Multicore support not enabled. Proceeding with single-core trimming. Path to Cutadapt set as: '/usr/lusers/yaaminiv/.local/bin/cutadapt' (user defined) Cutadapt seems to be working fine (tested command '/usr/lusers/yaaminiv/.local/bin/cutadapt --version') Cutadapt version: 3.1 single-core operation. No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) Output will be written into the directory: /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/ Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_1_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_1_R1.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j 1 Writing final adapter and quality trimmed output to zr3616_1_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_1_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_1_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4579.51 s (28 µs/read; 2.13 M reads/minute). === Summary === Total reads processed: 162,780,101 Reads with adapters: 62,282,524 (38.3%) Reads written (passing filters): 162,780,101 (100.0%) Total basepairs processed: 19,464,055,669 bp Quality-trimmed: 3,949,688 bp (0.0%) Total written (filtered): 19,380,382,323 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 62282524 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.9% C: 10.1% G: 7.6% T: 38.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 52535873 40695025.2 0 52535873 2 6572350 10173756.3 0 6572350 3 1405861 2543439.1 0 1405861 4 1125266 635859.8 0 1125266 5 369656 158964.9 0 369656 6 90653 39741.2 0 90653 7 59410 9935.3 0 59410 8 35804 2483.8 0 35804 9 6859 621.0 0 5163 1696 10 62774 155.2 1 59511 3263 11 666 38.8 1 132 534 12 181 9.7 1 79 102 13 73 2.4 1 44 29 14 44 2.4 1 34 10 15 91 2.4 1 78 13 16 34 2.4 1 27 7 17 38 2.4 1 26 12 18 98 2.4 1 87 11 19 91 2.4 1 84 7 20 102 2.4 1 92 10 21 52 2.4 1 42 10 22 47 2.4 1 37 10 23 108 2.4 1 92 16 24 74 2.4 1 64 10 25 80 2.4 1 73 7 26 76 2.4 1 68 8 27 81 2.4 1 71 10 28 56 2.4 1 47 9 29 75 2.4 1 65 10 30 71 2.4 1 65 6 31 69 2.4 1 50 19 32 61 2.4 1 51 10 33 75 2.4 1 66 9 34 61 2.4 1 55 6 35 60 2.4 1 56 4 36 66 2.4 1 60 6 37 66 2.4 1 55 11 38 71 2.4 1 62 9 39 73 2.4 1 64 9 40 82 2.4 1 73 9 41 108 2.4 1 97 11 42 75 2.4 1 69 6 43 104 2.4 1 91 13 44 101 2.4 1 88 13 45 77 2.4 1 72 5 46 83 2.4 1 77 6 47 104 2.4 1 90 14 48 86 2.4 1 74 12 49 97 2.4 1 90 7 50 116 2.4 1 105 11 51 107 2.4 1 90 17 52 113 2.4 1 104 9 53 90 2.4 1 74 16 54 112 2.4 1 94 18 55 111 2.4 1 99 12 56 106 2.4 1 96 10 57 108 2.4 1 98 10 58 87 2.4 1 77 10 59 132 2.4 1 123 9 60 132 2.4 1 111 21 61 102 2.4 1 91 11 62 103 2.4 1 93 10 63 105 2.4 1 86 19 64 86 2.4 1 76 10 65 121 2.4 1 117 4 66 130 2.4 1 115 15 67 109 2.4 1 93 16 68 119 2.4 1 104 15 69 124 2.4 1 108 16 70 139 2.4 1 123 16 71 131 2.4 1 125 6 72 112 2.4 1 99 13 73 136 2.4 1 126 10 74 156 2.4 1 136 20 75 165 2.4 1 152 13 76 146 2.4 1 127 19 77 109 2.4 1 96 13 78 145 2.4 1 125 20 79 129 2.4 1 115 14 80 156 2.4 1 142 14 81 149 2.4 1 134 15 82 124 2.4 1 110 14 83 136 2.4 1 114 22 84 121 2.4 1 109 12 85 168 2.4 1 152 16 86 141 2.4 1 125 16 87 132 2.4 1 118 14 88 155 2.4 1 144 11 89 157 2.4 1 139 18 90 152 2.4 1 137 15 91 139 2.4 1 126 13 92 143 2.4 1 130 13 93 147 2.4 1 131 16 94 131 2.4 1 117 14 95 155 2.4 1 130 25 96 125 2.4 1 107 18 97 161 2.4 1 146 15 98 146 2.4 1 135 11 99 158 2.4 1 145 13 100 132 2.4 1 123 9 101 180 2.4 1 152 28 102 140 2.4 1 131 9 103 136 2.4 1 122 14 104 150 2.4 1 140 10 105 139 2.4 1 122 17 106 173 2.4 1 149 24 107 161 2.4 1 137 24 108 200 2.4 1 179 21 109 183 2.4 1 161 22 110 200 2.4 1 177 23 111 176 2.4 1 162 14 112 160 2.4 1 143 17 113 192 2.4 1 168 24 114 223 2.4 1 203 20 115 202 2.4 1 179 23 116 220 2.4 1 193 27 117 193 2.4 1 173 20 118 244 2.4 1 223 21 119 198 2.4 1 177 21 120 198 2.4 1 177 21 121 206 2.4 1 182 24 122 204 2.4 1 178 26 123 227 2.4 1 193 34 124 221 2.4 1 199 22 125 210 2.4 1 181 29 126 211 2.4 1 189 22 127 230 2.4 1 209 21 128 274 2.4 1 250 24 129 283 2.4 1 254 29 130 293 2.4 1 275 18 131 284 2.4 1 250 34 132 331 2.4 1 292 39 133 362 2.4 1 305 57 134 296 2.4 1 223 73 135 452 2.4 1 194 258 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_1_R1.fq.gz ============================================= 162780101 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_1_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_1_R2.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_1_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_1_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_1_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4611.37 s (28 µs/read; 2.12 M reads/minute). === Summary === Total reads processed: 162,780,101 Reads with adapters: 62,280,853 (38.3%) Reads written (passing filters): 162,780,101 (100.0%) Total basepairs processed: 19,461,874,095 bp Quality-trimmed: 3,835,880 bp (0.0%) Total written (filtered): 19,378,440,979 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 62280853 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.1% C: 9.8% G: 7.6% T: 38.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 52600766 40695025.2 0 52600766 2 6526277 10173756.3 0 6526277 3 1379477 2543439.1 0 1379477 4 1137096 635859.8 0 1137096 5 366365 158964.9 0 366365 6 89932 39741.2 0 89932 7 59322 9935.3 0 59322 8 35528 2483.8 0 35528 9 6643 621.0 0 5024 1619 10 61870 155.2 1 58490 3380 11 580 38.8 1 125 455 12 220 9.7 1 123 97 13 155 2.4 1 135 20 14 41 2.4 1 30 11 15 81 2.4 1 76 5 16 37 2.4 1 32 5 17 43 2.4 1 31 12 18 87 2.4 1 80 7 19 72 2.4 1 65 7 20 102 2.4 1 84 18 21 66 2.4 1 49 17 22 39 2.4 1 32 7 23 86 2.4 1 78 8 24 71 2.4 1 64 7 25 71 2.4 1 64 7 26 72 2.4 1 63 9 27 68 2.4 1 62 6 28 55 2.4 1 46 9 29 67 2.4 1 54 13 30 48 2.4 1 42 6 31 56 2.4 1 48 8 32 86 2.4 1 73 13 33 56 2.4 1 53 3 34 57 2.4 1 44 13 35 63 2.4 1 57 6 36 66 2.4 1 58 8 37 68 2.4 1 56 12 38 62 2.4 1 56 6 39 54 2.4 1 43 11 40 73 2.4 1 65 8 41 83 2.4 1 75 8 42 64 2.4 1 56 8 43 58 2.4 1 53 5 44 81 2.4 1 73 8 45 80 2.4 1 72 8 46 93 2.4 1 81 12 47 106 2.4 1 94 12 48 99 2.4 1 89 10 49 72 2.4 1 62 10 50 103 2.4 1 93 10 51 113 2.4 1 97 16 52 80 2.4 1 69 11 53 109 2.4 1 100 9 54 106 2.4 1 100 6 55 110 2.4 1 95 15 56 108 2.4 1 96 12 57 114 2.4 1 105 9 58 110 2.4 1 99 11 59 89 2.4 1 79 10 60 109 2.4 1 100 9 61 125 2.4 1 108 17 62 118 2.4 1 102 16 63 91 2.4 1 80 11 64 117 2.4 1 110 7 65 117 2.4 1 107 10 66 95 2.4 1 85 10 67 129 2.4 1 118 11 68 123 2.4 1 112 11 69 114 2.4 1 102 12 70 131 2.4 1 124 7 71 137 2.4 1 125 12 72 89 2.4 1 79 10 73 150 2.4 1 126 24 74 147 2.4 1 126 21 75 118 2.4 1 101 17 76 110 2.4 1 96 14 77 141 2.4 1 120 21 78 141 2.4 1 129 12 79 143 2.4 1 130 13 80 144 2.4 1 134 10 81 157 2.4 1 135 22 82 140 2.4 1 127 13 83 151 2.4 1 128 23 84 137 2.4 1 118 19 85 120 2.4 1 105 15 86 131 2.4 1 115 16 87 133 2.4 1 120 13 88 160 2.4 1 140 20 89 139 2.4 1 127 12 90 172 2.4 1 153 19 91 158 2.4 1 138 20 92 138 2.4 1 123 15 93 142 2.4 1 130 12 94 150 2.4 1 132 18 95 162 2.4 1 142 20 96 149 2.4 1 129 20 97 188 2.4 1 163 25 98 135 2.4 1 119 16 99 163 2.4 1 149 14 100 170 2.4 1 147 23 101 169 2.4 1 151 18 102 148 2.4 1 121 27 103 141 2.4 1 119 22 104 143 2.4 1 124 19 105 131 2.4 1 118 13 106 163 2.4 1 140 23 107 173 2.4 1 148 25 108 154 2.4 1 128 26 109 163 2.4 1 137 26 110 216 2.4 1 200 16 111 185 2.4 1 161 24 112 212 2.4 1 185 27 113 169 2.4 1 151 18 114 194 2.4 1 171 23 115 184 2.4 1 173 11 116 184 2.4 1 165 19 117 208 2.4 1 183 25 118 216 2.4 1 193 23 119 182 2.4 1 154 28 120 249 2.4 1 232 17 121 222 2.4 1 205 17 122 187 2.4 1 172 15 123 194 2.4 1 176 18 124 193 2.4 1 167 26 125 232 2.4 1 198 34 126 204 2.4 1 191 13 127 252 2.4 1 225 27 128 261 2.4 1 232 29 129 273 2.4 1 239 34 130 279 2.4 1 247 32 131 286 2.4 1 262 24 132 296 2.4 1 249 47 133 293 2.4 1 248 45 134 321 2.4 1 243 78 135 436 2.4 1 198 238 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_1_R2.fq.gz ============================================= 162780101 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_1_R1_trimmed.fq.gz and zr3616_1_R2_trimmed.fq.gz file_1: zr3616_1_R1_trimmed.fq.gz, file_2: zr3616_1_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_1_R1_trimmed.fq.gz and zr3616_1_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_1_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_1_R2_val_2.fq.gz Total number of sequences analysed: 162780101 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1543746 (0.95%) >>> Now running FastQC on the validated data zr3616_1_R1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 651120404. >>> Now running FastQC on the validated data zr3616_1_R2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 651120404. Deleting both intermediate output files zr3616_1_R1_trimmed.fq.gz and zr3616_1_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_2_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_2_R1.