Starting /dee2/code/volunteer_pipeline.sh SRR11462733 current disk space = 3051296092160 free memory = 1581915356 SRR11462733 SRAfilesize b83322f8845ff55840df98d8c49b0b8b SRR11462733.sra SRR11462733.sra file validated SRR11462733 is single end SRR11462733 is conventional basespace SRR11462733 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462733_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 44 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 22.55125 32.0 2.0 32.0 2.0 32.0 2 31.75 32.0 32.0 32.0 32.0 32.0 3 34.42875 37.0 32.0 37.0 32.0 37.0 4 36.12375 37.0 37.0 37.0 32.0 37.0 5 36.435 37.0 37.0 37.0 37.0 37.0 6 39.944 41.0 41.0 41.0 37.0 41.0 7 40.1015 41.0 41.0 41.0 37.0 41.0 8 40.0725 41.0 41.0 41.0 37.0 41.0 9 40.137 41.0 41.0 41.0 37.0 41.0 10-14 40.18204999999999 41.0 41.0 41.0 37.0 41.0 15-19 40.133300000000006 41.0 41.0 41.0 37.0 41.0 20-24 40.0662 41.0 41.0 41.0 37.0 41.0 25-29 40.02535 41.0 41.0 41.0 37.0 41.0 30-34 39.88615 41.0 41.0 41.0 37.0 41.0 35-39 39.824250000000006 41.0 41.0 41.0 37.0 41.0 40-44 39.880399999999995 41.0 41.0 41.0 37.0 41.0 45-49 39.874700000000004 41.0 41.0 41.0 37.0 41.0 50-54 39.84115 41.0 41.0 41.0 37.0 41.0 55-59 39.6533 41.0 41.0 41.0 37.0 41.0 60-64 39.68635 41.0 41.0 41.0 37.0 41.0 65-69 39.6728 41.0 41.0 41.0 37.0 41.0 70-74 39.5528 41.0 41.0 41.0 37.0 41.0 75-79 39.50385 41.0 40.2 41.0 37.0 41.0 80-84 39.87605 41.0 41.0 41.0 37.0 41.0 85-89 39.83005 41.0 41.0 41.0 37.0 41.0 90-94 39.755700000000004 41.0 41.0 41.0 37.0 41.0 95-99 39.63995 41.0 41.0 41.0 37.0 41.0 100-104 39.64354999999999 41.0 41.0 41.0 37.0 41.0 105-109 39.58585000000001 41.0 41.0 41.0 37.0 41.0 110-114 39.4674 41.0 41.0 41.0 37.0 41.0 115-119 39.5304 41.0 41.0 41.0 37.0 41.0 120-124 39.35175 41.0 41.0 41.0 37.0 41.0 125-129 39.03830000000001 41.0 41.0 41.0 34.0 41.0 130-134 38.909850000000006 41.0 41.0 41.0 33.0 41.0 135-139 38.62115 41.0 41.0 41.0 32.0 41.0 140-144 38.5577 41.0 41.0 41.0 32.0 41.0 145-149 38.2663 41.0 41.0 41.0 32.0 41.0 150-151 37.461625 41.0 39.0 41.0 27.0 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 2.0 23 3.0 24 1.0 25 5.0 26 5.0 27 7.0 28 16.0 29 32.0 30 47.0 31 39.0 32 49.0 33 69.0 34 83.0 35 82.0 36 116.0 37 159.0 38 139.0 39 274.0 40 2872.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 5.924855491329479 35.26011560693642 43.786127167630056 15.028901734104046 2 24.85 43.075 21.075 11.0 3 21.5 29.299999999999997 38.75 10.45 4 32.5 23.925 27.800000000000004 15.775 5 26.75 27.3 28.7 17.25 6 25.474999999999998 25.825 28.625 20.075000000000003 7 23.35 27.375 29.125 20.150000000000002 8 24.075 25.6 30.425 19.900000000000002 9 20.1 25.5 31.65 22.75 10-14 24.87 25.415 29.310000000000002 20.405 15-19 23.611180559027954 27.76638831941597 29.176458822941147 19.44597229861493 20-24 24.995 26.419999999999998 28.345 20.24 25-29 25.124999999999996 26.369999999999997 29.28 19.225 30-34 24.706235311765585 25.43627181359068 28.891444572228615 20.96604830241512 35-39 24.03 25.85 28.57 21.55 40-44 23.225 26.52 29.270000000000003 20.985 45-49 22.89114455722786 26.80134006700335 29.75148757437872 20.55602780139007 50-54 23.866193309665483 27.27136356817841 28.026401320066004 