Starting /dee2/code/volunteer_pipeline.sh SRR6793149 current disk space = 3089389912064 free memory = 1449521680 SRR6793149 SRAfilesize 70c38a5fc098a0d0d0e4b6ad78aa7e6e SRR6793149.sra SRR6793149.sra file validated SRR6793149 is single end SRR6793149 is conventional basespace SRR6793149 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6793149_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.6305 32.0 32.0 32.0 32.0 32.0 2 31.60175 32.0 32.0 32.0 32.0 32.0 3 31.676 32.0 32.0 32.0 32.0 32.0 4 31.69075 32.0 32.0 32.0 32.0 32.0 5 31.7185 32.0 32.0 32.0 32.0 32.0 6 35.218 36.0 36.0 36.0 36.0 36.0 7 35.33375 36.0 36.0 36.0 36.0 36.0 8 35.417 36.0 36.0 36.0 36.0 36.0 9 35.27475 36.0 36.0 36.0 36.0 36.0 10-14 35.354 36.0 36.0 36.0 36.0 36.0 15-19 35.325599999999994 36.0 36.0 36.0 36.0 36.0 20-24 35.2956 36.0 36.0 36.0 36.0 36.0 25-29 35.2635 36.0 36.0 36.0 36.0 36.0 30-34 35.214150000000004 36.0 36.0 36.0 36.0 36.0 35-39 35.1016 36.0 36.0 36.0 36.0 36.0 40-44 35.1685 36.0 36.0 36.0 36.0 36.0 45-49 35.0221 36.0 36.0 36.0 36.0 36.0 50-54 35.0481 36.0 36.0 36.0 36.0 36.0 55-59 34.993900000000004 36.0 36.0 36.0 36.0 36.0 60-64 34.860150000000004 36.0 36.0 36.0 34.4 36.0 65-69 34.823449999999994 36.0 36.0 36.0 33.6 36.0 70-74 34.67615 36.0 36.0 36.0 32.0 36.0 75-79 34.6058 36.0 36.0 36.0 32.0 36.0 80-84 34.5059 36.0 36.0 36.0 32.0 36.0 85-89 34.5938 36.0 36.0 36.0 32.0 36.0 90-94 34.435249999999996 36.0 36.0 36.0 32.0 36.0 95-99 34.3909 36.0 36.0 36.0 32.0 36.0 100-104 34.39675 36.0 36.0 36.0 32.0 36.0 105-109 34.312349999999995 36.0 36.0 36.0 32.0 36.0 110-114 34.1761 36.0 36.0 36.0 32.0 36.0 115-119 34.14975 36.0 36.0 36.0 32.0 36.0 120-124 34.0672 36.0 36.0 36.0 32.0 36.0 125-129 33.90335 36.0 35.2 36.0 28.0 36.0 130-134 33.8306 36.0 34.4 36.0 27.0 36.0 135-139 33.262950000000004 36.0 32.0 36.0 27.0 36.0 140-144 33.39635 36.0 32.0 36.0 27.0 36.0 145-149 32.65135 36.0 32.0 36.0 27.0 36.0 150-151 30.53625 34.0 29.5 36.0 20.5 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 2.0 21 2.0 22 7.0 23 16.0 24 12.0 25 14.0 26 28.0 27 24.0 28 48.0 29 82.0 30 82.0 31 109.0 32 165.0 33 250.0 34 681.0 35 2477.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 22.325 13.450000000000001 9.175 55.05 2 19.825 18.224999999999998 40.825 21.125 3 20.150000000000002 22.975 26.0 30.875000000000004 4 26.25 31.15 17.375 25.224999999999998 5 28.525 30.85 19.875 20.75 6 21.24937280481686 35.474159558454595 22.955343702960363 20.321123933768188 7 18.525 17.299999999999997 42.3 21.875 8 20.8 18.625 30.275000000000002 30.3 9 20.974999999999998 21.525 32.9 24.6 10-14 22.54 27.694999999999997 24.975 24.79 15-19 24.64 25.96 26.36 23.04 20-24 24.525 25.330000000000002 26.150000000000002 23.995 25-29 23.535 25.840000000000003 25.44 25.185000000000002 30-34 23.825 25.585 25.755 24.834999999999997 35-39 23.655 26.215 25.56 24.57 40-44 23.794999999999998 25.495 26.47 24.240000000000002 45-49 23.78 25.775 25.919999999999998 24.525 50-54 23.59 26.584999999999997 25.990000000000002 23.835 55-59 23.39850977646647 25.81387208081212 26.47397109566435 24.313647047057056 60-64 24.545 25.374999999999996 25.97 24.11 65-69 24.169999999999998 25.95 25.855 24.025 70-74 23.995 25.4 25.8 24.805 75-79 24.415 25.919999999999998 25.355 24.310000000000002 80-84 24.72623631181559 24.7862393119656 25.956297814890743 24.53122656132807 85-89 24.362436243624362 26.552655265526553 26.142614261426147 22.94229422942294 90-94 24.844968993798762 25.6501300260052 25.820164032806563 23.684736947389478 95-99 23.632089626888067 26.12783835150545 26.698009402820844 23.542062618785636 100-104 