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_2_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_2_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_2_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4803.25 s (28 µs/read; 2.11 M reads/minute). === Summary === Total reads processed: 168,555,919 Reads with adapters: 64,789,951 (38.4%) Reads written (passing filters): 168,555,919 (100.0%) Total basepairs processed: 20,136,253,714 bp Quality-trimmed: 4,613,448 bp (0.0%) Total written (filtered): 20,048,443,536 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64789951 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.8% C: 10.0% G: 7.6% T: 38.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 54553749 42138979.8 0 54553749 2 6934950 10534744.9 0 6934950 3 1459472 2633686.2 0 1459472 4 1175875 658421.6 0 1175875 5 382331 164605.4 0 382331 6 95249 41151.3 0 95249 7 61926 10287.8 0 61926 8 36466 2572.0 0 36466 9 6653 643.0 0 4823 1830 10 62077 160.7 1 58567 3510 11 661 40.2 1 144 517 12 233 10.0 1 136 97 13 80 2.5 1 56 24 14 69 2.5 1 52 17 15 100 2.5 1 84 16 16 53 2.5 1 38 15 17 50 2.5 1 41 9 18 113 2.5 1 94 19 19 140 2.5 1 115 25 20 138 2.5 1 124 14 21 68 2.5 1 56 12 22 75 2.5 1 56 19 23 126 2.5 1 117 9 24 81 2.5 1 64 17 25 100 2.5 1 87 13 26 81 2.5 1 74 7 27 97 2.5 1 85 12 28 79 2.5 1 63 16 29 76 2.5 1 65 11 30 61 2.5 1 51 10 31 86 2.5 1 65 21 32 103 2.5 1 96 7 33 100 2.5 1 86 14 34 92 2.5 1 82 10 35 106 2.5 1 94 12 36 83 2.5 1 69 14 37 91 2.5 1 79 12 38 74 2.5 1 64 10 39 106 2.5 1 91 15 40 99 2.5 1 86 13 41 96 2.5 1 84 12 42 90 2.5 1 80 10 43 97 2.5 1 87 10 44 101 2.5 1 89 12 45 115 2.5 1 104 11 46 103 2.5 1 87 16 47 111 2.5 1 95 16 48 121 2.5 1 108 13 49 99 2.5 1 89 10 50 123 2.5 1 105 18 51 110 2.5 1 99 11 52 102 2.5 1 93 9 53 117 2.5 1 97 20 54 118 2.5 1 105 13 55 102 2.5 1 88 14 56 121 2.5 1 106 15 57 116 2.5 1 94 22 58 137 2.5 1 119 18 59 158 2.5 1 144 14 60 141 2.5 1 128 13 61 124 2.5 1 111 13 62 148 2.5 1 120 28 63 121 2.5 1 108 13 64 145 2.5 1 130 15 65 166 2.5 1 155 11 66 130 2.5 1 120 10 67 126 2.5 1 113 13 68 178 2.5 1 157 21 69 156 2.5 1 145 11 70 136 2.5 1 119 17 71 162 2.5 1 146 16 72 142 2.5 1 127 15 73 139 2.5 1 125 14 74 141 2.5 1 124 17 75 148 2.5 1 129 19 76 183 2.5 1 157 26 77 153 2.5 1 138 15 78 184 2.5 1 167 17 79 161 2.5 1 138 23 80 182 2.5 1 168 14 81 183 2.5 1 164 19 82 162 2.5 1 144 18 83 162 2.5 1 138 24 84 177 2.5 1 158 19 85 196 2.5 1 181 15 86 156 2.5 1 128 28 87 170 2.5 1 150 20 88 218 2.5 1 201 17 89 179 2.5 1 160 19 90 186 2.5 1 173 13 91 168 2.5 1 155 13 92 211 2.5 1 203 8 93 173 2.5 1 158 15 94 170 2.5 1 150 20 95 184 2.5 1 164 20 96 212 2.5 1 188 24 97 204 2.5 1 183 21 98 187 2.5 1 165 22 99 211 2.5 1 174 37 100 192 2.5 1 169 23 101 179 2.5 1 158 21 102 154 2.5 1 143 11 103 154 2.5 1 147 7 104 174 2.5 1 147 27 105 212 2.5 1 182 30 106 172 2.5 1 151 21 107 211 2.5 1 186 25 108 199 2.5 1 179 20 109 211 2.5 1 192 19 110 213 2.5 1 189 24 111 218 2.5 1 202 16 112 209 2.5 1 185 24 113 239 2.5 1 214 25 114 172 2.5 1 166 6 115 225 2.5 1 196 29 116 219 2.5 1 197 22 117 249 2.5 1 218 31 118 246 2.5 1 222 24 119 282 2.5 1 252 30 120 218 2.5 1 198 20 121 232 2.5 1 206 26 122 234 2.5 1 204 30 123 240 2.5 1 214 26 124 252 2.5 1 214 38 125 254 2.5 1 211 43 126 274 2.5 1 246 28 127 294 2.5 1 263 31 128 303 2.5 1 264 39 129 294 2.5 1 266 28 130 343 2.5 1 295 48 131 373 2.5 1 332 41 132 327 2.5 1 295 32 133 329 2.5 1 287 42 134 370 2.5 1 278 92 135 503 2.5 1 239 264 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_2_R1.fq.gz ============================================= 168555919 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_2_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_2_R2.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_2_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_2_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_2_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4774.64 s (28 µs/read; 2.12 M reads/minute). === Summary === Total reads processed: 168,555,919 Reads with adapters: 64,689,343 (38.4%) Reads written (passing filters): 168,555,919 (100.0%) Total basepairs processed: 20,137,031,441 bp Quality-trimmed: 4,088,114 bp (0.0%) Total written (filtered): 20,050,187,834 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64689343 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 44.1% C: 9.8% G: 7.4% T: 38.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 54711066 42138979.8 0 54711066 2 6708849 10534744.9 0 6708849 3 1429411 2633686.2 0 1429411 4 1180167 658421.6 0 1180167 5 380029 164605.4 0 380029 6 93234 41151.3 0 93234 7 61148 10287.8 0 61148 8 36803 2572.0 0 36803 9 6988 643.0 0 5364 1624 10 60809 160.7 1 57364 3445 11 657 40.2 1 121 536 12 274 10.0 1 157 117 13 176 2.5 1 147 29 14 51 2.5 1 39 12 15 104 2.5 1 84 20 16 46 2.5 1 31 15 17 46 2.5 1 36 10 18 108 2.5 1 97 11 19 115 2.5 1 100 15 20 110 2.5 1 97 13 21 84 2.5 1 75 9 22 68 2.5 1 59 9 23 125 2.5 1 119 6 24 61 2.5 1 53 8 25 76 2.5 1 69 7 26 75 2.5 1 59 16 27 72 2.5 1 58 14 28 71 2.5 1 59 12 29 69 2.5 1 59 10 30 68 2.5 1 59 9 31 76 2.5 1 68 8 32 92 2.5 1 77 15 33 85 2.5 1 78 7 34 104 2.5 1 93 11 35 95 2.5 1 90 5 36 88 2.5 1 81 7 37 97 2.5 1 85 12 38 102 2.5 1 92 10 39 117 2.5 1 103 14 40 99 2.5 1 93 6 41 91 2.5 1 82 9 42 108 2.5 1 98 10 43 101 2.5 1 85 16 44 102 2.5 1 89 13 45 127 2.5 1 115 12 46 120 2.5 1 103 17 47 107 2.5 1 100 7 48 99 2.5 1 88 11 49 102 2.5 1 89 13 50 101 2.5 1 88 13 51 98 2.5 1 86 12 52 134 2.5 1 124 10 53 121 2.5 1 100 21 54 107 2.5 1 97 10 55 111 2.5 1 101 10 56 104 2.5 1 87 17 57 149 2.5 1 129 20 58 135 2.5 1 121 14 59 127 2.5 1 121 6 60 142 2.5 1 116 26 61 131 2.5 1 113 18 62 114 2.5 1 93 21 63 145 2.5 1 136 9 64 107 2.5 1 94 13 65 149 2.5 1 130 19 66 160 2.5 1 141 19 67 169 2.5 1 149 20 68 118 2.5 1 105 13 69 150 2.5 1 136 14 70 147 2.5 1 134 13 71 157 2.5 1 135 22 72 153 2.5 1 122 31 73 132 2.5 1 119 13 74 167 2.5 1 148 19 75 154 2.5 1 135 19 76 165 2.5 1 145 20 77 148 2.5 1 123 25 78 173 2.5 1 149 24 79 172 2.5 1 154 18 80 139 2.5 1 119 20 81 192 2.5 1 172 20 82 163 2.5 1 147 16 83 144 2.5 1 122 22 84 180 2.5 1 156 24 85 159 2.5 1 142 17 86 157 2.5 1 140 17 87 173 2.5 1 155 18 88 154 2.5 1 147 7 89 162 2.5 1 144 18 90 210 2.5 1 191 19 91 159 2.5 1 138 21 92 200 2.5 1 172 28 93 147 2.5 1 127 20 94 162 2.5 1 140 22 95 197 2.5 1 180 17 96 194 2.5 1 176 18 97 178 2.5 1 149 29 98 185 2.5 1 169 16 99 204 2.5 1 182 22 100 157 2.5 1 141 16 101 191 2.5 1 157 34 102 189 2.5 1 164 25 103 200 2.5 1 182 18 104 197 2.5 1 176 21 105 173 2.5 1 141 32 106 197 2.5 1 177 20 107 169 2.5 1 157 12 108 210 2.5 1 183 27 109 194 2.5 1 172 22 110 207 2.5 1 172 35 111 246 2.5 1 215 31 112 193 2.5 1 175 18 113 212 2.5 1 181 31 114 223 2.5 1 194 29 115 225 2.5 1 200 25 116 218 2.5 1 189 29 117 215 2.5 1 195 20 118 252 2.5 1 227 25 119 261 2.5 1 245 16 120 234 2.5 1 213 21 121 257 2.5 1 225 32 122 285 2.5 1 253 32 123 195 2.5 1 180 15 124 226 2.5 1 202 24 125 275 2.5 1 242 33 126 262 2.5 1 222 40 127 299 2.5 1 268 31 128 294 2.5 1 278 16 129 296 2.5 1 256 40 130 318 2.5 1 288 30 131 296 2.5 1 250 46 132 338 2.5 1 306 32 133 320 2.5 1 278 42 134 361 2.5 1 260 101 135 487 2.5 1 243 244 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_2_R2.fq.gz ============================================= 168555919 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_2_R1_trimmed.fq.gz and zr3616_2_R2_trimmed.fq.gz file_1: zr3616_2_R1_trimmed.fq.gz, file_2: zr3616_2_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_2_R1_trimmed.fq.gz and zr3616_2_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_2_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_2_R2_val_2.fq.gz Total number of sequences analysed: 168555919 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1587165 (0.94%) >>> Now running FastQC on the validated data zr3616_2_R1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 1325344080. >>> Now running FastQC on the validated data zr3616_2_R2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 1325344080. Deleting both intermediate output files zr3616_2_R1_trimmed.fq.gz and zr3616_2_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_3_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_3_R1.