 166 80 69 52 40 502 0.0 4 170 100 64 70 98 41 447 0.0 4 135 92 58 70 92 42 499 0.0 4 149 112 66 72 100 43 408 0.0 4 117 78 59 60 94 44 450 0.0 4 148 71 79 56 96 45 426 0.0 4 142 86 70 67 61 46 440 0.0 4 148 87 73 61 71 47 424 0.0 4 152 104 61 45 62 48 498 0.0 4 195 124 70 57 52 49 926 0.0 4 405 214 117 114 76 50 1105 0.0 5 515 200 131 104 85 70 51 843 0.0 5 504 146 74 43 46 30 52 776 0.0 5 480 139 70 42 25 20 53 683 0.0 5 387 131 81 43 23 18 54 730 0.0 5 462 134 64 42 13 15 55 810 0.0 5 574 117 50 35 23 11 56 933 0.0 5 686 134 49 30 19 15 57 884 0.0 5 650 120 56 27 19 12 58 994 0.0 5 763 124 51 24 21 11 59 1022 0.0 5 810 100 49 35 13 15 60 797 0.0 5 575 127 54 24 8 9 61 786 0.0 5 604 101 43 19 13 6 62 1004 0.0 5 800 110 45 25 11 13 63 1105 0.0 5 922 101 47 18 10 7 64 1319 0.0 5 1136 103 32 24 16 8 65 942 0.0 5 778 97 33 19 8 7 66 1201 0.0 5 998 126 46 16 7 8 67 1423 0.0 5 1221 127 42 16 11 6 68 1894 0.0 5 1688 131 33 22 12 8 69 2677 0.0 5 2467 149 26 23 7 5 70 4936 0.0 5 4681 172 43 26 7 7 71 10257 0.0 5 9979 216 38 14 6 4 72 28978 0.0 5 28618 288 47 8 11 6 73 92859 0.0 5 92352 417 60 18 5 7 74 261127 0.0 5 260311 698 92 12 12 2 75 25742 0.0 5 25542 136 34 13 12 5 76 22922 0.0 5 22751 127 21 11 5 7 77 53728 0.0 5 53507 163 35 11 5 7 78 13512 0.0 5 13401 76 23 8 3 1 79 35724 0.0 5 35563 123 15 14 5 4 80 10588 0.0 5 10515 50 15 5 1 2 81 7424 0.0 5 7344 54 15 3 7 1 82 10621 0.0 5 10519 63 13 7 14 5 83 3980 0.0 5 3883 68 16 8 2 3 84 5419 0.0 5 5323 68 10 6 8 4 85 1040 0.0 5 984 35 10 3 4 4 86 165 0.0 5 126 20 9 5 3 2 87 171 0.0 5 125 20 13 6 3 4 88 138 0.0 5 90 21 15 6 3 3 89 123 0.0 5 79 21 13 6 4 90 130 0.0 5 84 24 9 7 4 2 91 113 0.0 5 72 21 7 5 2 6 92 87 0.0 5 65 15 3 3 1 93 113 0.0 5 75 14 11 6 3 4 94 95 0.0 5 63 15 4 4 7 2 95 101 0.0 5 72 13 6 3 4 3 96 86 0.0 5 42 20 9 8 5 2 97 81 0.0 5 56 9 8 6 2 98 64 0.0 5 41 10 6 2 4 1 99 59 0.0 5 41 5 5 3 3 2 100 53 0.0 5 44 5 1 1 1 1 101 66 0.0 5 41 9 9 5 1 1 102 49 0.0 5 33 5 7 1 1 2 103 31 0.0 5 23 3 1 3 1 104 36 0.0 5 20 6 4 1 5 105 25 0.0 5 16 3 1 4 1 106 22 0.0 5 12 2 1 3 1 3 107 25 0.0 5 18 2 1 1 1 2 108 16 0.0 5 13 1 0 1 0 1 109 18 0.0 5 11 0 2 1 3 1 110 17 0.0 5 13 1 0 1 0 2 111 18 0.0 5 13 2 1 0 2 112 11 0.0 5 9 1 0 1 113 8 0.0 5 6 1 0 1 114 10 0.0 5 9 1 115 83 0.0 5 77 4 1 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_23_R1_val_1_val_1.fq.gz ============================================= 40515907 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_23_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_23_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/Hawes/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 zr3644_23_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/Hawes/analyses/trimgalore-2/zr3644_23_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 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/Hawes/analyses/trimgalore-2/zr3644_23_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1098.87 s (27 µs/read; 2.21 M reads/minute). === Summary === Total reads processed: 40,515,907 Reads with adapters: 3,950,552 (9.8%) Reads written (passing filters): 40,515,907 (100.0%) Total basepairs processed: 4,252,298,832 bp Quality-trimmed: 1,994,244 bp (0.0%) Total written (filtered): 4,174,781,678 bp (98.2%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 3950552 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: 13.4% C: 5.1% G: 0.0% T: 81.4% 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 