20.836041802090104 55-59 24.781239061953098 26.846342317115855 27.85139256962848 20.521026051302567 60-64 24.46122306115306 25.92129606480324 29.946497324866243 19.67098354917746 65-69 24.915000000000003 26.634999999999998 27.750000000000004 20.7 70-74 24.493674051107668 26.974046106916038 27.93919087863179 20.593088963344503 75-79 24.03 26.545 29.439999999999998 19.985 80-84 24.88 27.295 28.505000000000003 19.32 85-89 23.891194559727985 27.65638281914096 28.581429071453574 19.870993549677486 90-94 25.481274063703186 25.6112805640282 28.506425321266065 20.40102005100255 95-99 24.895 26.06 28.34 20.705000000000002 100-104 25.324999999999996 26.16 27.935 20.580000000000002 105-109 22.855 26.229999999999997 28.055000000000003 22.86 110-114 24.065 26.755000000000003 28.599999999999998 20.580000000000002 115-119 24.175 26.275 29.04 20.51 120-124 24.060000000000002 27.169999999999998 28.525 20.244999999999997 125-129 23.815 27.675 27.405 21.105 130-134 23.07 28.749999999999996 27.605 20.575 135-139 23.945 27.215 26.215 22.625 140-144 24.94 27.529999999999998 25.669999999999998 21.86 145-149 23.655 27.325 25.96 23.06 150-151 21.9625 26.6 26.950000000000003 24.4875 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 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 0.5 16 0.5 17 0.5 18 0.5 19 0.0 20 0.0 21 0.0 22 1.5 23 2.0 24 1.5 25 3.0 26 4.0 27 5.5 28 8.5 29 10.5 30 20.0 31 35.5 32 46.5 33 54.5 34 64.5 35 92.0 36 111.5 37 118.5 38 149.5 39 182.5 40 183.5 41 185.5 42 212.0 43 240.5 44 294.5 45 293.5 46 239.0 47 220.0 48 188.0 49 144.5 50 127.5 51 100.0 52 122.0 53 130.0 54 72.5 55 60.5 56 53.0 57 38.5 58 29.5 59 17.0 60 23.5 61 24.5 62 18.5 63 20.0 64 9.0 65 2.5 66 2.5 67 3.5 68 6.5 69 6.0 70 5.5 71 6.0 72 3.5 73 2.0 74 1.0 75 0.5 76 0.0 77 0.0 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 30.8 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 0.005 20-24 0.0 25-29 0.0 30-34 0.005 35-39 0.0 40-44 0.0 45-49 0.005 50-54 0.005 55-59 0.005 60-64 0.005 65-69 0.0 70-74 0.015 75-79 0.0 80-84 0.0 85-89 0.005 90-94 0.005 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 85.775 #Duplication Level Percentage of deduplicated Percentage of total 1 93.35470708248324 80.075 2 4.750801515593121 8.15 3 0.728650539201399 1.875 4 0.34975225881667155 1.2 5 0.20402215097639173 0.8750000000000001 6 0.05829204313611192 0.3 7 0.1457301078402798 0.8750000000000001 8 0.08743806470416789 0.6 9 0.02914602156805596 0.22499999999999998 >10 0.2623141941125036 4.2 >50 0.02914602156805596 1.625 >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 fail #Sequence Count Percentage Possible Source TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 65 1.625 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 48 1.2 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 21 0.525 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 20 0.5 No Hit NTGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 17 0.42500000000000004 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 15 0.375 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 14 0.35000000000000003 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 12 0.3 No Hit TATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCAT 11 0.27499999999999997 No Hit TGGAACAAAAGGGTAAAAGCTCGTTTGATTCTGATTTCCAGTACGAATAC 10 0.25 No Hit TACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCCG 9 0.22499999999999998 No Hit AGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTA 8 0.2 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 8 0.2 No Hit TAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGG 8 0.2 No Hit NAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGG 7 0.17500000000000002 No Hit CTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 7 0.17500000000000002 No Hit TGCAACAAACCCCGACTTCTGGAAGGGACGCATTTATTAGATAAAAGGTC 7 0.17500000000000002 No Hit NTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 7 0.17500000000000002 No Hit AAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAAT 7 0.17500000000000002 No Hit TGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 6 0.15 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 6 0.15 No Hit TGCAGTAGGGGCCTCTTGGCCCCGGAGGCACGTGCCGTTGGCCAAGCCCT 5 0.125 No Hit TAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACAC 5 0.125 No Hit NATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 5 0.125 No Hit TTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTA 5 0.125 No Hit TTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGA 5 0.125 No Hit AGTTAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTC 5 0.125 No Hit TTTTGTCAATTGGGCACTCGGTGTTCGTAAAGGGAGATCACACCAACTTC 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 0.0125 0.0 0.0 0.0 0.0 16-17 0.037500000000000006 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.1 0.0 0.0 0.0 0.0 22-23 0.1125 0.0 0.0 0.0 0.0 24-25 0.1375 0.0 0.0 0.0 0.0 26-27 0.15 0.0 0.0 0.0 0.0 28-29 0.15 0.0 0.0 0.0 0.0 30-31 0.15 0.0 0.0 0.0 0.0 32-33 0.15 0.0 0.0 0.0 0.0 34-35 0.15 0.0 0.0 0.0 0.0 36-37 0.21250000000000002 0.0 0.0 0.0 0.0 38-39 0.25 0.0 0.0 0.0 0.0 40-41 0.32499999999999996 0.0 0.0 0.0 0.0 42-43 0.35 0.0 0.0 0.0 0.0 44-45 0.4 0.0 0.0 0.0 0.0 46-47 0.4375 0.0 0.0 0.0 0.0 48-49 0.525 0.0 0.0 0.0 0.0 50-51 0.575 0.0 0.0 0.0 0.0 52-53 0.6375 0.0 0.0 0.0 0.0 54-55 0.675 0.0 0.0 0.0 0.0 56-57 0.725 0.0 0.0 0.0 0.0 58-59 0.875 0.0 0.0 0.0 0.0 60-61 0.9375 0.0 0.0 0.0 0.0 62-63 1.0875 0.0 0.0 0.0 0.0 64-65 1.225 0.0 0.0 0.0 0.0 66-67 1.2999999999999998 0.0 0.0 0.0 0.0 68-69 1.3875 0.0 0.0 0.0 0.0 70-71 1.475 0.0 0.0 0.0 0.0 72-73 1.6375 0.0 0.0 0.0 0.0 74-75 1.875 0.0 0.0 0.0 0.0 76-77 2.05 0.0 0.0 0.0 0.0 78-79 2.2625 0.0 0.0 0.0 0.0 80-81 2.5375 0.0 0.0 0.0 0.0 82-83 2.6875 0.0 0.0 0.0 0.0 84-85 2.875 0.0 0.0 0.0 0.0 86-87 3.15 0.0 0.0 0.0 0.0 88-89 3.525 0.0 0.0 0.0 0.0 90-91 4.0625 0.0 0.0 0.0 0.0 92-93 4.4625 0.0 0.0 0.0 0.0 94-95 4.887499999999999 0.0 0.0 0.0 0.0 96-97 5.5125 0.0 0.0 0.0 0.0 98-99 6.125 0.0 0.0 0.0 0.0 100-101 6.6625 0.0 0.0 0.0 0.0 102-103 7.1 0.0 0.0 0.0 0.0 104-105 7.65 0.0 0.0 0.0 0.0 106-107 8.0125 0.0 0.0 0.0 0.0 108-109 8.6125 0.0 0.0 0.0 0.0 110-111 9.7 0.0 0.0 0.0 0.0 112-113 10.75 0.0 0.0 0.0 0.0 114-115 12.0375 0.0 0.0 0.0 0.0 116-117 12.975 0.0 0.0 0.0 0.0 118-119 14.275 0.0 0.0 0.0 0.0 120-121 15.3125 0.0 0.0 0.0 0.0 122-123 16.45 0.0 0.0 0.0 0.0 