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_3_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_3_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_3_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 5301.72 s (28 µs/read; 2.16 M reads/minute). === Summary === Total reads processed: 190,890,981 Reads with adapters: 67,946,267 (35.6%) Reads written (passing filters): 190,890,981 (100.0%) Total basepairs processed: 21,887,812,359 bp Quality-trimmed: 4,711,467 bp (0.0%) Total written (filtered): 21,792,339,028 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 67946267 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.0% C: 9.5% G: 8.2% T: 39.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 55407052 47722745.2 0 55407052 2 8405082 11930686.3 0 8405082 3 1609571 2982671.6 0 1609571 4 1478104 745667.9 0 1478104 5 578773 186417.0 0 578773 6 146091 46604.2 0 146091 7 102698 11651.1 0 102698 8 67699 2912.8 0 67699 9 12611 728.2 0 10073 2538 10 120983 182.0 1 116248 4735 11 969 45.5 1 189 780 12 240 11.4 1 83 157 13 70 2.8 1 42 28 14 49 2.8 1 39 10 15 105 2.8 1 89 16 16 37 2.8 1 24 13 17 32 2.8 1 20 12 18 89 2.8 1 77 12 19 87 2.8 1 70 17 20 126 2.8 1 111 15 21 58 2.8 1 50 8 22 41 2.8 1 31 10 23 115 2.8 1 107 8 24 83 2.8 1 74 9 25 74 2.8 1 67 7 26 61 2.8 1 48 13 27 62 2.8 1 56 6 28 67 2.8 1 59 8 29 66 2.8 1 56 10 30 53 2.8 1 43 10 31 54 2.8 1 41 13 32 76 2.8 1 66 10 33 68 2.8 1 64 4 34 61 2.8 1 52 9 35 61 2.8 1 53 8 36 79 2.8 1 68 11 37 75 2.8 1 65 10 38 94 2.8 1 74 20 39 82 2.8 1 67 15 40 78 2.8 1 64 14 41 74 2.8 1 69 5 42 87 2.8 1 75 12 43 80 2.8 1 74 6 44 90 2.8 1 83 7 45 93 2.8 1 83 10 46 85 2.8 1 75 10 47 73 2.8 1 66 7 48 80 2.8 1 72 8 49 104 2.8 1 97 7 50 103 2.8 1 86 17 51 102 2.8 1 89 13 52 92 2.8 1 76 16 53 91 2.8 1 77 14 54 86 2.8 1 76 10 55 99 2.8 1 90 9 56 115 2.8 1 98 17 57 101 2.8 1 88 13 58 113 2.8 1 91 22 59 125 2.8 1 114 11 60 114 2.8 1 107 7 61 108 2.8 1 104 4 62 115 2.8 1 97 18 63 92 2.8 1 83 9 64 88 2.8 1 80 8 65 112 2.8 1 104 8 66 125 2.8 1 114 11 67 132 2.8 1 117 15 68 111 2.8 1 100 11 69 133 2.8 1 115 18 70 135 2.8 1 127 8 71 141 2.8 1 123 18 72 110 2.8 1 92 18 73 129 2.8 1 121 8 74 117 2.8 1 105 12 75 149 2.8 1 133 16 76 149 2.8 1 128 21 77 138 2.8 1 112 26 78 114 2.8 1 94 20 79 138 2.8 1 120 18 80 143 2.8 1 126 17 81 125 2.8 1 111 14 82 133 2.8 1 122 11 83 162 2.8 1 154 8 84 142 2.8 1 126 16 85 158 2.8 1 131 27 86 147 2.8 1 131 16 87 153 2.8 1 140 13 88 148 2.8 1 136 12 89 164 2.8 1 141 23 90 165 2.8 1 138 27 91 145 2.8 1 130 15 92 157 2.8 1 138 19 93 181 2.8 1 154 27 94 141 2.8 1 120 21 95 138 2.8 1 121 17 96 161 2.8 1 143 18 97 154 2.8 1 120 34 98 152 2.8 1 120 32 99 167 2.8 1 149 18 100 177 2.8 1 162 15 101 179 2.8 1 157 22 102 169 2.8 1 143 26 103 161 2.8 1 123 38 104 146 2.8 1 132 14 105 154 2.8 1 135 19 106 180 2.8 1 162 18 107 153 2.8 1 132 21 108 157 2.8 1 132 25 109 162 2.8 1 149 13 110 179 2.8 1 161 18 111 216 2.8 1 193 23 112 154 2.8 1 131 23 113 165 2.8 1 148 17 114 185 2.8 1 163 22 115 172 2.8 1 150 22 116 175 2.8 1 151 24 117 198 2.8 1 177 21 118 168 2.8 1 140 28 119 219 2.8 1 187 32 120 198 2.8 1 168 30 121 170 2.8 1 148 22 122 227 2.8 1 204 23 123 182 2.8 1 160 22 124 194 2.8 1 151 43 125 193 2.8 1 172 21 126 201 2.8 1 183 18 127 211 2.8 1 186 25 128 231 2.8 1 199 32 129 248 2.8 1 214 34 130 230 2.8 1 205 25 131 255 2.8 1 223 32 132 239 2.8 1 195 44 133 247 2.8 1 209 38 134 248 2.8 1 187 61 135 369 2.8 1 169 200 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_3_R1.fq.gz ============================================= 190890981 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_3_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_3_R2.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_3_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_3_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_3_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 5277.20 s (28 µs/read; 2.17 M reads/minute). === Summary === Total reads processed: 190,890,981 Reads with adapters: 68,104,946 (35.7%) Reads written (passing filters): 190,890,981 (100.0%) Total basepairs processed: 21,887,510,700 bp Quality-trimmed: 6,137,470 bp (0.0%) Total written (filtered): 21,790,702,726 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 68104946 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.2% C: 9.5% G: 8.0% T: 39.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 55768543 47722745.2 0 55768543 2 8249585 11930686.3 0 8249585 3 1573556 2982671.6 0 1573556 4 1483247 745667.9 0 1483247 5 567788 186417.0 0 567788 6 143673 46604.2 0 143673 7 102236 11651.1 0 102236 8 67227 2912.8 0 67227 9 12764 728.2 0 10115 2649 10 117979 182.0 1 113181 4798 11 962 45.5 1 195 767 12 345 11.4 1 205 140 13 190 2.8 1 145 45 14 43 2.8 1 29 14 15 88 2.8 1 71 17 16 29 2.8 1 24 5 17 36 2.8 1 28 8 18 79 2.8 1 65 14 19 68 2.8 1 60 8 20 130 2.8 1 117 13 21 68 2.8 1 58 10 22 48 2.8 1 37 11 23 105 2.8 1 96 9 24 44 2.8 1 40 4 25 73 2.8 1 65 8 26 67 2.8 1 57 10 27 62 2.8 1 51 11 28 71 2.8 1 57 14 29 48 2.8 1 40 8 30 72 2.8 1 64 8 31 65 2.8 1 57 8 32 73 2.8 1 62 11 33 70 2.8 1 60 10 34 90 2.8 1 80 10 35 80 2.8 1 74 6 36 75 2.8 1 65 10 37 87 2.8 1 79 8 38 70 2.8 1 60 10 39 94 2.8 1 81 13 40 77 2.8 1 68 9 41 88 2.8 1 77 11 42 77 2.8 1 69 8 43 103 2.8 1 83 20 44 96 2.8 1 87 9 45 88 2.8 1 81 7 46 91 2.8 1 76 15 47 84 2.8 1 73 11 48 102 2.8 1 92 10 49 97 2.8 1 83 14 50 91 2.8 1 83 8 51 85 2.8 1 74 11 52 116 2.8 1 104 12 53 93 2.8 1 79 14 54 88 2.8 1 79 9 55 120 2.8 1 115 5 56 128 2.8 1 117 11 57 116 2.8 1 108 8 58 112 2.8 1 105 7 59 109 2.8 1 99 10 60 122 2.8 1 103 19 61 112 2.8 1 103 9 62 103 2.8 1 90 13 63 122 2.8 1 106 16 64 108 2.8 1 96 12 65 124 2.8 1 105 19 66 121 2.8 1 107 14 67 114 2.8 1 106 8 68 137 2.8 1 122 15 69 137 2.8 1 118 19 70 137 2.8 1 118 19 71 124 2.8 1 109 15 72 133 2.8 1 118 15 73 139 2.8 1 124 15 74 155 2.8 1 135 20 75 122 2.8 1 109 13 76 141 2.8 1 130 11 77 161 2.8 1 139 22 78 132 2.8 1 118 14 79 142 2.8 1 125 17 80 143 2.8 1 127 16 81 144 2.8 1 126 18 82 144 2.8 1 120 24 83 132 2.8 1 118 14 84 142 2.8 1 121 21 85 132 2.8 1 120 12 86 187 2.8 1 153 34 87 165 2.8 1 138 27 88 159 2.8 1 136 23 89 163 2.8 1 142 21 90 192 2.8 1 170 22 91 163 2.8 1 140 23 92 197 2.8 1 185 12 93 149 2.8 1 136 13 94 138 2.8 1 121 17 95 138 2.8 1 122 16 96 141 2.8 1 123 18 97 184 2.8 1 157 27 98 199 2.8 1 171 28 99 195 2.8 1 166 29 100 168 2.8 1 150 18 101 186 2.8 1 166 20 102 182 2.8 1 157 25 103 172 2.8 1 152 20 104 177 2.8 1 161 16 105 164 2.8 1 145 19 106 124 2.8 1 104 20 107 176 2.8 1 150 26 108 203 2.8 1 173 30 109 175 2.8 1 157 18 110 175 2.8 1 154 21 111 182 2.8 1 161 21 112 162 2.8 1 144 18 113 166 2.8 1 136 30 114 158 2.8 1 142 16 115 182 2.8 1 160 22 116 214 2.8 1 184 30 117 194 2.8 1 175 19 118 206 2.8 1 178 28 119 182 2.8 1 159 23 120 192 2.8 1 166 26 121 201 2.8 1 178 23 122 182 2.8 1 166 16 123 214 2.8 1 178 36 124 210 2.8 1 186 24 125 218 2.8 1 190 28 126 187 2.8 1 166 21 127 206 2.8 1 185 21 128 254 2.8 1 223 31 129 208 2.8 1 182 26 130 234 2.8 1 209 25 131 233 2.8 1 204 29 132 251 2.8 1 224 27 133 260 2.8 1 212 48 134 271 2.8 1 195 76 135 393 2.8 1 178 215 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_3_R2.fq.gz ============================================= 190890981 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_3_R1_trimmed.fq.gz and zr3616_3_R2_trimmed.fq.gz file_1: zr3616_3_R1_trimmed.fq.gz, file_2: zr3616_3_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_3_R1_trimmed.fq.gz and zr3616_3_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_3_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_3_R2_val_2.fq.gz Total number of sequences analysed: 190890981 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2320519 (1.22%) >>> Now running FastQC on the validated data zr3616_3_R1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 2088908004. >>> Now running FastQC on the validated data zr3616_3_R2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 2088908004. Deleting both intermediate output files zr3616_3_R1_trimmed.fq.gz and zr3616_3_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_4_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_4_R1.