2442623 10128976.8 0 2442623 2 659783 2532244.2 0 659783 3 143651 633061.0 0 143651 4 40134 158265.3 0 40134 5 11539 39566.3 0 11539 6 3365 9891.6 0 3365 7 1190 2472.9 0 1190 8 655 618.2 0 655 9 565 154.6 0 565 10 1997 38.6 1 513 1484 11 1600 9.7 1 406 1194 12 1225 2.4 1 380 845 13 1058 0.6 1 339 719 14 1006 0.2 1 338 668 15 846 0.0 1 274 572 16 725 0.0 1 237 488 17 534 0.0 1 191 343 18 372 0.0 1 178 194 19 334 0.0 1 162 172 20 911 0.0 2 235 182 494 21 856 0.0 2 215 157 484 22 790 0.0 2 232 168 390 23 658 0.0 2 188 140 330 24 618 0.0 2 171 148 299 25 608 0.0 2 165 133 310 26 495 0.0 2 158 122 215 27 428 0.0 2 169 81 178 28 368 0.0 2 154 105 109 29 370 0.0 2 152 86 132 30 616 0.0 3 140 88 99 289 31 604 0.0 3 159 74 96 275 32 558 0.0 3 134 72 101 251 33 513 0.0 3 106 78 98 231 34 491 0.0 3 131 61 80 219 35 454 0.0 3 114 67 93 180 36 427 0.0 3 118 78 76 155 37 375 0.0 3 125 55 67 128 38 324 0.0 3 90 71 72 91 39 296 0.0 3 101 58 54 83 40 498 0.0 4 105 61 59 81 192 41 511 0.0 4 115 53 56 80 207 42 486 0.0 4 105 50 47 87 197 43 489 0.0 4 110 53 60 76 190 44 454 0.0 4 103 64 54 77 156 45 413 0.0 4 96 55 52 59 151 46 451 0.0 4 121 65 49 73 143 47 403 0.0 4 117 63 65 48 110 48 427 0.0 4 112 89 83 79 64 49 1143 0.0 4 378 220 221 155 169 50 1237 0.0 5 297 241 215 168 168 148 51 904 0.0 5 262 170 154 126 99 93 52 823 0.0 5 329 173 100 84 68 69 53 766 0.0 5 313 164 114 62 64 49 54 705 0.0 5 301 115 104 65 71 49 55 636 0.0 5 302 109 96 57 40 32 56 656 0.0 5 320 129 66 47 53 41 57 597 0.0 5 313 121 74 31 33 25 58 519 0.0 5 263 94 61 40 33 28 59 496 0.0 5 272 86 51 26 37 24 60 497 0.0 5 272 98 41 45 16 25 61 459 0.0 5 220 83 58 45 32 21 62 449 0.0 5 263 62 55 29 17 23 63 492 0.0 5 297 81 48 28 20 18 64 490 0.0 5 301 84 52 23 19 11 65 514 0.0 5 322 86 42 26 22 16 66 442 0.0 5 265 73 43 23 24 14 67 483 0.0 5 309 79 25 26 26 18 68 482 0.0 5 325 68 33 26 16 14 69 564 0.0 5 436 56 30 20 14 8 70 573 0.0 5 440 57 33 19 12 12 71 422 0.0 5 315 52 24 11 12 8 72 387 0.0 5 283 53 29 10 7 5 73 390 0.0 5 301 42 15 10 14 8 74 418 0.0 5 314 42 16 17 14 15 75 460 0.0 5 348 56 23 17 9 7 76 415 0.0 5 314 45 23 13 7 13 77 410 0.0 5 322 42 20 8 7 11 78 307 0.0 5 228 40 18 8 9 4 79 407 0.0 5 319 44 23 12 7 2 80 343 0.0 5 257 44 23 7 7 5 81 315 0.0 5 239 43 11 10 6 6 82 293 0.0 5 244 23 13 4 3 6 83 311 0.0 5 242 38 9 7 10 5 84 275 0.0 5 222 22 14 7 5 5 85 281 0.0 5 213 31 9 13 8 7 86 319 0.0 5 256 30 13 9 6 5 87 240 0.0 5 208 11 9 5 4 3 88 333 0.0 5 272 27 15 8 5 6 89 292 0.0 5 239 24 12 7 9 1 90 286 0.0 5 229 33 8 5 5 6 91 238 0.0 5 200 14 11 4 3 6 92 277 0.0 5 231 18 9 9 7 3 93 221 0.0 5 174 24 10 5 5 3 94 218 0.0 5 176 18 9 4 5 6 95 263 0.0 5 220 21 11 6 2 3 96 222 0.0 5 168 32 14 3 4 1 97 222 0.0 5 170 26 9 7 2 8 98 172 0.0 5 139 21 6 0 4 2 99 283 0.0 5 253 16 4 7 1 2 100 181 0.0 5 149 15 6 2 5 4 101 330 0.0 5 293 19 7 2 7 2 102 273 0.0 5 229 25 9 5 2 3 103 279 0.0 5 246 13 5 6 6 3 104 201 0.0 5 164 16 9 8 2 2 105 327 0.0 5 290 23 8 3 1 2 106 217 0.0 5 180 17 8 6 4 2 107 241 0.0 5 197 30 5 3 3 3 108 222 0.0 5 183 19 8 7 3 2 109 385 0.0 5 263 46 53 12 6 5 110 341 0.0 5 280 27 15 6 6 7 111 307 0.0 5 245 15 13 14 11 9 112 681 0.0 5 591 40 20 9 13 8 113 815 0.0 5 702 59 18 13 9 14 114 2706 0.0 5 2505 96 44 31 15 15 115 592005 0.0 5 591243 600 85 33 25 19 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/Hawes/analyses/trimgalore-2/zr3644_23_R2_val_2_val_2.fq.gz ============================================= 