Starting /dee2/code/volunteer_pipeline.sh SRR11462700 current disk space = 3050274979840 free memory = 1497531816 SRR11462700 SRAfilesize 6ff61e9a44e8356da424213f6ba0d6b3 SRR11462700.sra SRR11462700.sra file validated SRR11462700 is single end SRR11462700 is conventional basespace SRR11462700 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462700_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 45 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 23.065 32.0 2.0 32.0 2.0 32.0 2 31.77 32.0 32.0 32.0 32.0 32.0 3 34.59125 37.0 32.0 37.0 32.0 37.0 4 36.315 37.0 37.0 37.0 32.0 37.0 5 36.41125 37.0 37.0 37.0 37.0 37.0 6 40.05 41.0 41.0 41.0 37.0 41.0 7 40.22975 41.0 41.0 41.0 37.0 41.0 8 40.32025 41.0 41.0 41.0 37.0 41.0 9 40.29875 41.0 41.0 41.0 37.0 41.0 10-14 40.356049999999996 41.0 41.0 41.0 41.0 41.0 15-19 40.35635 41.0 41.0 41.0 41.0 41.0 20-24 40.2408 41.0 41.0 41.0 39.4 41.0 25-29 40.24035 41.0 41.0 41.0 41.0 41.0 30-34 40.127050000000004 41.0 41.0 41.0 40.2 41.0 35-39 40.1226 41.0 41.0 41.0 39.4 41.0 40-44 40.22355 41.0 41.0 41.0 40.2 41.0 45-49 40.144800000000004 41.0 41.0 41.0 39.4 41.0 50-54 40.15435 41.0 41.0 41.0 39.4 41.0 55-59 40.14465 41.0 41.0 41.0 38.6 41.0 60-64 40.0257 41.0 41.0 41.0 37.0 41.0 65-69 40.091049999999996 41.0 41.0 41.0 37.0 41.0 70-74 39.8999 41.0 41.0 41.0 37.0 41.0 75-79 39.858850000000004 41.0 40.2 41.0 37.0 41.0 80-84 40.22115 41.0 41.0 41.0 40.2 41.0 85-89 40.1857 41.0 41.0 41.0 40.2 41.0 90-94 40.109500000000004 41.0 41.0 41.0 37.8 41.0 95-99 40.056799999999996 41.0 41.0 41.0 37.0 41.0 100-104 39.90555 41.0 41.0 41.0 37.0 41.0 105-109 39.93065 41.0 41.0 41.0 37.0 41.0 110-114 39.8935 41.0 41.0 41.0 37.0 41.0 115-119 39.8546 41.0 41.0 41.0 37.0 41.0 120-124 39.792350000000006 41.0 41.0 41.0 37.0 41.0 125-129 39.53565 41.0 41.0 41.0 37.0 41.0 130-134 39.451049999999995 41.0 41.0 41.0 37.0 41.0 135-139 39.218650000000004 41.0 41.0 41.0 37.0 41.0 140-144 39.1589 41.0 41.0 41.0 37.0 41.0 145-149 38.956050000000005 41.0 41.0 41.0 37.0 41.0 150-151 38.019999999999996 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 1.0 25 2.0 26 3.0 27 3.0 28 11.0 29 12.0 30 18.0 31 32.0 32 46.0 33 50.0 34 67.0 35 74.0 36 59.0 37 135.0 38 163.0 39 261.0 40 3062.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 6.179378531073446 37.67655367231638 41.03107344632768 15.112994350282486 2 27.500000000000004 41.8 19.75 10.95 3 23.5 28.9 36.225 11.375 4 32.85 25.674999999999997 26.775 14.7 5 27.450000000000003 26.474999999999998 28.525 17.549999999999997 6 26.25 25.924999999999997 28.4 19.425 7 22.55 27.375 30.599999999999998 19.475 8 24.575 26.674999999999997 30.099999999999998 18.65 9 22.775000000000002 24.55 31.2 21.475 10-14 25.240000000000002 25.779999999999998 29.244999999999997 19.735 15-19 24.865000000000002 27.474999999999998 27.994999999999997 19.665 20-24 25.465 26.855 27.73 19.950000000000003 25-29 25.295 26.66 28.16 19.885 30-34 24.47 26.135 28.985 20.41 35-39 24.39 26.16 28.51 20.94 40-44 23.674999999999997 26.950000000000003 28.62 20.755000000000003 45-49 23.49 27.11 28.7 20.7 50-54 24.81 26.87 27.875 20.445 55-59 25.290000000000003 26.955000000000002 28.065 