124-125 17.7875 0.0 0.0 0.0 0.0 126-127 19.275 0.0 0.0 0.0 0.0 128-129 20.5 0.0 0.0 0.0 0.0 130-131 22.025 0.0 0.0 0.0 0.0 132-133 23.8375 0.0 0.0 0.0 0.0 134-135 25.575000000000003 0.0 0.0 0.0 0.0 136-137 26.7875 0.0 0.0 0.0 0.0 138-139 28.525 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGACCTT 10 0.00687326 144.7 9 >>END_MODULE Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697894 READS because READLEN < 1 Read 1697894 spots for SRR11462733.sra Written 1697894 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra Rejected 1697879 READS because READLEN < 1 Read 1697879 spots for SRR11462733.sra Written 1697879 spots for SRR11462733.sra SRR ids: ['SRR11462733.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_op1esdnn SRR11462733.sra spots: 33957595 blocks: [[1, 1697879], [1697880, 3395758], [3395759, 5093637], [5093638, 6791516], [6791517, 8489395], [8489396, 10187274], [10187275, 11885153], [11885154, 13583032], [13583033, 15280911], [15280912, 16978790], [16978791, 18676669], [18676670, 20374548], [20374549, 22072427], [22072428, 23770306], [23770307, 25468185], [25468186, 27166064], [27166065, 28863943], [28863944, 30561822], [30561823, 32259701], [32259702, 33957595]] SRR11462733 file size 11518576 SRR11462733 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 SRR11462733 SRR11462733_1.fastq Input file: SRR11462733_1.fastq trimmed: SRR11462733-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 11:19:33 2025 >> started Wed Feb 12 11:19:52 2025 >> done (19.676s) 33957595 reads processed; of these: 10506 ( 0.03%) short reads filtered out after trimming by size control 566 ( 0.00%) empty reads filtered out after trimming by size control 33946523 (99.97%) reads available; of these: 5287644 (15.58%) trimmed reads available after processing 28658879 (84.42%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2443 0.01% 19 2499 0.01% 20 2748 0.01% 21 3068 0.01% 22 3547 0.01% 23 3819 0.01% 24 4174 0.01% 25 4179 0.01% 26 4146 0.01% 27 5589 0.02% 28 4790 0.01% 29 5068 0.01% 30 5279 0.02% 31 5461 0.02% 32 5588 0.02% 33 5737 0.02% 34 6029 0.02% 35 6187 0.02% 36 6402 0.02% 37 8127 0.02% 38 6776 0.02% 39 7343 0.02% 40 7519 0.02% 41 7519 0.02% 42 8864 0.03% 43 10093 0.03% 44 8270 0.02% 45 9815 0.03% 46 9893 0.03% 47 13407 0.04% 48 11526 0.03% 49 14263 0.04% 50 11065 0.03% 51 12045 0.04% 52 12495 0.04% 53 13422 0.04% 54 14708 0.04% 55 14228 0.04% 56 14417 0.04% 57 17013 0.05% 58 16718 0.05% 59 17553 0.05% 60 18886 0.06% 61 18449 0.05% 62 49865 0.15% 63 19554 0.06% 64 23145 0.07% 65 20724 0.06% 66 21930 0.06% 67 23973 0.07% 68 23492 0.07% 69 33558 0.10% 70 26578 0.08% 71 29001 0.09% 72 32076 0.09% 73 43652 0.13% 74 40588 0.12% 75 34295 0.10% 76 32798 0.10% 77 46008 0.14% 78 37287 0.11% 79 48434 0.14% 80 39518 0.12% 81 40410 0.12% 82 45309 0.13% 83 46711 0.14% 84 51306 0.15% 85 49877 0.15% 86 52591 0.15% 87 60754 0.18% 88 56628 0.17% 89 110978 0.33% 90 63001 0.19% 91 72803 0.21% 92 64411 0.19% 93 67550 0.20% 94 74239 0.22% 95 75516 0.22% 96 86517 0.25% 97 98576 0.29% 98 84193 0.25% 99 87955 0.26% 100 88888 0.26% 101 97853 0.29% 102 119675 0.35% 103 103477 0.30% 104 108799 0.32% 105 109930 0.32% 106 114940 0.34% 