40515907 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_23_R1_val_1_val_1_trimmed.fq.gz and zr3644_23_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_23_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_23_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_23_R1_val_1_val_1_trimmed.fq.gz and zr3644_23_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_23_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_23_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 40515907 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 613398 (1.51%) >>> Now running FastQC on the validated data zr3644_23_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_23_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_23_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_23_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_23_R1_val_1_val_1_trimmed.fq.gz and zr3644_23_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G/zr3644_24_R1_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_24_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/Hawes/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 zr3644_24_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/Hawes/analyses/trimgalore-2/zr3644_24_R1_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_24_R1_val_1_val_1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1454.88 s (28 µs/read; 2.18 M reads/minute). === Summary === Total reads processed: 52,894,890 Reads with adapters: 5,345,542 (10.1%) Reads written (passing filters): 52,894,890 (100.0%) Total basepairs processed: 5,591,025,465 bp Quality-trimmed: 2,078,621 bp (0.0%) Total written (filtered): 5,532,987,899 bp (99.0%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 5345542 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: 20.4% C: 4.7% G: 0.0% T: 74.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 3419026 13223722.5 0 3419026 2 945995 3305930.6 0 945995 3 203892 826482.7 0 203892 4 56264 206620.7 0 56264 5 16625 51655.2 0 16625 6 4936 12913.8 0 4936 7 2260 3228.4 0 2260 8 1533 807.1 0 1533 9 1456 201.8 0 1456 10 3023 50.4 1 1343 1680 11 2694 12.6 1 1320 1374 12 2404 3.2 1 1186 1218 13 2253 0.8 1 1134 1119 14 1869 0.2 1 953 916 15 1716 0.0 1 850 866 16 1420 0.0 1 711 709 17 1167 0.0 1 612 555 18 920 0.0 1 548 372 19 871 0.0 1 528 343 20 1433 0.0 2 557 369 507 21 1275 0.0 2 486 338 451 22 1201 0.0 2 506 316 379 23 1093 0.0 2 472 279 342 24 988 0.0 2 463 247 278 25 937 0.0 2 417 258 262 26 807 0.0 2 347 230 230 27 775 0.0 2 374 199 202 28 689 0.0 2 353 191 145 29 684 0.0 2 325 211 148 30 919 0.0 3 315 230 150 224 31 895 0.0 3 333 184 155 223 32 823 0.0 3 335 155 142 191 33 810 0.0 3 283 199 136 192 34 798 0.0 3 292 162 169 175 35 737 0.0 3 262 179 139 157 36 721 0.0 3 269 166 129 157 37 688 0.0 3 269 170 114 135 38 623 0.0 3 270 156 102 95 39 567 0.0 3 237 132 86 112 40 711 0.0 4 237 146 94 83 151 41 776 0.0 4 268 140 112 98 158 42 745 0.0 4 262 124 118 93 148 43 640 0.0 4 213 150 86 74 117 44 642 0.0 4 203 132 98 82 127 45 612 0.0 4 219 117 88 76 112 46 644 0.0 4 220 127 105 79 113 47 634 0.0 4 251 129 90 70 94 48 701 0.0 4 268 160 105 80 88 49 1321 0.0 4 535 286 201 157 142 50 1524 0.0 5 618 320 214 148 116 108 51 1081 0.0 5 587 167 123 96 67 41 52 1080 0.0 5 616 184 103 93 49 35 53 979 0.0 5 552 182 120 58 45 22 54 931 0.0 5 569 154 86 61 30 31 55 1033 0.0 5 683 163 86 44 28 29 56 1109 0.0 5 742 191 73 47 40 16 57 1064 0.0 5 756 