19.689999999999998 60-64 25.495 26.565 28.685 19.255 65-69 25.509999999999998 25.995 27.775 20.72 70-74 25.295 26.945000000000004 27.73 20.03 75-79 25.215 26.235000000000003 28.4 20.150000000000002 80-84 25.314999999999998 27.169999999999998 27.61 19.905 85-89 25.305 27.175 27.589999999999996 19.93 90-94 25.36 27.275 27.435 19.93 95-99 24.82 26.365 27.894999999999996 20.919999999999998 100-104 25.445 26.16 28.09 20.305 105-109 23.815 26.889999999999997 28.01 21.285 110-114 24.52 26.810000000000002 27.884999999999998 20.785 115-119 24.665 27.450000000000003 27.435 20.45 120-124 24.09 27.884999999999998 27.045 20.979999999999997 125-129 24.04 28.425 26.455000000000002 21.08 130-134 23.84 28.849999999999998 26.145000000000003 21.165 135-139 24.235 27.975 25.66 22.13 140-144 23.69 28.165000000000003 25.335 22.81 145-149 23.995 27.96 25.16 22.884999999999998 150-151 22.6125 27.474999999999998 25.4 24.5125 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.5 18 0.5 19 0.0 20 0.0 21 0.0 22 1.0 23 2.0 24 2.0 25 2.0 26 2.0 27 2.5 28 5.5 29 11.0 30 15.5 31 25.5 32 31.0 33 36.0 34 65.5 35 92.5 36 116.0 37 137.0 38 149.5 39 163.5 40 186.0 41 204.0 42 217.5 43 247.0 44 282.0 45 265.0 46 229.5 47 206.0 48 180.0 49 169.5 50 135.0 51 102.0 52 118.0 53 117.5 54 83.0 55 71.5 56 58.5 57 43.5 58 35.5 59 27.5 60 26.5 61 24.0 62 18.5 63 20.0 64 16.5 65 6.5 66 2.5 67 3.5 68 5.0 69 4.5 70 9.5 71 12.5 72 6.5 73 2.0 74 0.5 75 0.0 76 0.5 77 0.5 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content fail #Base N-Count 1 29.2 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 88.7 #Duplication Level Percentage of deduplicated Percentage of total 1 93.85569334836528 83.25 2 4.453213077790305 7.9 3 0.5918827508455468 1.575 4 0.3382187147688839 1.2 5 0.16910935738444194 0.75 6 0.1972942502818489 1.05 7 0.02818489289740699 0.17500000000000002 8 0.08455467869222097 0.6 9 0.02818489289740699 0.22499999999999998 >10 0.2536640360766629 3.2750000000000004 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 28 0.7000000000000001 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 26 0.65 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 13 0.325 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 13 0.325 No Hit CGGTGAAAGAGCCGCGCGGGCCGCCTTGAAGTACAATTCCCACCGAGCGG 11 0.27499999999999997 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 10 0.25 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 10 0.25 No Hit NTGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 10 0.25 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 10 0.25 No Hit CGTGCCGGCCGGGGGACGGGCTGGGAACGGCCCCTTCGGGGGCCTTCCCC 9 0.22499999999999998 No Hit CTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 8 0.2 No Hit TATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCAT 8 0.2 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 8 0.2 No Hit AGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGAT 7 0.17500000000000002 No Hit AGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACT 6 0.15 No Hit ACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGGACCCAA 6 0.15 No Hit NATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 6 0.15 