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_4_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_4_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_4_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 5518.47 s (28 µs/read; 2.17 M reads/minute). === Summary === Total reads processed: 199,920,896 Reads with adapters: 74,214,434 (37.1%) Reads written (passing filters): 199,920,896 (100.0%) Total basepairs processed: 23,462,606,601 bp Quality-trimmed: 5,081,221 bp (0.0%) Total written (filtered): 23,360,095,022 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 74214434 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.3% C: 9.8% G: 7.9% T: 39.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 61435800 49980224.0 0 61435800 2 8622690 12495056.0 0 8622690 3 1721129 3123764.0 0 1721129 4 1486347 780941.0 0 1486347 5 522326 195235.2 0 522326 6 133103 48808.8 0 133103 7 92467 12202.2 0 92467 8 60243 3050.6 0 60243 9 11091 762.6 0 8625 2466 10 105760 190.7 1 101028 4732 11 1009 47.7 1 203 806 12 316 11.9 1 140 176 13 69 3.0 1 42 27 14 66 3.0 1 55 11 15 126 3.0 1 113 13 16 33 3.0 1 27 6 17 47 3.0 1 35 12 18 127 3.0 1 111 16 19 105 3.0 1 95 10 20 146 3.0 1 121 25 21 77 3.0 1 67 10 22 57 3.0 1 49 8 23 175 3.0 1 161 14 24 92 3.0 1 83 9 25 109 3.0 1 96 13 26 89 3.0 1 80 9 27 114 3.0 1 95 19 28 83 3.0 1 79 4 29 72 3.0 1 64 8 30 99 3.0 1 82 17 31 81 3.0 1 67 14 32 101 3.0 1 89 12 33 89 3.0 1 82 7 34 100 3.0 1 88 12 35 99 3.0 1 85 14 36 95 3.0 1 84 11 37 102 3.0 1 90 12 38 110 3.0 1 97 13 39 105 3.0 1 94 11 40 95 3.0 1 77 18 41 126 3.0 1 114 12 42 110 3.0 1 95 15 43 112 3.0 1 104 8 44 122 3.0 1 110 12 45 110 3.0 1 98 12 46 140 3.0 1 126 14 47 147 3.0 1 137 10 48 154 3.0 1 134 20 49 115 3.0 1 95 20 50 148 3.0 1 129 19 51 139 3.0 1 120 19 52 118 3.0 1 102 16 53 137 3.0 1 123 14 54 140 3.0 1 127 13 55 154 3.0 1 135 19 56 147 3.0 1 132 15 57 134 3.0 1 116 18 58 155 3.0 1 138 17 59 172 3.0 1 155 17 60 152 3.0 1 142 10 61 178 3.0 1 164 14 62 177 3.0 1 162 15 63 141 3.0 1 131 10 64 152 3.0 1 129 23 65 150 3.0 1 142 8 66 182 3.0 1 156 26 67 192 3.0 1 173 19 68 189 3.0 1 170 19 69 156 3.0 1 134 22 70 191 3.0 1 174 17 71 189 3.0 1 170 19 72 178 3.0 1 167 11 73 194 3.0 1 178 16 74 192 3.0 1 176 16 75 174 3.0 1 156 18 76 176 3.0 1 156 20 77 173 3.0 1 159 14 78 191 3.0 1 164 27 79 207 3.0 1 193 14 80 187 3.0 1 165 22 81 189 3.0 1 169 20 82 187 3.0 1 171 16 83 196 3.0 1 178 18 84 198 3.0 1 182 16 85 181 3.0 1 154 27 86 214 3.0 1 186 28 87 181 3.0 1 163 18 88 207 3.0 1 180 27 89 183 3.0 1 169 14 90 194 3.0 1 173 21 91 210 3.0 1 192 18 92 204 3.0 1 181 23 93 174 3.0 1 159 15 94 170 3.0 1 150 20 95 224 3.0 1 193 31 96 188 3.0 1 166 22 97 199 3.0 1 168 31 98 241 3.0 1 223 18 99 230 3.0 1 205 25 100 212 3.0 1 190 22 101 223 3.0 1 199 24 102 216 3.0 1 192 24 103 211 3.0 1 192 19 104 200 3.0 1 179 21 105 185 3.0 1 163 22 106 227 3.0 1 198 29 107 235 3.0 1 210 25 108 219 3.0 1 190 29 109 235 3.0 1 201 34 110 224 3.0 1 191 33 111 225 3.0 1 190 35 112 222 3.0 1 201 21 113 209 3.0 1 194 15 114 229 3.0 1 193 36 115 236 3.0 1 209 27 116 239 3.0 1 217 22 117 242 3.0 1 210 32 118 245 3.0 1 229 16 119 258 3.0 1 237 21 120 266 3.0 1 236 30 121 236 3.0 1 202 34 122 269 3.0 1 233 36 123 272 3.0 1 246 26 124 260 3.0 1 239 21 125 270 3.0 1 240 30 126 294 3.0 1 263 31 127 298 3.0 1 267 31 128 305 3.0 1 261 44 129 307 3.0 1 278 29 130 294 3.0 1 262 32 131 295 3.0 1 255 40 132 344 3.0 1 313 31 133 384 3.0 1 326 58 134 335 3.0 1 227 108 135 498 3.0 1 245 253 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_4_R1.fq.gz ============================================= 199920896 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_4_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_4_R2.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_4_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_4_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_4_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 5752.90 s (29 µs/read; 2.09 M reads/minute). === Summary === Total reads processed: 199,920,896 Reads with adapters: 74,522,650 (37.3%) Reads written (passing filters): 199,920,896 (100.0%) Total basepairs processed: 23,464,661,406 bp Quality-trimmed: 5,134,686 bp (0.0%) Total written (filtered): 23,362,142,591 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 74522650 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.6% C: 9.7% G: 7.8% T: 39.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 62047657 49980224.0 0 62047657 2 8370995 12495056.0 0 8370995 3 1677009 3123764.0 0 1677009 4 1491904 780941.0 0 1491904 5 514799 195235.2 0 514799 6 131657 48808.8 0 131657 7 90622 12202.2 0 90622 8 60206 3050.6 0 60206 9 11770 762.6 0 9369 2401 10 102131 190.7 1 97298 4833 11 888 47.7 1 204 684 12 318 11.9 1 156 162 13 196 3.0 1 161 35 14 41 3.0 1 34 7 15 117 3.0 1 98 19 16 53 3.0 1 38 15 17 44 3.0 1 32 12 18 108 3.0 1 99 9 19 90 3.0 1 79 11 20 174 3.0 1 156 18 21 91 3.0 1 83 8 22 63 3.0 1 56 7 23 148 3.0 1 133 15 24 96 3.0 1 86 10 25 109 3.0 1 95 14 26 88 3.0 1 79 9 27 86 3.0 1 74 12 28 64 3.0 1 56 8 29 116 3.0 1 107 9 30 81 3.0 1 68 13 31 84 3.0 1 78 6 32 100 3.0 1 86 14 33 88 3.0 1 67 21 34 100 3.0 1 84 16 35 93 3.0 1 82 11 36 92 3.0 1 80 12 37 116 3.0 1 102 14 38 88 3.0 1 71 17 39 120 3.0 1 99 21 40 102 3.0 1 88 14 41 128 3.0 1 109 19 42 110 3.0 1 94 16 43 93 3.0 1 82 11 44 122 3.0 1 110 12 45 120 3.0 1 116 4 46 114 3.0 1 98 16 47 118 3.0 1 110 8 48 119 3.0 1 109 10 49 143 3.0 1 121 22 50 157 3.0 1 133 24 51 148 3.0 1 130 18 52 129 3.0 1 116 13 53 127 3.0 1 111 16 54 152 3.0 1 137 15 55 146 3.0 1 128 18 56 143 3.0 1 132 11 57 196 3.0 1 175 21 58 143 3.0 1 132 11 59 166 3.0 1 153 13 60 164 3.0 1 148 16 61 145 3.0 1 132 13 62 151 3.0 1 132 19 63 164 3.0 1 150 14 64 167 3.0 1 158 9 65 184 3.0 1 159 25 66 173 3.0 1 152 21 67 187 3.0 1 175 12 68 174 3.0 1 150 24 69 142 3.0 1 124 18 70 205 3.0 1 178 27 71 167 3.0 1 145 22 72 168 3.0 1 157 11 73 186 3.0 1 170 16 74 173 3.0 1 160 13 75 175 3.0 1 157 18 76 162 3.0 1 144 18 77 199 3.0 1 179 20 78 174 3.0 1 155 19 79 211 3.0 1 181 30 80 239 3.0 1 220 19 81 248 3.0 1 222 26 82 227 3.0 1 201 26 83 211 3.0 1 185 26 84 171 3.0 1 152 19 85 178 3.0 1 162 16 86 192 3.0 1 173 19 87 211 3.0 1 180 31 88 215 3.0 1 194 21 89 211 3.0 1 185 26 90 223 3.0 1 195 28 91 224 3.0 1 204 20 92 234 3.0 1 211 23 93 203 3.0 1 187 16 94 236 3.0 1 212 24 95 229 3.0 1 199 30 96 211 3.0 1 193 18 97 207 3.0 1 174 33 98 242 3.0 1 216 26 99 231 3.0 1 200 31 100 237 3.0 1 209 28 101 216 3.0 1 185 31 102 235 3.0 1 198 37 103 215 3.0 1 193 22 104 184 3.0 1 168 16 105 242 3.0 1 214 28 106 237 3.0 1 209 28 107 203 3.0 1 181 22 108 231 3.0 1 212 19 109 247 3.0 1 206 41 110 275 3.0 1 240 35 111 221 3.0 1 190 31 112 233 3.0 1 204 29 113 205 3.0 1 186 19 114 239 3.0 1 219 20 115 233 3.0 1 213 20 116 204 3.0 1 180 24 117 224 3.0 1 199 25 118 285 3.0 1 257 28 119 240 3.0 1 217 23 120 256 3.0 1 225 31 121 293 3.0 1 263 30 122 256 3.0 1 221 35 123 277 3.0 1 256 21 124 260 3.0 1 235 25 125 250 3.0 1 214 36 126 226 3.0 1 200 26 127 280 3.0 1 241 39 128 276 3.0 1 239 37 129 305 3.0 1 268 37 130 342 3.0 1 302 40 131 314 3.0 1 269 45 132 307 3.0 1 258 49 133 338 3.0 1 289 49 134 423 3.0 1 317 106 135 549 3.0 1 236 313 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_4_R2.fq.gz ============================================= 199920896 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_4_R1_trimmed.fq.gz and zr3616_4_R2_trimmed.fq.gz file_1: zr3616_4_R1_trimmed.fq.gz, file_2: zr3616_4_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_4_R1_trimmed.fq.gz and zr3616_4_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_4_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_4_R2_val_2.fq.gz Total number of sequences analysed: 199920896 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1926681 (0.96%) >>> Now running FastQC on the validated data zr3616_4_R1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 2888591588. >>> Now running FastQC on the validated data zr3616_4_R2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 2888591588. Deleting both intermediate output files zr3616_4_R1_trimmed.fq.gz and zr3616_4_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_5_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_5_R1.