145 74 51 24 14 58 1142 0.0 5 831 143 76 51 19 22 59 1160 0.0 5 891 146 53 40 17 13 60 961 0.0 5 675 167 49 35 20 15 61 956 0.0 5 687 138 54 38 27 12 62 1174 0.0 5 889 154 69 33 19 10 63 1363 0.0 5 1138 121 48 23 27 6 64 1576 0.0 5 1279 162 73 27 26 9 65 1119 0.0 5 864 150 51 27 18 9 66 1292 0.0 5 1028 143 54 32 23 12 67 1609 0.0 5 1350 151 45 33 26 4 68 2034 0.0 5 1722 183 63 30 21 15 69 2680 0.0 5 2358 216 52 27 21 6 70 4688 0.0 5 4375 197 49 40 21 6 71 9885 0.0 5 9554 238 54 25 7 7 72 27109 0.0 5 26663 347 59 21 12 7 73 101919 0.0 5 101288 511 79 24 14 3 74 261916 0.0 5 260984 787 98 29 12 6 75 27362 0.0 5 27129 160 39 17 9 8 76 24783 0.0 5 24568 140 37 21 9 8 77 55829 0.0 5 55599 162 34 12 14 8 78 14567 0.0 5 14406 91 42 13 9 6 79 36347 0.0 5 36149 138 33 11 10 6 80 11836 0.0 5 11699 78 21 15 18 5 81 8384 0.0 5 8245 87 24 12 10 6 82 11853 0.0 5 11742 71 17 12 9 2 83 8864 0.0 5 8736 77 22 12 10 7 84 13721 0.0 5 13581 87 26 15 6 6 85 2499 0.0 5 2388 70 18 9 7 7 86 418 0.0 5 348 36 20 6 6 2 87 203 0.0 5 124 35 17 17 7 3 88 187 0.0 5 118 33 14 15 5 2 89 180 0.0 5 111 35 12 6 11 5 90 207 0.0 5 113 42 28 9 11 4 91 171 0.0 5 109 30 14 7 6 5 92 144 0.0 5 85 19 17 14 4 5 93 154 0.0 5 101 24 15 8 3 3 94 120 0.0 5 80 15 9 12 2 2 95 134 0.0 5 81 26 8 10 6 3 96 110 0.0 5 64 18 13 6 6 3 97 112 0.0 5 64 19 10 6 8 5 98 83 0.0 5 55 7 8 5 3 5 99 87 0.0 5 62 8 3 7 4 3 100 82 0.0 5 46 12 10 6 3 5 101 78 0.0 5 52 10 5 4 3 4 102 71 0.0 5 50 5 2 6 3 5 103 55 0.0 5 35 7 4 5 3 1 104 36 0.0 5 21 5 5 1 3 1 105 25 0.0 5 15 2 1 1 3 3 106 24 0.0 5 12 4 1 3 2 2 107 31 0.0 5 19 2 4 1 2 3 108 17 0.0 5 13 1 0 1 0 2 109 11 0.0 5 5 2 0 0 1 3 110 15 0.0 5 12 0 1 0 0 2 111 22 0.0 5 19 2 0 0 1 112 5 0.0 5 4 0 0 0 1 113 9 0.0 5 5 2 1 1 114 15 0.0 5 10 3 1 0 1 115 94 0.0 5 89 3 1 0 1 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_24_R1_val_1_val_1.fq.gz ============================================= 52894890 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/Hawes/analyses/trimgalore-2/poly-G/zr3644_24_R2_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/zr3644_24_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/Hawes/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 zr3644_24_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/Hawes/analyses/trimgalore-2/zr3644_24_R2_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 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/Hawes/analyses/trimgalore-2/zr3644_24_R2_val_2_val_2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 1450.22 s (27 µs/read; 2.19 M reads/minute). === Summary === Total reads processed: 52,894,890 Reads with adapters: 4,990,032 (9.4%) Reads written (passing filters): 52,894,890 (100.0%) Total basepairs processed: 5,589,271,116 bp Quality-trimmed: 2,547,797 bp (0.0%) Total written (filtered): 5,505,351,532 bp (98.5%) === Adapter 1 === Sequence: GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG; Type: regular 3'; Length: 50; Trimmed: 4990032 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: 13.4% C: 5.1% G: 0.0% T: 81.4% 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 3175227 13223722.5 0 3175227 2 856267 3305930.6 0 856267 3 187098 826482.7 0 187098 4 52094 206620.7 0 52094 5 15535 51655.2 0 15535 6 4474 12913.8 0 4474 7 1660 3228.4 0 1660 8 837 807.1 0 837 9 796 201.8 0 796 10 2687 50.4 1 703 1984 11 2205 12.6 1 616 1589 12 1767 3.2 1 547 1220 13 1628 0.8 1 527 1101 14 1366 0.2 1 455 911 15 1179 0.0 1 