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 6 0.15 No Hit TAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGG 6 0.15 No Hit AAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAAT 6 0.15 No Hit AGTACGAATACGAACCGTGAAAGCGTGGCCTATCGATCCTTTAGACCTTC 6 0.15 No Hit NGGTGAAAGAGCCGCGCGGGCCGCCTTGAAGTACAATTCCCACCGAGCGG 5 0.125 No Hit CGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGA 5 0.125 No Hit AGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTA 5 0.125 No Hit NTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 5 0.125 No Hit CGGGCCGCCTTGAAGTACAATTCCCACCGAGCGGCGGGTAGAATCCTTTG 5 0.125 No Hit TTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.05 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.07500000000000001 0.0 0.0 0.0 0.0 26-27 0.1125 0.0 0.0 0.0 0.0 28-29 0.15 0.0 0.0 0.0 0.0 30-31 0.175 0.0 0.0 0.0 0.0 32-33 0.2 0.0 0.0 0.0 0.0 34-35 0.2375 0.0 0.0 0.0 0.0 36-37 0.275 0.0 0.0 0.0 0.0 38-39 0.3625 0.0 0.0 0.0 0.0 40-41 0.4 0.0 0.0 0.0 0.0 42-43 0.4125 0.0 0.0 0.0 0.0 44-45 0.425 0.0 0.0 0.0 0.0 46-47 0.4625 0.0 0.0 0.0 0.0 48-49 0.525 0.0 0.0 0.0 0.0 50-51 0.5375000000000001 0.0 0.0 0.0 0.0 52-53 0.6125 0.0 0.0 0.0 0.0 54-55 0.6375 0.0 0.0 0.0 0.0 56-57 0.6625000000000001 0.0 0.0 0.0 0.0 58-59 0.7 0.0 0.0 0.0 0.0 60-61 0.825 0.0 0.0 0.0 0.0 62-63 1.0 0.0 0.0 0.0 0.0 64-65 1.1375 0.0 0.0 0.0 0.0 66-67 1.225 0.0 0.0 0.0 0.0 68-69 1.35 0.0 0.0 0.0 0.0 70-71 1.4625 0.0 0.0 0.0 0.0 72-73 1.5375 0.0 0.0 0.0 0.0 74-75 1.8125 0.0 0.0 0.0 0.0 76-77 2.0625 0.0 0.0 0.0 0.0 78-79 2.1875 0.0 0.0 0.0 0.0 80-81 2.4375 0.0 0.0 0.0 0.0 82-83 2.725 0.0 0.0 0.0 0.0 84-85 3.125 0.0 0.0 0.0 0.0 86-87 3.45 0.0 0.0 0.0 0.0 88-89 3.7 0.0 0.0 0.0 0.0 90-91 4.225 0.0 0.0 0.0 0.0 92-93 4.6375 0.0 0.0 0.0 0.0 94-95 5.15 0.0 0.0 0.0 0.0 96-97 5.7125 0.0 0.0 0.0 0.0 98-99 6.475 0.0 0.0 0.0 0.0 100-101 7.0625 0.0 0.0 0.0 0.0 102-103 8.1125 0.0 0.0 0.0 0.0 104-105 8.899999999999999 0.0 0.0 0.0 0.0 106-107 9.712499999999999 0.0 0.0 0.0 0.0 108-109 10.725 0.0 0.0 0.0 0.0 110-111 11.675 0.0 0.0 0.0 0.0 112-113 12.6875 0.0 0.0 0.0 0.0 114-115 13.8625 0.0 0.0 0.0 0.0 116-117 14.95 0.0 0.0 0.0 0.0 118-119 16.175 0.0 0.0 0.0 0.0 120-121 17.5375 0.0 0.0 0.0 0.0 122-123 18.9125 0.0 0.0 0.0 0.0 124-125 20.3625 0.0 0.0 0.0 0.0 126-127 21.9375 0.0 0.0 0.0 0.0 128-129 23.5375 0.0 0.0 0.0 0.0 130-131 25.125 0.0 0.0 0.0 0.0 132-133 26.9 0.0 0.0 0.0 0.0 134-135 28.5875 0.0 0.0 0.0 0.0 136-137 30.05 0.0 0.0 0.0 0.0 138-139 32.0125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACTCCAG 105 0.0069067967 27.564285 145 CGTCTGA 125 0.0051748413 11.577 145 GAACTCC 105 0.001215948 11.025714 140-144 AAAAAAA 140 0.0012308282 9.302946 120-124 >>END_MODULE Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804885 READS because READLEN < 1 Read 1804885 spots for SRR11462700.sra Written 1804885 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra Rejected 1804870 READS because READLEN < 1 Read 1804870 spots for SRR11462700.sra Written 1804870 spots for SRR11462700.sra SRR ids: ['SRR11462700.