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_5_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_5_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_5_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4110.42 s (27 µs/read; 2.20 M reads/minute). === Summary === Total reads processed: 150,419,008 Reads with adapters: 55,059,110 (36.6%) Reads written (passing filters): 150,419,008 (100.0%) Total basepairs processed: 17,427,703,814 bp Quality-trimmed: 4,672,609 bp (0.0%) Total written (filtered): 17,350,375,657 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 55059110 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.1% C: 9.7% G: 8.1% T: 39.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 45286525 37604752.0 0 45286525 2 6611329 9401188.0 0 6611329 3 1310029 2350297.0 0 1310029 4 1131557 587574.2 0 1131557 5 401467 146893.6 0 401467 6 101925 36723.4 0 101925 7 71237 9180.8 0 71237 8 46703 2295.2 0 46703 9 8117 573.8 0 6313 1804 10 73478 143.5 1 69860 3618 11 673 35.9 1 134 539 12 201 9.0 1 96 105 13 65 2.2 1 40 25 14 46 2.2 1 37 9 15 79 2.2 1 67 12 16 34 2.2 1 28 6 17 27 2.2 1 21 6 18 90 2.2 1 74 16 19 98 2.2 1 81 17 20 106 2.2 1 88 18 21 78 2.2 1 67 11 22 47 2.2 1 39 8 23 111 2.2 1 100 11 24 62 2.2 1 60 2 25 86 2.2 1 75 11 26 59 2.2 1 54 5 27 85 2.2 1 74 11 28 57 2.2 1 48 9 29 59 2.2 1 52 7 30 77 2.2 1 65 12 31 67 2.2 1 56 11 32 56 2.2 1 50 6 33 92 2.2 1 83 9 34 64 2.2 1 53 11 35 68 2.2 1 57 11 36 52 2.2 1 47 5 37 68 2.2 1 58 10 38 66 2.2 1 59 7 39 82 2.2 1 76 6 40 74 2.2 1 63 11 41 114 2.2 1 103 11 42 85 2.2 1 82 3 43 86 2.2 1 70 16 44 90 2.2 1 81 9 45 80 2.2 1 70 10 46 77 2.2 1 66 11 47 81 2.2 1 65 16 48 95 2.2 1 84 11 49 93 2.2 1 76 17 50 105 2.2 1 77 28 51 86 2.2 1 83 3 52 92 2.2 1 80 12 53 84 2.2 1 73 11 54 80 2.2 1 74 6 55 122 2.2 1 112 10 56 101 2.2 1 95 6 57 109 2.2 1 91 18 58 104 2.2 1 96 8 59 140 2.2 1 130 10 60 109 2.2 1 87 22 61 115 2.2 1 102 13 62 115 2.2 1 98 17 63 136 2.2 1 117 19 64 136 2.2 1 119 17 65 107 2.2 1 95 12 66 119 2.2 1 106 13 67 128 2.2 1 114 14 68 115 2.2 1 98 17 69 115 2.2 1 106 9 70 119 2.2 1 106 13 71 110 2.2 1 98 12 72 142 2.2 1 128 14 73 123 2.2 1 114 9 74 123 2.2 1 110 13 75 103 2.2 1 84 19 76 139 2.2 1 126 13 77 184 2.2 1 170 14 78 145 2.2 1 130 15 79 128 2.2 1 116 12 80 142 2.2 1 130 12 81 115 2.2 1 104 11 82 137 2.2 1 126 11 83 143 2.2 1 128 15 84 119 2.2 1 111 8 85 138 2.2 1 125 13 86 132 2.2 1 119 13 87 140 2.2 1 126 14 88 135 2.2 1 123 12 89 155 2.2 1 141 14 90 143 2.2 1 127 16 91 135 2.2 1 120 15 92 124 2.2 1 112 12 93 152 2.2 1 133 19 94 129 2.2 1 114 15 95 112 2.2 1 93 19 96 146 2.2 1 131 15 97 146 2.2 1 124 22 98 146 2.2 1 126 20 99 182 2.2 1 163 19 100 165 2.2 1 147 18 101 142 2.2 1 127 15 102 154 2.2 1 133 21 103 150 2.2 1 136 14 104 176 2.2 1 155 21 105 155 2.2 1 132 23 106 153 2.2 1 141 12 107 142 2.2 1 122 20 108 149 2.2 1 132 17 109 162 2.2 1 146 16 110 155 2.2 1 136 19 111 162 2.2 1 132 30 112 167 2.2 1 156 11 113 189 2.2 1 173 16 114 162 2.2 1 152 10 115 134 2.2 1 121 13 116 157 2.2 1 138 19 117 198 2.2 1 170 28 118 187 2.2 1 168 19 119 213 2.2 1 190 23 120 196 2.2 1 178 18 121 183 2.2 1 157 26 122 203 2.2 1 179 24 123 140 2.2 1 117 23 124 186 2.2 1 157 29 125 185 2.2 1 149 36 126 192 2.2 1 169 23 127 229 2.2 1 212 17 128 233 2.2 1 205 28 129 235 2.2 1 211 24 130 246 2.2 1 223 23 131 222 2.2 1 189 33 132 234 2.2 1 215 19 133 240 2.2 1 195 45 134 246 2.2 1 167 79 135 366 2.2 1 152 214 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_5_R1.fq.gz ============================================= 150419008 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_5_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_5_R2.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_5_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_5_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_5_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4093.54 s (27 µs/read; 2.20 M reads/minute). === Summary === Total reads processed: 150,419,008 Reads with adapters: 54,717,652 (36.4%) Reads written (passing filters): 150,419,008 (100.0%) Total basepairs processed: 17,426,503,375 bp Quality-trimmed: 4,558,367 bp (0.0%) Total written (filtered): 17,349,807,948 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 54717652 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.3% C: 9.6% G: 8.0% T: 39.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 45101075 37604752.0 0 45101075 2 6503750 9401188.0 0 6503750 3 1259619 2350297.0 0 1259619 4 1135277 587574.2 0 1135277 5 401524 146893.6 0 401524 6 100353 36723.4 0 100353 7 71462 9180.8 0 71462 8 46543 2295.2 0 46543 9 8283 573.8 0 6448 1835 10 72512 143.5 1 69038 3474 11 690 35.9 1 158 532 12 243 9.0 1 116 127 13 173 2.2 1 150 23 14 36 2.2 1 27 9 15 95 2.2 1 84 11 16 21 2.2 1 20 1 17 37 2.2 1 30 7 18 78 2.2 1 73 5 19 72 2.2 1 59 13 20 106 2.2 1 98 8 21 50 2.2 1 46 4 22 51 2.2 1 41 10 23 101 2.2 1 95 6 24 54 2.2 1 43 11 25 70 2.2 1 57 13 26 63 2.2 1 54 9 27 83 2.2 1 76 7 28 66 2.2 1 60 6 29 52 2.2 1 41 11 30 64 2.2 1 49 15 31 68 2.2 1 63 5 32 52 2.2 1 43 9 33 72 2.2 1 55 17 34 61 2.2 1 51 10 35 81 2.2 1 64 17 36 62 2.2 1 53 9 37 66 2.2 1 61 5 38 73 2.2 1 61 12 39 94 2.2 1 75 19 40 89 2.2 1 76 13 41 87 2.2 1 75 12 42 85 2.2 1 72 13 43 82 2.2 1 74 8 44 85 2.2 1 71 14 45 84 2.2 1 74 10 46 95 2.2 1 82 13 47 96 2.2 1 80 16 48 103 2.2 1 88 15 49 114 2.2 1 107 7 50 109 2.2 1 94 15 51 95 2.2 1 82 13 52 127 2.2 1 111 16 53 78 2.2 1 64 14 54 101 2.2 1 88 13 55 124 2.2 1 106 18 56 129 2.2 1 117 12 57 120 2.2 1 104 16 58 111 2.2 1 98 13 59 106 2.2 1 91 15 60 111 2.2 1 100 11 61 114 2.2 1 93 21 62 123 2.2 1 113 10 63 110 2.2 1 102 8 64 122 2.2 1 115 7 65 121 2.2 1 104 17 66 123 2.2 1 113 10 67 111 2.2 1 97 14 68 139 2.2 1 115 24 69 133 2.2 1 121 12 70 129 2.2 1 117 12 71 128 2.2 1 120 8 72 119 2.2 1 105 14 73 116 2.2 1 108 8 74 141 2.2 1 129 12 75 140 2.2 1 126 14 76 156 2.2 1 148 8 77 163 2.2 1 147 16 78 142 2.2 1 123 19 79 131 2.2 1 116 15 80 141 2.2 1 121 20 81 125 2.2 1 105 20 82 144 2.2 1 125 19 83 142 2.2 1 126 16 84 143 2.2 1 122 21 85 169 2.2 1 142 27 86 143 2.2 1 133 10 87 136 2.2 1 116 20 88 122 2.2 1 105 17 89 162 2.2 1 148 14 90 164 2.2 1 153 11 91 147 2.2 1 119 28 92 147 2.2 1 130 17 93 132 2.2 1 105 27 94 151 2.2 1 131 20 95 186 2.2 1 169 17 96 156 2.2 1 125 31 97 140 2.2 1 128 12 98 140 2.2 1 129 11 99 183 2.2 1 163 20 100 191 2.2 1 164 27 101 133 2.2 1 117 16 102 183 2.2 1 161 22 103 120 2.2 1 108 12 104 156 2.2 1 128 28 105 126 2.2 1 107 19 106 158 2.2 1 139 19 107 161 2.2 1 140 21 108 150 2.2 1 138 12 109 172 2.2 1 151 21 110 134 2.2 1 125 9 111 172 2.2 1 150 22 112 196 2.2 1 176 20 113 172 2.2 1 149 23 114 194 2.2 1 167 27 115 139 2.2 1 120 19 116 148 2.2 1 133 15 117 169 2.2 1 152 17 118 178 2.2 1 150 28 119 162 2.2 1 149 13 120 191 2.2 1 168 23 121 223 2.2 1 194 29 122 202 2.2 1 178 24 123 193 2.2 1 167 26 124 181 2.2 1 142 39 125 192 2.2 1 169 23 126 222 2.2 1 192 30 127 204 2.2 1 178 26 128 204 2.2 1 181 23 129 202 2.2 1 179 23 130 236 2.2 1 200 36 131 261 2.2 1 233 28 132 266 2.2 1 244 22 133 270 2.2 1 227 43 134 233 2.2 1 160 73 135 361 2.2 1 141 220 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_5_R2.fq.gz ============================================= 150419008 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_5_R1_trimmed.fq.gz and zr3616_5_R2_trimmed.fq.gz file_1: zr3616_5_R1_trimmed.fq.gz, file_2: zr3616_5_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_5_R1_trimmed.fq.gz and zr3616_5_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_5_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_5_R2_val_2.fq.gz Total number of sequences analysed: 150419008 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1715117 (1.14%) >>> Now running FastQC on the validated data zr3616_5_R1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 3490267620. >>> Now running FastQC on the validated data zr3616_5_R2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 3490267620. Deleting both intermediate output files zr3616_5_R1_trimmed.fq.gz and zr3616_5_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_6_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_6_R1.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_6_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_6_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_6_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 5409.37 s (27 µs/read; 2.19 M reads/minute). === Summary === Total reads processed: 197,572,800 Reads with adapters: 70,288,569 (35.6%) Reads written (passing filters): 197,572,800 (100.0%) Total basepairs processed: 22,541,948,875 bp Quality-trimmed: 5,531,625 bp (0.0%) Total written (filtered): 22,442,009,492 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 70288569 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 42.9% C: 9.7% G: 8.3% T: 39.