393 786 16 949 0.0 1 343 606 17 734 0.0 1 266 468 18 537 0.0 1 267 270 19 515 0.0 1 246 269 20 1232 0.0 2 309 248 675 21 1175 0.0 2 279 257 639 22 1053 0.0 2 249 236 568 23 969 0.0 2 276 215 478 24 844 0.0 2 246 176 422 25 774 0.0 2 249 171 354 26 687 0.0 2 223 156 308 27 580 0.0 2 237 100 243 28 471 0.0 2 194 112 165 29 465 0.0 2 201 117 147 30 849 0.0 3 205 106 166 372 31 813 0.0 3 177 115 157 364 32 722 0.0 3 165 108 130 319 33 680 0.0 3 179 95 109 297 34 684 0.0 3 178 102 115 289 35 623 0.0 3 156 107 122 238 36 580 0.0 3 167 92 97 224 37 493 0.0 3 153 80 89 171 38 453 0.0 3 152 91 90 120 39 429 0.0 3 164 80 70 115 40 719 0.0 4 133 85 85 109 307 41 626 0.0 4 136 80 66 92 252 42 625 0.0 4 124 73 64 111 253 43 605 0.0 4 122 73 57 108 245 44 522 0.0 4 103 51 69 101 198 45 607 0.0 4 143 67 83 108 206 46 502 0.0 4 123 69 69 74 167 47 528 0.0 4 163 90 72 53 150 48 571 0.0 4 188 105 89 99 90 49 1529 0.0 4 423 310 317 253 226 50 1605 0.0 5 393 292 255 253 226 186 51 1297 0.0 5 402 250 200 175 143 127 52 1081 0.0 5 340 215 184 130 111 101 53 1048 0.0 5 419 228 141 105 95 60 54 843 0.0 5 348 149 115 83 74 74 55 891 0.0 5 373 176 113 93 77 59 56 886 0.0 5 421 175 95 88 50 57 57 771 0.0 5 357 146 98 76 57 37 58 685 0.0 5 332 140 72 57 51 33 59 673 0.0 5 341 124 88 49 40 31 60 649 0.0 5 340 119 65 64 38 23 61 655 0.0 5 351 117 77 50 30 30 62 575 0.0 5 325 116 50 39 24 21 63 631 0.0 5 368 107 69 33 29 25 64 587 0.0 5 341 108 53 36 25 24 65 640 0.0 5 409 98 56 25 28 24 66 562 0.0 5 354 93 46 32 20 17 67 666 0.0 5 449 103 51 32 15 16 68 591 0.0 5 388 92 43 29 27 12 69 713 0.0 5 528 88 36 25 20 16 70 616 0.0 5 453 67 38 21 17 20 71 529 0.0 5 372 74 40 21 11 11 72 491 0.0 5 345 62 38 21 13 12 73 491 0.0 5 351 60 32 20 15 13 74 497 0.0 5 376 46 27 20 16 12 75 573 0.0 5 429 62 32 20 23 7 76 462 0.0 5 359 44 21 16 9 13 77 501 0.0 5 385 60 23 15 9 9 78 423 0.0 5 310 49 18 17 17 12 79 475 0.0 5 346 62 27 16 15 9 80 371 0.0 5 278 37 19 16 10 11 81 376 0.0 5 283 44 18 12 10 9 82 372 0.0 5 263 50 31 12 9 7 83 343 0.0 5 267 33 18 9 5 11 84 400 0.0 5 314 40 24 14 6 2 85 325 0.0 5 257 30 16 6 8 8 86 381 0.0 5 288 38 26 12 10 7 87 322 0.0 5 247 31 16 15 7 6 88 401 0.0 5 333 26 15 10 11 6 89 299 0.0 5 249 28 7 4 5 6 90 337 0.0 5 273 27 18 6 6 7 91 291 0.0 5 223 35 16 6 7 4 92 356 0.0 5 294 31 9 8 7 7 93 272 0.0 5 214 26 11 10 4 7 94 245 0.0 5 193 20 10 11 7 4 95 300 0.0 5 238 29 9 12 5 7 96 295 0.0 5 222 37 17 8 5 6 97 278 0.0 5 214 28 12 10 7 7 98 210 0.0 5 150 28 12 9 6 5 99 295 0.0 5 259 18 8 5 5 100 206 0.0 5 147 26 14 7 8 4 101 337 0.0 5 290 18 12 7 7 3 102 334 0.0 5 274 25 19 5 5 6 103 276 0.0 5 229 22 6 7 9 3 104 231 0.0 5 175 23 14 5 9 5 105 315 0.0 5 271 17 11 6 6 4 106 283 0.0 5 233 18 14 6 7 5 107 301 0.0 5 243 31 8 5 7 7 108 263 0.0 5 207 23 10 5 8 10 109 424 0.0 5 296 44 56 12 6 10 110 391 0.0 5 324 34 8 8 10 7 111 347 0.0 5 252 41 11 12 16 15 112 763 0.0 5 620 56 32 25 14 16 113 948 0.0 5 811 52 31 20 22 12 114 3179 0.0 5 2906 135 50 40 24 24 115 624893 0.0 5 623953 715 102 64 31 28 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/Hawes/analyses/trimgalore-2/zr3644_24_R2_val_2_val_2.fq.gz ============================================= 52894890 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3644_24_R1_val_1_val_1_trimmed.fq.gz and zr3644_24_R2_val_2_val_2_trimmed.fq.gz file_1: zr3644_24_R1_val_1_val_1_trimmed.fq.gz, file_2: zr3644_24_R2_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3644_24_R1_val_1_val_1_trimmed.fq.gz