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_rwhr60ee SRR11462700.sra spots: 36097415 blocks: [[1, 1804870], [1804871, 3609740], [3609741, 5414610], [5414611, 7219480], [7219481, 9024350], [9024351, 10829220], [10829221, 12634090], [12634091, 14438960], [14438961, 16243830], [16243831, 18048700], [18048701, 19853570], [19853571, 21658440], [21658441, 23463310], [23463311, 25268180], [25268181, 27073050], [27073051, 28877920], [28877921, 30682790], [30682791, 32487660], [32487661, 34292530], [34292531, 36097415]] SRR11462700 file size 12245780 SRR11462700 completed basic pipeline successfully skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -q 10 -k inf -t 20 -o SRR11462700 SRR11462700_1.fastq Input file: SRR11462700_1.fastq trimmed: SRR11462700-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Wed Feb 12 06:23:00 2025 >> started Wed Feb 12 06:23:22 2025 >> done (22.141s) 36097415 reads processed; of these: 10884 ( 0.03%) short reads filtered out after trimming by size control 1202 ( 0.00%) empty reads filtered out after trimming by size control 36085329 (99.97%) reads available; of these: 6309799 (17.49%) trimmed reads available after processing 29775530 (82.51%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2463 0.01% 19 2554 0.01% 20 3171 0.01% 21 3255 0.01% 22 3740 0.01% 23 3921 0.01% 24 4336 0.01% 25 4144 0.01% 26 4373 0.01% 27 5042 0.01% 28 5013 0.01% 29 5122 0.01% 30 5381 0.01% 31 5639 0.02% 32 5564 0.02% 33 5912 0.02% 34 6474 0.02% 35 6514 0.02% 36 6582 0.02% 37 9174 0.03% 38 7335 0.02% 39 7591 0.02% 40 7845 0.02% 41 8101 0.02% 42 9203 0.03% 43 9413 0.03% 44 8889 0.02% 45 9776 0.03% 46 10417 0.03% 47 13587 0.04% 48 12692 0.04% 49 14112 0.04% 50 12268 0.03% 51 13330 0.04% 52 13818 0.04% 53 14465 0.04% 54 16948 0.05% 55 15764 0.04% 56 16479 0.05% 57 19811 0.05% 58 18639 0.05% 59 19338 0.05% 60 21020 0.06% 61 21741 0.06% 62 42046 0.12% 63 23112 0.06% 64 26126 0.07% 65 24716 0.07% 66 25538 0.07% 67 28042 0.08% 68 27764 0.08% 69 35171 0.10% 70 31066 0.09% 71 35267 0.10% 72 38039 0.11% 73 44834 0.12% 74 45433 0.13% 75 41566 0.12% 76 39204 0.11% 77 49257 0.14% 78 45847 0.13% 79 58353 0.16% 80 47956 0.13% 81 50487 0.14% 82 57825 0.16% 83 60579 0.17% 84 64941 0.18% 85 63064 0.17% 86 67759 0.19% 87 78195 0.22% 88 75566 0.21% 89 108707 0.30% 90 78885 0.22% 91 87516 0.24% 92 79746 0.22% 93 85715 0.24% 94 94759 0.26% 95 97900 0.27% 96 109358 0.30% 97 114737 0.32% 98 106143 0.29% 99 114177 0.32% 100 113860 0.32% 101 125620 0.35% 102 143689 0.40% 103 138524 0.38% 104 137444 0.38% 105 138932 0.39% 106 145789 0.40% 107 152624 0.42% 108 166837 0.46% 109 184687 0.51% 110 172096 0.48% 111 176756 0.49% 112 334678 0.93% 113 191592 0.53% 114 191122 0.53% 115 190598 0.53% 116 204251 0.57% 117 220440 0.61% 118 220189 0.61% 119 233600 0.65% 120 0 0.00% 121 0 0.00% 122 0 0.00% 123 0 0.00% 124 0 0.00% 125 0 0.00% 126 0 0.00% 127 0 0.00% 128 0 0.00% 129 0 0.00% 130 0 0.00% 131 0 0.00% 132 0 0.00% 133 0 0.00% 134 0 0.00% 135 0 0.00% 136 0 0.00% 137 0 0.00% 138 0 0.00% 139 0 0.00% 140 0 0.00% 141 0 0.00% 142 0 0.00% 143 0 0.00% 144 0 0.00% 145 0 0.00% 146 0 0.00% 147 0 0.00% 148 0 0.00% 149 0 0.00% 150 119 0.00% 151 29775530 82.51% 36085329 reads passed initial QC criterion=sequence-density sequence-density=14.44 sequence-density-rank=1 