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 57128669 49393200.0 0 57128669 2 8853172 12348300.0 0 8853172 3 1746170 3087075.0 0 1746170 4 1549392 771768.8 0 1549392 5 570617 192942.2 0 570617 6 143035 48235.5 0 143035 7 99889 12058.9 0 99889 8 63778 3014.7 0 63778 9 11204 753.7 0 8840 2364 10 96284 188.4 1 91445 4839 11 970 47.1 1 181 789 12 301 11.8 1 124 177 13 97 2.9 1 67 30 14 78 2.9 1 57 21 15 164 2.9 1 137 27 16 57 2.9 1 46 11 17 62 2.9 1 46 16 18 130 2.9 1 106 24 19 146 2.9 1 126 20 20 204 2.9 1 179 25 21 102 2.9 1 86 16 22 66 2.9 1 60 6 23 171 2.9 1 159 12 24 117 2.9 1 102 15 25 129 2.9 1 121 8 26 90 2.9 1 74 16 27 124 2.9 1 103 21 28 110 2.9 1 88 22 29 85 2.9 1 77 8 30 104 2.9 1 91 13 31 104 2.9 1 92 12 32 96 2.9 1 82 14 33 79 2.9 1 75 4 34 128 2.9 1 107 21 35 128 2.9 1 113 15 36 144 2.9 1 126 18 37 144 2.9 1 134 10 38 119 2.9 1 105 14 39 134 2.9 1 118 16 40 139 2.9 1 127 12 41 138 2.9 1 121 17 42 165 2.9 1 149 16 43 134 2.9 1 127 7 44 115 2.9 1 100 15 45 143 2.9 1 134 9 46 163 2.9 1 142 21 47 174 2.9 1 159 15 48 181 2.9 1 164 17 49 185 2.9 1 170 15 50 150 2.9 1 135 15 51 164 2.9 1 150 14 52 153 2.9 1 135 18 53 149 2.9 1 136 13 54 171 2.9 1 159 12 55 159 2.9 1 142 17 56 189 2.9 1 166 23 57 180 2.9 1 155 25 58 196 2.9 1 177 19 59 200 2.9 1 183 17 60 149 2.9 1 134 15 61 177 2.9 1 149 28 62 188 2.9 1 165 23 63 209 2.9 1 186 23 64 187 2.9 1 163 24 65 157 2.9 1 142 15 66 192 2.9 1 170 22 67 209 2.9 1 186 23 68 164 2.9 1 150 14 69 175 2.9 1 159 16 70 250 2.9 1 227 23 71 210 2.9 1 189 21 72 226 2.9 1 207 19 73 233 2.9 1 218 15 74 201 2.9 1 189 12 75 248 2.9 1 227 21 76 230 2.9 1 203 27 77 208 2.9 1 176 32 78 256 2.9 1 229 27 79 242 2.9 1 210 32 80 277 2.9 1 246 31 81 224 2.9 1 202 22 82 256 2.9 1 236 20 83 219 2.9 1 193 26 84 223 2.9 1 194 29 85 255 2.9 1 228 27 86 190 2.9 1 172 18 87 209 2.9 1 186 23 88 222 2.9 1 196 26 89 190 2.9 1 175 15 90 231 2.9 1 204 27 91 216 2.9 1 192 24 92 240 2.9 1 225 15 93 246 2.9 1 220 26 94 232 2.9 1 202 30 95 232 2.9 1 210 22 96 250 2.9 1 227 23 97 254 2.9 1 230 24 98 250 2.9 1 217 33 99 244 2.9 1 211 33 100 235 2.9 1 209 26 101 233 2.9 1 205 28 102 242 2.9 1 219 23 103 210 2.9 1 187 23 104 240 2.9 1 210 30 105 241 2.9 1 208 33 106 229 2.9 1 206 23 107 224 2.9 1 195 29 108 247 2.9 1 205 42 109 218 2.9 1 194 24 110 235 2.9 1 209 26 111 262 2.9 1 234 28 112 234 2.9 1 213 21 113 234 2.9 1 209 25 114 236 2.9 1 211 25 115 240 2.9 1 210 30 116 240 2.9 1 223 17 117 267 2.9 1 228 39 118 260 2.9 1 236 24 119 296 2.9 1 266 30 120 290 2.9 1 246 44 121 253 2.9 1 224 29 122 254 2.9 1 227 27 123 270 2.9 1 243 27 124 293 2.9 1 268 25 125 276 2.9 1 246 30 126 279 2.9 1 247 32 127 278 2.9 1 241 37 128 356 2.9 1 315 41 129 329 2.9 1 275 54 130 295 2.9 1 268 27 131 376 2.9 1 336 40 132 353 2.9 1 309 44 133 330 2.9 1 270 60 134 368 2.9 1 261 107 135 534 2.9 1 237 297 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_6_R1.fq.gz ============================================= 197572800 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_6_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_6_R2.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_6_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_6_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_6_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 5262.54 s (27 µs/read; 2.25 M reads/minute). === Summary === Total reads processed: 197,572,800 Reads with adapters: 70,057,307 (35.5%) Reads written (passing filters): 197,572,800 (100.0%) Total basepairs processed: 22,544,053,643 bp Quality-trimmed: 5,055,245 bp (0.0%) Total written (filtered): 22,445,212,917 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 70057307 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.3% C: 9.4% G: 8.1% T: 39.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 57214116 49393200.0 0 57214116 2 8670692 12348300.0 0 8670692 3 1627836 3087075.0 0 1627836 4 1538525 771768.8 0 1538525 5 568835 192942.2 0 568835 6 141297 48235.5 0 141297 7 99862 12058.9 0 99862 8 63665 3014.7 0 63665 9 10903 753.7 0 8510 2393 10 94034 188.4 1 89381 4653 11 956 47.1 1 191 765 12 350 11.8 1 210 140 13 222 2.9 1 187 35 14 73 2.9 1 49 24 15 186 2.9 1 159 27 16 40 2.9 1 35 5 17 56 2.9 1 43 13 18 145 2.9 1 128 17 19 137 2.9 1 126 11 20 207 2.9 1 182 25 21 135 2.9 1 119 16 22 70 2.9 1 56 14 23 154 2.9 1 149 5 24 101 2.9 1 89 12 25 123 2.9 1 114 9 26 113 2.9 1 103 10 27 129 2.9 1 119 10 28 116 2.9 1 106 10 29 114 2.9 1 98 16 30 102 2.9 1 85 17 31 117 2.9 1 104 13 32 88 2.9 1 75 13 33 107 2.9 1 97 10 34 103 2.9 1 87 16 35 125 2.9 1 112 13 36 118 2.9 1 102 16 37 134 2.9 1 117 17 38 131 2.9 1 109 22 39 107 2.9 1 98 9 40 161 2.9 1 140 21 41 141 2.9 1 128 13 42 130 2.9 1 118 12 43 152 2.9 1 138 14 44 123 2.9 1 108 15 45 136 2.9 1 123 13 46 155 2.9 1 139 16 47 155 2.9 1 141 14 48 168 2.9 1 147 21 49 150 2.9 1 133 17 50 181 2.9 1 159 22 51 160 2.9 1 145 15 52 134 2.9 1 120 14 53 183 2.9 1 161 22 54 160 2.9 1 143 17 55 180 2.9 1 170 10 56 174 2.9 1 154 20 57 196 2.9 1 177 19 58 157 2.9 1 138 19 59 207 2.9 1 184 23 60 184 2.9 1 165 19 61 175 2.9 1 155 20 62 185 2.9 1 175 10 63 209 2.9 1 189 20 64 190 2.9 1 163 27 65 200 2.9 1 180 20 66 196 2.9 1 170 26 67 210 2.9 1 190 20 68 212 2.9 1 188 24 69 205 2.9 1 197 8 70 194 2.9 1 175 19 71 234 2.9 1 214 20 72 202 2.9 1 182 20 73 227 2.9 1 202 25 74 202 2.9 1 180 22 75 242 2.9 1 213 29 76 242 2.9 1 215 27 77 247 2.9 1 220 27 78 288 2.9 1 251 37 79 267 2.9 1 234 33 80 259 2.9 1 243 16 81 229 2.9 1 202 27 82 235 2.9 1 215 20 83 248 2.9 1 224 24 84 227 2.9 1 210 17 85 251 2.9 1 223 28 86 225 2.9 1 208 17 87 255 2.9 1 221 34 88 273 2.9 1 241 32 89 271 2.9 1 243 28 90 278 2.9 1 249 29 91 250 2.9 1 225 25 92 224 2.9 1 195 29 93 227 2.9 1 200 27 94 261 2.9 1 227 34 95 259 2.9 1 228 31 96 246 2.9 1 208 38 97 212 2.9 1 178 34 98 262 2.9 1 232 30 99 270 2.9 1 236 34 100 260 2.9 1 234 26 101 262 2.9 1 238 24 102 253 2.9 1 231 22 103 258 2.9 1 219 39 104 253 2.9 1 231 22 105 258 2.9 1 228 30 106 269 2.9 1 245 24 107 276 2.9 1 242 34 108 218 2.9 1 191 27 109 268 2.9 1 237 31 110 259 2.9 1 215 44 111 298 2.9 1 266 32 112 272 2.9 1 234 38 113 255 2.9 1 225 30 114 244 2.9 1 222 22 115 290 2.9 1 251 39 116 278 2.9 1 244 34 117 289 2.9 1 251 38 118 282 2.9 1 252 30 119 276 2.9 1 231 45 120 287 2.9 1 261 26 121 279 2.9 1 248 31 122 303 2.9 1 275 28 123 262 2.9 1 238 24 124 283 2.9 1 249 34 125 256 2.9 1 220 36 126 297 2.9 1 268 29 127 308 2.9 1 262 46 128 292 2.9 1 246 46 129 324 2.9 1 277 47 130 340 2.9 1 296 44 131 330 2.9 1 292 38 132 338 2.9 1 289 49 133 393 2.9 1 299 94 134 368 2.9 1 273 95 135 529 2.9 1 227 302 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_6_R2.fq.gz ============================================= 197572800 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_6_R1_trimmed.fq.gz and zr3616_6_R2_trimmed.fq.gz file_1: zr3616_6_R1_trimmed.fq.gz, file_2: zr3616_6_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_6_R1_trimmed.fq.gz and zr3616_6_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_6_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_6_R2_val_2.fq.gz Total number of sequences analysed: 197572800 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2541198 (1.29%) >>> Now running FastQC on the validated data zr3616_6_R1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 4280558820. >>> Now running FastQC on the validated data zr3616_6_R2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 4280558820. Deleting both intermediate output files zr3616_6_R1_trimmed.fq.gz and zr3616_6_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_7_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_7_R1.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_7_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_7_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_7_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4204.58 s (28 µs/read; 2.15 M reads/minute). === Summary === Total reads processed: 150,811,300 Reads with adapters: 55,728,162 (37.0%) Reads written (passing filters): 150,811,300 (100.0%) Total basepairs processed: 17,548,799,698 bp Quality-trimmed: 4,591,455 bp (0.0%) Total written (filtered): 17,470,764,290 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 55728162 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.1% C: 9.6% G: 7.9% T: 39.