and zr3644_24_R2_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3644_24_R1_val_1_val_1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3644_24_R2_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 52894890 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 650845 (1.23%) >>> Now running FastQC on the validated data zr3644_24_R1_val_1_val_1_val_1.fq.gz<<< Started analysis of zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 5% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 10% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 15% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 20% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 25% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 30% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 35% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 40% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 45% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 50% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 55% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 60% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 65% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 70% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 75% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 80% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 85% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 90% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Approx 95% complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz Analysis complete for zr3644_24_R1_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr3644_24_R2_val_2_val_2_val_2.fq.gz<<< Started analysis of zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 5% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 10% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 15% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 20% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 25% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 30% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 35% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 40% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 45% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 50% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 55% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 60% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 65% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 70% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 75% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 80% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 85% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 90% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Approx 95% complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Analysis complete for zr3644_24_R2_val_2_val_2_val_2.fq.gz Deleting both intermediate output files zr3644_24_R1_val_1_val_1_trimmed.fq.gz and zr3644_24_R2_val_2_val_2_trimmed.fq.gz ==================================================================================================== [INFO ] multiqc : This is MultiQC v1.8 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching : /gscratch/scrubbed/yaaminiv/Hawes/analyses/trimgalore-2/poly-G [INFO ] cutadapt : Found 48 reports [INFO ] fastqc : Found 48 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