fanout-score=39.90 fanout-score-rank=1 prefix-density=17.07 prefix-fanout=33.8 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCATCTCGTATGCCGTCTTCTGCTTG criterion=fanout-score sequence-density=14.44 sequence-density-rank=1 fanout-score=39.90 fanout-score-rank=1 prefix-density=17.07 prefix-fanout=33.8 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCATCTCGTATGCCGTCTTCTGCTTG Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCATCTCGTATGCCGTCTTCTGCTTG -o SRR11462700 - Input file: STDIN trimmed: SRR11462700-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACAGTTCCATCTCGTATGCCGTCTTCTGCTTG -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Wed Feb 12 06:24:43 2025 >> started Wed Feb 12 06:25:25 2025 >> done (42.809s) 31273952 reads processed; of these: 322 ( 0.00%) short reads filtered out after trimming by size control 6 ( 0.00%) empty reads filtered out after trimming by size control 31273624 (100.00%) reads available; of these: 8305939 (26.56%) trimmed reads available after processing 22967685 (73.44%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2193 0.01% 19 2292 0.01% 20 2860 0.01% 21 2765 0.01% 22 3266 0.01% 23 3487 0.01% 24 3778 0.01% 25 3598 0.01% 26 3828 0.01% 27 4397 0.01% 28 4455 0.01% 29 4511 0.01% 30 4651 0.01% 31 4871 0.02% 32 4874 0.02% 33 5133 0.02% 34 5661 0.02% 35 5649 0.02% 36 5791 0.02% 37 7985 0.03% 38 6393 0.02% 39 6558 0.02% 40 6865 0.02% 41 7094 0.02% 42 8033 0.03% 43 8235 0.03% 44 7851 0.03% 45 8522 0.03% 46 9151 0.03% 47 11847 0.04% 48 11044 0.04% 49 12295 0.04% 50 10783 0.03% 51 11606 0.04% 52 12090 0.04% 53 12932 0.04% 54 14773 0.05% 55 13868 0.04% 56 14084 0.05% 57 17327 0.06% 58 16134 0.05% 59 16799 0.05% 60 18455 0.06% 61 19037 0.06% 62 36665 0.12% 63 20271 0.06% 64 22865 0.07% 65 21510 0.07% 66 22364 0.07% 67 24491 0.08% 68 24373 0.08% 69 30618 0.10% 70 27451 0.09% 71 30631 0.10% 72 33278 0.11% 73 39059 0.12% 74 39760 0.13% 75 35951 0.11% 76 34106 0.11% 77 42944 0.14% 78 40038 0.13% 79 51012 0.16% 80 41905 0.13% 81 45128 0.14% 82 50402 0.16% 83 52689 0.17% 84 55424 0.18% 85 54963 0.18% 86 59171 0.19% 87 68351 0.22% 88 66166 0.21% 89 94528 0.30% 90 70138 0.22% 91 76207 0.24% 92 69964 0.22% 93 74500 0.24% 94 82527 0.26% 95 84966 0.27% 96 95515 0.31% 97 99430 0.32% 98 92606 0.30% 99 100041 0.32% 100 99080 0.32% 101 110267 0.35% 102 124794 0.40% 103 120969 0.39% 104 119335 0.38% 105 121011 0.39% 106 126772 0.41% 107 132829 0.42% 108 146184 0.47% 109 161526 0.52% 110 150778 0.48% 111 154101 0.49% 112 291688 0.93% 113 165409 0.53% 114 165569 0.53% 115 164225 0.53% 116 177107 0.57% 117 185587 0.59% 118 185496 0.59% 119 200081 0.64% 120 217950 0.70% 121 223633 0.72% 122 213104 0.68% 123 262487 0.84% 124 264643 0.85% 125 221300 0.71% 126 242046 0.77% 127 250406 0.80% 128 238657 0.76% 129 239699 0.77% 130 235107 0.75% 131 245072 0.78% 132 301334 0.96% 133 283106 0.91% 134 259748 0.83% 135 282180 0.90% 136 257652 0.82% 137 278177 0.89% 138 303569 0.97% 139 278314 0.89% 140 280476 0.90% 141 266987 0.85% 142 283799 0.91% 143 278475 0.89% 144 262734 0.84% 145 383480 1.23% 146 284283 0.91% 147 368555 1.18% 148 619738 1.98% 149 0 0.00% 150 68 0.00% 151 17664208 