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 46056625 37702825.0 0 46056625 2 6594663 9425706.2 0 6594663 3 1319173 2356426.6 0 1319173 4 1125771 589106.6 0 1125771 5 361289 147276.7 0 361289 6 88158 36819.2 0 88158 7 58900 9204.8 0 58900 8 35648 2301.2 0 35648 9 6354 575.3 0 4742 1612 10 56808 143.8 1 53528 3280 11 645 36.0 1 128 517 12 237 9.0 1 143 94 13 77 2.2 1 54 23 14 68 2.2 1 52 16 15 168 2.2 1 153 15 16 38 2.2 1 28 10 17 72 2.2 1 56 16 18 105 2.2 1 94 11 19 133 2.2 1 108 25 20 149 2.2 1 134 15 21 119 2.2 1 111 8 22 92 2.2 1 78 14 23 167 2.2 1 156 11 24 88 2.2 1 76 12 25 97 2.2 1 90 7 26 74 2.2 1 64 10 27 109 2.2 1 96 13 28 99 2.2 1 92 7 29 118 2.2 1 108 10 30 82 2.2 1 74 8 31 119 2.2 1 105 14 32 108 2.2 1 101 7 33 97 2.2 1 90 7 34 135 2.2 1 125 10 35 111 2.2 1 90 21 36 103 2.2 1 96 7 37 115 2.2 1 101 14 38 129 2.2 1 108 21 39 114 2.2 1 97 17 40 136 2.2 1 116 20 41 144 2.2 1 131 13 42 157 2.2 1 137 20 43 128 2.2 1 115 13 44 102 2.2 1 99 3 45 114 2.2 1 102 12 46 134 2.2 1 122 12 47 140 2.2 1 131 9 48 157 2.2 1 147 10 49 128 2.2 1 117 11 50 139 2.2 1 127 12 51 133 2.2 1 117 16 52 155 2.2 1 144 11 53 158 2.2 1 147 11 54 130 2.2 1 116 14 55 177 2.2 1 151 26 56 138 2.2 1 127 11 57 168 2.2 1 139 29 58 147 2.2 1 129 18 59 170 2.2 1 152 18 60 179 2.2 1 156 23 61 169 2.2 1 154 15 62 134 2.2 1 122 12 63 183 2.2 1 170 13 64 164 2.2 1 145 19 65 175 2.2 1 149 26 66 175 2.2 1 155 20 67 190 2.2 1 168 22 68 221 2.2 1 212 9 69 178 2.2 1 162 16 70 182 2.2 1 170 12 71 205 2.2 1 181 24 72 207 2.2 1 180 27 73 212 2.2 1 191 21 74 209 2.2 1 186 23 75 174 2.2 1 158 16 76 182 2.2 1 170 12 77 213 2.2 1 194 19 78 205 2.2 1 175 30 79 207 2.2 1 186 21 80 217 2.2 1 189 28 81 205 2.2 1 181 24 82 226 2.2 1 202 24 83 222 2.2 1 197 25 84 184 2.2 1 165 19 85 183 2.2 1 169 14 86 185 2.2 1 157 28 87 207 2.2 1 174 33 88 221 2.2 1 208 13 89 239 2.2 1 210 29 90 231 2.2 1 215 16 91 212 2.2 1 195 17 92 245 2.2 1 216 29 93 237 2.2 1 213 24 94 217 2.2 1 187 30 95 199 2.2 1 179 20 96 228 2.2 1 198 30 97 214 2.2 1 191 23 98 224 2.2 1 197 27 99 240 2.2 1 209 31 100 240 2.2 1 209 31 101 255 2.2 1 226 29 102 235 2.2 1 215 20 103 237 2.2 1 210 27 104 201 2.2 1 178 23 105 264 2.2 1 235 29 106 211 2.2 1 175 36 107 232 2.2 1 201 31 108 221 2.2 1 187 34 109 304 2.2 1 277 27 110 237 2.2 1 210 27 111 245 2.2 1 218 27 112 219 2.2 1 184 35 113 225 2.2 1 187 38 114 233 2.2 1 195 38 115 231 2.2 1 215 16 116 223 2.2 1 191 32 117 249 2.2 1 228 21 118 285 2.2 1 254 31 119 297 2.2 1 252 45 120 284 2.2 1 257 27 121 289 2.2 1 252 37 122 286 2.2 1 251 35 123 274 2.2 1 249 25 124 267 2.2 1 223 44 125 269 2.2 1 250 19 126 287 2.2 1 249 38 127 278 2.2 1 252 26 128 313 2.2 1 263 50 129 355 2.2 1 324 31 130 376 2.2 1 338 38 131 332 2.2 1 290 42 132 339 2.2 1 294 45 133 388 2.2 1 314 74 134 358 2.2 1 247 111 135 511 2.2 1 205 306 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_7_R1.fq.gz ============================================= 150811300 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_7_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_7_R2.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_7_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_7_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_7_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4267.50 s (28 µs/read; 2.12 M reads/minute). === Summary === Total reads processed: 150,811,300 Reads with adapters: 55,622,993 (36.9%) Reads written (passing filters): 150,811,300 (100.0%) Total basepairs processed: 17,546,903,399 bp Quality-trimmed: 4,282,115 bp (0.0%) Total written (filtered): 17,469,617,103 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 55622993 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.5% C: 9.7% G: 7.7% T: 39.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 46232463 37702825.0 0 46232463 2 6383119 9425706.2 0 6383119 3 1263005 2356426.6 0 1263005 4 1119159 589106.6 0 1119159 5 357925 147276.7 0 357925 6 86321 36819.2 0 86321 7 58304 9204.8 0 58304 8 36108 2301.2 0 36108 9 6434 575.3 0 4845 1589 10 54733 143.8 1 51602 3131 11 574 36.0 1 108 466 12 304 9.0 1 201 103 13 181 2.2 1 158 23 14 76 2.2 1 64 12 15 169 2.2 1 156 13 16 78 2.2 1 63 15 17 55 2.2 1 43 12 18 130 2.2 1 104 26 19 135 2.2 1 115 20 20 171 2.2 1 149 22 21 92 2.2 1 83 9 22 107 2.2 1 84 23 23 166 2.2 1 148 18 24 110 2.2 1 97 13 25 110 2.2 1 102 8 26 111 2.2 1 97 14 27 96 2.2 1 81 15 28 109 2.2 1 94 15 29 107 2.2 1 97 10 30 94 2.2 1 84 10 31 102 2.2 1 94 8 32 89 2.2 1 79 10 33 112 2.2 1 102 10 34 116 2.2 1 105 11 35 128 2.2 1 110 18 36 126 2.2 1 111 15 37 118 2.2 1 105 13 38 115 2.2 1 101 14 39 101 2.2 1 86 15 40 128 2.2 1 108 20 41 127 2.2 1 117 10 42 147 2.2 1 120 27 43 123 2.2 1 109 14 44 129 2.2 1 115 14 45 123 2.2 1 110 13 46 96 2.2 1 93 3 47 136 2.2 1 117 19 48 140 2.2 1 133 7 49 138 2.2 1 120 18 50 162 2.2 1 146 16 51 116 2.2 1 97 19 52 151 2.2 1 133 18 53 141 2.2 1 131 10 54 143 2.2 1 128 15 55 150 2.2 1 135 15 56 128 2.2 1 120 8 57 174 2.2 1 152 22 58 172 2.2 1 156 16 59 170 2.2 1 159 11 60 166 2.2 1 148 18 61 146 2.2 1 136 10 62 166 2.2 1 146 20 63 167 2.2 1 152 15 64 156 2.2 1 140 16 65 203 2.2 1 187 16 66 147 2.2 1 133 14 67 171 2.2 1 158 13 68 192 2.2 1 176 16 69 161 2.2 1 142 19 70 206 2.2 1 185 21 71 262 2.2 1 240 22 72 212 2.2 1 185 27 73 228 2.2 1 195 33 74 197 2.2 1 179 18 75 194 2.2 1 173 21 76 214 2.2 1 196 18 77 214 2.2 1 190 24 78 186 2.2 1 160 26 79 213 2.2 1 197 16 80 252 2.2 1 220 32 81 209 2.2 1 191 18 82 192 2.2 1 174 18 83 226 2.2 1 197 29 84 187 2.2 1 164 23 85 214 2.2 1 194 20 86 235 2.2 1 192 43 87 222 2.2 1 198 24 88 249 2.2 1 214 35 89 256 2.2 1 224 32 90 221 2.2 1 196 25 91 265 2.2 1 235 30 92 227 2.2 1 210 17 93 220 2.2 1 201 19 94 226 2.2 1 199 27 95 210 2.2 1 185 25 96 277 2.2 1 236 41 97 227 2.2 1 204 23 98 244 2.2 1 207 37 99 230 2.2 1 199 31 100 246 2.2 1 215 31 101 225 2.2 1 202 23 102 272 2.2 1 235 37 103 236 2.2 1 217 19 104 221 2.2 1 191 30 105 207 2.2 1 181 26 106 194 2.2 1 162 32 107 239 2.2 1 202 37 108 281 2.2 1 242 39 109 282 2.2 1 239 43 110 271 2.2 1 238 33 111 239 2.2 1 207 32 112 239 2.2 1 215 24 113 242 2.2 1 215 27 114 251 2.2 1 223 28 115 234 2.2 1 212 22 116 257 2.2 1 224 33 117 307 2.2 1 272 35 118 246 2.2 1 226 20 119 288 2.2 1 267 21 120 278 2.2 1 249 29 121 302 2.2 1 266 36 122 284 2.2 1 260 24 123 296 2.2 1 263 33 124 258 2.2 1 229 29 125 312 2.2 1 265 47 126 274 2.2 1 237 37 127 321 2.2 1 273 48 128 309 2.2 1 261 48 129 338 2.2 1 302 36 130 392 2.2 1 352 40 131 320 2.2 1 272 48 132 334 2.2 1 285 49 133 373 2.2 1 313 60 134 397 2.2 1 294 103 135 491 2.2 1 219 272 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_7_R2.fq.gz ============================================= 150811300 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_7_R1_trimmed.fq.gz and zr3616_7_R2_trimmed.fq.gz file_1: zr3616_7_R1_trimmed.fq.gz, file_2: zr3616_7_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_7_R1_trimmed.fq.gz and zr3616_7_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_7_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_7_R2_val_2.fq.gz Total number of sequences analysed: 150811300 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1589275 (1.05%) >>> Now running FastQC on the validated data zr3616_7_R1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 4883804020. >>> Now running FastQC on the validated data zr3616_7_R2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 4883804020. Deleting both intermediate output files zr3616_7_R1_trimmed.fq.gz and zr3616_7_R2_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_8_R1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_8_R1.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_8_R1_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_8_R1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_8_R1.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4519.25 s (28 µs/read; 2.17 M reads/minute). === Summary === Total reads processed: 163,170,949 Reads with adapters: 60,377,927 (37.0%) Reads written (passing filters): 163,170,949 (100.0%) Total basepairs processed: 19,050,779,988 bp Quality-trimmed: 4,388,508 bp (0.0%) Total written (filtered): 18,967,646,504 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 60377927 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.4% C: 9.7% G: 7.9% T: 39.