107 120870 0.36% 108 130468 0.38% 109 149778 0.44% 110 136547 0.40% 111 141742 0.42% 112 384705 1.13% 113 157293 0.46% 114 153291 0.45% 115 153091 0.45% 116 163697 0.48% 117 179548 0.53% 118 179814 0.53% 119 186245 0.55% 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 25 0.00% 151 28658879 84.42% 33946523 reads passed initial QC criterion=sequence-density sequence-density=13.63 sequence-density-rank=1 fanout-score=39.19 fanout-score-rank=1 prefix-density=16.21 prefix-fanout=33.0 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC criterion=fanout-score sequence-density=13.63 sequence-density-rank=1 fanout-score=39.19 fanout-score-rank=1 prefix-density=16.21 prefix-fanout=33.0 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -o SRR11462733 - Input file: STDIN trimmed: SRR11462733-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 -- 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 11:21:04 2025 >> started Wed Feb 12 11:21:36 2025 >> done (31.924s) 29097020 reads processed; of these: 251 ( 0.00%) short reads filtered out after trimming by size control 1 ( 0.00%) empty reads filtered out after trimming by size control 29096768 (100.00%) reads available; of these: 7310560 (25.12%) trimmed reads available after processing 21786208 (74.88%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2109 0.01% 19 2175 0.01% 20 2436 0.01% 21 2680 0.01% 22 3059 0.01% 23 3303 0.01% 24 3568 0.01% 25 3606 0.01% 26 3553 0.01% 27 4796 0.02% 28 4117 0.01% 29 4357 0.01% 30 4495 0.02% 31 4694 0.02% 32 4859 0.02% 33 4928 0.02% 34 5160 0.02% 35 5262 0.02% 36 5482 0.02% 37 7044 0.02% 38 5809 0.02% 39 6261 0.02% 40 6487 0.02% 41 6529 0.02% 42 7697 0.03% 43 8651 0.03% 44 7144 0.02% 45 8403 0.03% 46 8502 0.03% 47 11484 0.04% 48 9927 0.03% 49 12197 0.04% 50 9659 0.03% 51 10358 0.04% 52 10826 0.04% 53 11646 0.04% 54 12585 0.04% 55 12230 0.04% 56 12249 0.04% 57 14670 0.05% 58 14290 0.05% 59 15157 0.05% 60 16156 0.06% 61 15948 0.05% 62 42931 0.15% 63 16841 0.06% 64 19875 0.07% 65 17849 0.06% 66 18815 0.06% 67 20475 0.07% 68 20241 0.07% 69 28904 0.10% 70 23390 0.08% 71 24750 0.09% 72 27633 0.09% 73 37462 0.13% 74 34995 0.12% 75 29026 0.10% 76 28313 0.10% 77 39604 0.14% 78 32018 0.11% 79 41649 0.14% 80 33911 0.12% 81 35462 0.12% 82 39151 0.13% 83 40168 0.14% 84 43539 0.15% 85 42865 0.15% 86 45339 0.16% 87 52244 0.18% 88 48799 0.17% 89 95268 0.33% 90 54678 0.19% 91 62746 0.22% 92 55508 0.19% 93 57852 0.20% 94 63476 0.22% 95 64990 0.22% 96 74320 0.26% 97 84502 0.29% 98 72395 0.25% 99 75926 0.26% 100 76624 0.26% 101 84536 0.29% 102 102763 0.35% 103 89258 0.31% 104 93259 0.32% 105 94439 0.32% 106 98810 0.34% 107 103832 0.36% 108 112665 0.39% 109 128632 0.44% 110 117619 0.40% 111 121508 0.42% 112 330921 1.14% 113 134400 0.46% 114 131914 0.45% 115 130353 0.45% 116 140279 0.48% 117 149747 0.51% 118 150267 0.52% 119 157849 0.54% 120 177935 0.61% 121 179333 0.62% 122 180171 0.62% 123 202670 0.70% 124 222755 0.77% 125 183623 0.63% 126 199580 0.69% 127 205992 0.71% 128 207961 0.71% 129 209243 0.72% 130 200238 0.69% 131 210360 0.72% 132 328044 1.13% 133 268913 0.92% 134 228031 0.78% 135 246072 0.85% 136 231460 0.80% 137 248248 0.85% 138 267206 