56.48% criterion=sequence-density sequence-density=0.81 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=27 prefix-density=0.79 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTACTCTGCT criterion=fanout-score sequence-density=0.02 sequence-density-rank=31 fanout-score=158.16 fanout-score-rank=1 prefix-density=0.37 prefix-fanout=7.1 sequence=TGTTGAAGAATGAGCCGGCGACTCATAGGCAGTGGCTTGGTTAAGGGAACCCACCGGAGCCGTAGCGAAAGCGAGTCTTCATAGGGCAATTGTCACTGCTTATGGACCCGAACCTGGGTGATCTATCCATGACCAGGATGAAGCTTGGGTGAAACTAAGTGGAGGTCCGAACCGACTGATGTTGAAGAATCAGCGGATGAGTTGTGGTTAGGGGTGAAATGCCACTCGAACCCAGAGCTAGCTGGTTCTCCCCGAAATGCGTTGAGGCGCAGCAGTTGACTGGACATCTAGGGGTAAAGCACTGTTTCGGTGCGGGCCGCGAGAGCGGTACCAAATCGAGGCAAACTCTGAATACTAGATATGACCTCAAAATAACAGGGGTCAAGGTCGGCCAGTGAGACGGTGGGGGATAAGCTTCATCGTCGAGAGGGAAACAGCCCGGATCACCAGCTAAGGCCCCTAAATGACCGCTCAGTGATAAAGGAGGTAGGGGTGCAGAGACAGCCAGGAG Started job on | Feb 12 06:26:00 Started mapping on | Feb 12 06:26:00 Finished on | Feb 12 06:27:43 Mapping speed, Million of reads per hour | 1261.22 Number of input reads | 36085001 Average input read length | 138 UNIQUE READS: Uniquely mapped reads number | 27666510 Uniquely mapped reads % | 76.67% Average mapped length | 135.04 Number of splices: Total | 11841775 Number of splices: Annotated (sjdb) | 11544393 Number of splices: GT/AG | 11647343 Number of splices: GC/AG | 144155 Number of splices: AT/AC | 6534 Number of splices: Non-canonical | 43743 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.02% Deletion average length | 2.13 Insertion rate per base | 0.01% Insertion average length | 1.78 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 883702 % of reads mapped to multiple loci | 2.45% Number of reads mapped to too many loci | 5466414 % of reads mapped to too many loci | 15.15% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.57% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7534789 7534789 7534789 N_multimapping 883702 883702 883702 N_noFeature 1772199 2336111 26729609 N_ambiguous 478338 105565 645 UnstrandedReadsAssigned:25415973 PositiveStrandReadsAssigned:25224834 NegativeStrandReadsAssigned:936256 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=123 echo kmer=119 SRR11462700 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in single-end mode [quant] will process file 1: SRR11462700-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 36,085,001 reads, 27,639,451 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,227 rounds 52401 SRR11462700.ke.tsv 34699 SRR11462700.se.tsv 87100 total ==> SRR11462700.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 2658 55.3586 Potri.005G024800.1.v4.1 1035 936 1148 49.0197 Potri.004G059700.1.v4.1 961 862 8 0.370926 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 2832.74 39.809 Potri.016G087400.1.v4.1 270 171 1493 348.954 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 2205.99 52.6688 Potri.012G127500.1.v4.1 977 878 18 0.819376 ==> SRR11462700.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 2 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 276 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 19 SRR11462700 completed mapping pipeline successfully