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 50084126 40792737.2 0 50084126 2 7045447 10198184.3 0 7045447 3 1408521 2549546.1 0 1408521 4 1194884 637386.5 0 1194884 5 371081 159346.6 0 371081 6 91420 39836.7 0 91420 7 61796 9959.2 0 61796 8 38927 2489.8 0 38927 9 6561 622.4 0 4812 1749 10 53488 155.6 1 50006 3482 11 580 38.9 1 108 472 12 222 9.7 1 114 108 13 71 2.4 1 57 14 14 55 2.4 1 45 10 15 133 2.4 1 119 14 16 44 2.4 1 33 11 17 60 2.4 1 52 8 18 117 2.4 1 104 13 19 114 2.4 1 95 19 20 148 2.4 1 132 16 21 85 2.4 1 75 10 22 67 2.4 1 60 7 23 152 2.4 1 128 24 24 96 2.4 1 88 8 25 107 2.4 1 94 13 26 104 2.4 1 87 17 27 99 2.4 1 87 12 28 91 2.4 1 86 5 29 66 2.4 1 56 10 30 80 2.4 1 74 6 31 83 2.4 1 74 9 32 85 2.4 1 78 7 33 90 2.4 1 79 11 34 101 2.4 1 91 10 35 117 2.4 1 102 15 36 83 2.4 1 72 11 37 112 2.4 1 98 14 38 109 2.4 1 94 15 39 98 2.4 1 90 8 40 107 2.4 1 98 9 41 100 2.4 1 91 9 42 120 2.4 1 110 10 43 88 2.4 1 77 11 44 116 2.4 1 98 18 45 116 2.4 1 106 10 46 121 2.4 1 113 8 47 96 2.4 1 80 16 48 133 2.4 1 126 7 49 106 2.4 1 98 8 50 117 2.4 1 110 7 51 139 2.4 1 131 8 52 142 2.4 1 124 18 53 131 2.4 1 116 15 54 135 2.4 1 115 20 55 143 2.4 1 127 16 56 145 2.4 1 124 21 57 150 2.4 1 136 14 58 137 2.4 1 124 13 59 117 2.4 1 107 10 60 126 2.4 1 118 8 61 130 2.4 1 119 11 62 147 2.4 1 137 10 63 154 2.4 1 137 17 64 117 2.4 1 102 15 65 159 2.4 1 144 15 66 174 2.4 1 150 24 67 145 2.4 1 122 23 68 159 2.4 1 143 16 69 169 2.4 1 156 13 70 156 2.4 1 143 13 71 151 2.4 1 136 15 72 187 2.4 1 172 15 73 180 2.4 1 162 18 74 156 2.4 1 145 11 75 150 2.4 1 139 11 76 174 2.4 1 147 27 77 206 2.4 1 184 22 78 174 2.4 1 157 17 79 147 2.4 1 130 17 80 166 2.4 1 154 12 81 200 2.4 1 187 13 82 165 2.4 1 148 17 83 178 2.4 1 156 22 84 159 2.4 1 143 16 85 191 2.4 1 168 23 86 204 2.4 1 179 25 87 189 2.4 1 170 19 88 207 2.4 1 182 25 89 193 2.4 1 175 18 90 189 2.4 1 169 20 91 187 2.4 1 180 7 92 178 2.4 1 157 21 93 186 2.4 1 169 17 94 189 2.4 1 165 24 95 211 2.4 1 195 16 96 185 2.4 1 161 24 97 213 2.4 1 188 25 98 208 2.4 1 190 18 99 199 2.4 1 180 19 100 227 2.4 1 203 24 101 224 2.4 1 199 25 102 219 2.4 1 197 22 103 214 2.4 1 191 23 104 192 2.4 1 171 21 105 216 2.4 1 187 29 106 224 2.4 1 193 31 107 199 2.4 1 182 17 108 170 2.4 1 148 22 109 199 2.4 1 162 37 110 192 2.4 1 164 28 111 224 2.4 1 198 26 112 214 2.4 1 178 36 113 190 2.4 1 165 25 114 233 2.4 1 194 39 115 188 2.4 1 163 25 116 209 2.4 1 181 28 117 233 2.4 1 212 21 118 242 2.4 1 214 28 119 242 2.4 1 202 40 120 238 2.4 1 201 37 121 235 2.4 1 204 31 122 220 2.4 1 189 31 123 248 2.4 1 222 26 124 244 2.4 1 217 27 125 250 2.4 1 220 30 126 251 2.4 1 226 25 127 273 2.4 1 243 30 128 277 2.4 1 243 34 129 290 2.4 1 264 26 130 309 2.4 1 274 35 131 308 2.4 1 262 46 132 312 2.4 1 283 29 133 317 2.4 1 256 61 134 361 2.4 1 258 103 135 506 2.4 1 222 284 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_8_R1.fq.gz ============================================= 163170949 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore/zr3616_8_R2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_8_R2.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore --threads 28' Output file(s) will be GZIP compressed Cutadapt seems to be fairly up-to-date (version 3.1). Setting -j -j 1 Writing final adapter and quality trimmed output to zr3616_8_R2_trimmed.fq.gz >>> Now performing quality (cutoff '-q 20') and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_8_R2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed This is cutadapt 3.1 with Python 3.8.5 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_8_R2.fq.gz Processing reads on 1 core in single-end mode ... Finished in 4610.64 s (28 µs/read; 2.12 M reads/minute). === Summary === Total reads processed: 163,170,949 Reads with adapters: 60,258,226 (36.9%) Reads written (passing filters): 163,170,949 (100.0%) Total basepairs processed: 19,053,229,657 bp Quality-trimmed: 4,238,850 bp (0.0%) Total written (filtered): 18,970,596,628 bp (99.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 60258226 times No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 43.5% C: 9.7% G: 7.7% T: 39.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 50222130 40792737.2 0 50222130 2 6829661 10198184.3 0 6829661 3 1365339 2549546.1 0 1365339 4 1200059 637386.5 0 1200059 5 369955 159346.6 0 369955 6 88415 39836.7 0 88415 7 62111 9959.2 0 62111 8 39241 2489.8 0 39241 9 6798 622.4 0 5105 1693 10 51956 155.6 1 48511 3445 11 579 38.9 1 108 471 12 192 9.7 1 119 73 13 142 2.4 1 126 16 14 50 2.4 1 38 12 15 149 2.4 1 128 21 16 42 2.4 1 33 9 17 62 2.4 1 51 11 18 101 2.4 1 89 12 19 109 2.4 1 86 23 20 124 2.4 1 109 15 21 67 2.4 1 57 10 22 68 2.4 1 58 10 23 130 2.4 1 117 13 24 86 2.4 1 73 13 25 112 2.4 1 98 14 26 67 2.4 1 57 10 27 92 2.4 1 81 11 28 75 2.4 1 65 10 29 93 2.4 1 81 12 30 78 2.4 1 71 7 31 98 2.4 1 78 20 32 79 2.4 1 72 7 33 94 2.4 1 78 16 34 111 2.4 1 96 15 35 103 2.4 1 89 14 36 98 2.4 1 86 12 37 98 2.4 1 88 10 38 87 2.4 1 85 2 39 109 2.4 1 94 15 40 110 2.4 1 96 14 41 110 2.4 1 97 13 42 134 2.4 1 106 28 43 116 2.4 1 104 12 44 125 2.4 1 111 14 45 124 2.4 1 110 14 46 122 2.4 1 110 12 47 140 2.4 1 127 13 48 152 2.4 1 136 16 49 127 2.4 1 110 17 50 138 2.4 1 123 15 51 152 2.4 1 137 15 52 142 2.4 1 131 11 53 154 2.4 1 137 17 54 114 2.4 1 106 8 55 133 2.4 1 123 10 56 123 2.4 1 107 16 57 167 2.4 1 154 13 58 161 2.4 1 135 26 59 142 2.4 1 125 17 60 123 2.4 1 111 12 61 121 2.4 1 104 17 62 163 2.4 1 144 19 63 135 2.4 1 125 10 64 166 2.4 1 153 13 65 148 2.4 1 134 14 66 162 2.4 1 150 12 67 187 2.4 1 164 23 68 177 2.4 1 155 22 69 176 2.4 1 173 3 70 141 2.4 1 131 10 71 176 2.4 1 155 21 72 159 2.4 1 139 20 73 167 2.4 1 146 21 74 177 2.4 1 158 19 75 183 2.4 1 162 21 76 202 2.4 1 179 23 77 214 2.4 1 199 15 78 195 2.4 1 174 21 79 183 2.4 1 168 15 80 179 2.4 1 161 18 81 195 2.4 1 167 28 82 215 2.4 1 199 16 83 192 2.4 1 169 23 84 183 2.4 1 158 25 85 188 2.4 1 161 27 86 177 2.4 1 151 26 87 184 2.4 1 164 20 88 201 2.4 1 179 22 89 189 2.4 1 172 17 90 217 2.4 1 192 25 91 210 2.4 1 190 20 92 227 2.4 1 210 17 93 210 2.4 1 190 20 94 154 2.4 1 135 19 95 200 2.4 1 172 28 96 166 2.4 1 139 27 97 205 2.4 1 177 28 98 222 2.4 1 204 18 99 202 2.4 1 174 28 100 185 2.4 1 166 19 101 202 2.4 1 178 24 102 208 2.4 1 176 32 103 220 2.4 1 193 27 104 196 2.4 1 156 40 105 197 2.4 1 171 26 106 197 2.4 1 176 21 107 220 2.4 1 188 32 108 239 2.4 1 221 18 109 238 2.4 1 208 30 110 243 2.4 1 220 23 111 222 2.4 1 194 28 112 228 2.4 1 205 23 113 231 2.4 1 205 26 114 234 2.4 1 199 35 115 245 2.4 1 213 32 116 220 2.4 1 195 25 117 235 2.4 1 213 22 118 239 2.4 1 212 27 119 262 2.4 1 229 33 120 294 2.4 1 265 29 121 278 2.4 1 241 37 122 242 2.4 1 218 24 123 238 2.4 1 208 30 124 219 2.4 1 183 36 125 234 2.4 1 204 30 126 261 2.4 1 228 33 127 296 2.4 1 241 55 128 342 2.4 1 303 39 129 289 2.4 1 263 26 130 300 2.4 1 251 49 131 343 2.4 1 294 49 132 308 2.4 1 273 35 133 351 2.4 1 285 66 134 357 2.4 1 265 92 135 496 2.4 1 213 283 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/yaaminiv/Manchester/data/zr3616_8_R2.fq.gz ============================================= 163170949 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr3616_8_R1_trimmed.fq.gz and zr3616_8_R2_trimmed.fq.gz file_1: zr3616_8_R1_trimmed.fq.gz, file_2: zr3616_8_R2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr3616_8_R1_trimmed.fq.gz and zr3616_8_R2_trimmed.fq.gz <<<<< Writing validated paired-end Read 1 reads to zr3616_8_R1_val_1.fq.gz Writing validated paired-end Read 2 reads to zr3616_8_R2_val_2.fq.gz Total number of sequences analysed: 163170949 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1712731 (1.05%) >>> Now running FastQC on the validated data zr3616_8_R1_val_1.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1525, line 5536487816. >>> Now running FastQC on the validated data zr3616_8_R2_val_2.fq.gz<<< Can't exec "fastqc": No such file or directory at /gscratch/srlab/programs/TrimGalore-0.6.6/trim_galore line 1535, line 5536487816. Deleting both intermediate output files zr3616_8_R1_trimmed.fq.gz and zr3616_8_R2_trimmed.fq.gz ==================================================================================================== TrimGalore 1 complete [INFO ] multiqc : This is MultiQC v1.8 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching : /gscratch/scrubbed/yaaminiv/Manchester/analyses/trimgalore [INFO ] cutadapt : Found 16 reports [INFO ] multiqc : Compressing plot data [INFO ] multiqc : Report : multiqc_report.html [INFO ] multiqc : Data : multiqc_data [INFO ] multiqc : MultiQC complete MultiQC 1 complete /var/spool/slurm/d/job1076838/slurm_script: line 63: cd: ../trimaglore-2: No such file or directory