0.92% 139 250552 0.86% 140 251749 0.87% 141 239371 0.82% 142 266495 0.92% 143 267861 0.92% 144 237830 0.82% 145 311345 1.07% 146 255427 0.88% 147 332373 1.14% 148 576672 1.98% 149 0 0.00% 150 17 0.00% 151 17375108 59.71% criterion=sequence-density sequence-density=1.03 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=34 prefix-density=1.03 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTACTCTGCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=246.26 fanout-score-rank=1 prefix-density=0.14 prefix-fanout=15.2 sequence=TGGATTTGATTAGATCCACCAATAAAAAGGGCTTGCCTTACACTCTTGGTCTTAATCAATTTGCTGATTGGACATGGCAAGAGTTCCAAAAGTACAGACTGGGAGCTGCCCAAAATTGCTCTGCAACCACAAGGGGCAATCACAAGCTTACGAACGCTCTTCTTCCTGAAACGAAAGACTGGAGGGAAGAAGGCATAGTCAGTCCCGTTAAGAATCAAGGTCACTGTGGATCTTGCTGGACTTTCAGCACCACTGGAGCTCTAGAGGCTGCTTACCACCAGGCTTTTGGGAAAGGAATCTCTCTGTCTGAACAGCAGCTTGTGGACTGTGCTAGAGCATTTAATAACTTTGGCTGCAATG Started job on | Feb 12 11:22:13 Started mapping on | Feb 12 11:22:14 Finished on | Feb 12 11:23:42 Mapping speed, Million of reads per hour | 1388.71 Number of input reads | 33946271 Average input read length | 139 UNIQUE READS: Uniquely mapped reads number | 24809515 Uniquely mapped reads % | 73.08% Average mapped length | 135.75 Number of splices: Total | 10537546 Number of splices: Annotated (sjdb) | 10294206 Number of splices: GT/AG | 10375899 Number of splices: GC/AG | 122265 Number of splices: AT/AC | 5900 Number of splices: Non-canonical | 33482 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.02% Deletion average length | 2.23 Insertion rate per base | 0.01% Insertion average length | 1.78 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 827263 % of reads mapped to multiple loci | 2.44% Number of reads mapped to too many loci | 5681975 % of reads mapped to too many loci | 16.74% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.52% % of reads unmapped: other | 0.22% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8309493 8309493 8309493 N_multimapping 827263 827263 827263 N_noFeature 1702022 2088138 24068922 N_ambiguous 448715 94531 568 UnstrandedReadsAssigned:22658778 PositiveStrandReadsAssigned:22626846 NegativeStrandReadsAssigned:740025 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=126 echo kmer=121 SRR11462733 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: SRR11462733-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 33,946,271 reads, 24,268,083 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,163 rounds 52401 SRR11462733.ke.tsv 34699 SRR11462733.se.tsv 87100 total ==> SRR11462733.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 1975 44.1833 Potri.005G024800.1.v4.1 1035 936 578 26.5105 Potri.004G059700.1.v4.1 961 862 0 0 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 2664.58 40.2222 Potri.016G087400.1.v4.1 270 171 1139 285.952 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 1147.98 29.4405 Potri.012G127500.1.v4.1 977 878 76 3.71608 ==> SRR11462733.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 16 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 218 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 12 SRR11462733 completed mapping pipeline successfully