24.124824964993 26.935387077415484 25.56011202240448 23.379675935187038 105-109 24.10102525631408 25.886471617904476 26.586646661665412 23.42585646411603 110-114 24.66616654163541 26.176544136034007 25.381345336334082 23.775943985996502 115-119 24.62246224622462 26.41764176417642 25.422542254225423 23.537353735373536 120-124 25.369999999999997 26.895000000000003 24.044999999999998 23.69 125-129 24.75871380707106 27.104065609841477 23.908586287943194 24.22863429514427 130-134 24.872487248724873 27.552755275527552 24.217421742174217 23.357335733573358 135-139 25.35260578173452 28.20846253876163 22.98189456837051 23.45703711113334 140-144 25.44517807122849 27.926170468187273 23.324329731892757 23.304321728691477 145-149 25.081270317579396 28.00200050012503 22.75068767191798 24.166041510377596 150-151 24.446667500312618 30.086282355883455 21.007877954232836 24.45917218957109 >>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 0.5 11 0.5 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 0.5 21 0.0 22 0.5 23 1.5 24 1.0 25 1.5 26 3.0 27 2.0 28 5.0 29 7.0 30 5.5 31 6.5 32 6.5 33 10.0 34 23.5 35 51.5 36 75.5 37 81.5 38 78.5 39 86.0 40 101.5 41 125.0 42 132.0 43 138.5 44 172.0 45 203.5 46 229.0 47 237.5 48 228.0 49 204.5 50 191.0 51 193.5 52 186.5 53 174.0 54 144.5 55 126.0 56 128.5 57 145.5 58 125.5 59 66.5 60 50.0 61 48.5 62 40.0 63 29.5 64 16.5 65 11.0 66 15.0 67 16.5 68 17.5 69 18.5 70 12.0 71 5.0 72 4.0 73 2.5 74 2.5 75 4.0 76 2.5 77 0.0 78 0.5 79 1.0 80 0.5 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 0.5 98 0.5 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.35000000000000003 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 0.015 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.005 85-89 0.01 90-94 0.02 95-99 0.03 100-104 0.02 105-109 0.025 110-114 0.025 115-119 0.01 120-124 0.0 125-129 0.015 130-134 0.01 135-139 0.03 140-144 0.04 145-149 0.025 150-151 0.0375 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 74.97500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 87.02900966988997 65.25 2 6.202067355785261 9.3 3 3.0010003334444817 6.75 4 1.2004001333777925 3.5999999999999996 5 0.8669556518839614 3.25 6 0.46682227409136384 2.1 7 0.266755585195065 1.4000000000000001 8 0.16672224074691563 1.0 9 0.23341113704568192 1.575 >10 0.5668556185395132 5.775 >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 CCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATA 21 0.525 No Hit CTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACAGCACCGGAGGCACGA 18 0.44999999999999996 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGA 18 0.44999999999999996 No Hit CTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCG 17 0.42500000000000004 No Hit CTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTT 15 0.375 No Hit ACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGAT 15 0.375 No Hit CTCGTCCCTTCTACCGGCGATGCGCTCCTGGCCTTAACTGGCCGGGTCGT 15 0.375 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 13 0.325 No Hit CCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAAT 12 0.3 No Hit CTCAGGTGTGCACCGGTCGCCTCGTCCCTTCTACCGGCGATGCGCTCCTG 12 0.3 No Hit GCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTA 12 0.3 No Hit CTTTTATCTAATAAATGCGTCCCTTCCAGAAGTCGGGGTTTGTTGCACGT 11 0.27499999999999997 No Hit CTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTC 11 0.27499999999999997 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAG 11 0.27499999999999997 No Hit CCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAA 10 0.25 No Hit CTGACTATGAAATACGAATGCCCCCGACTGTCCCTGTTAATCATTACTCC 10 0.25 No Hit CAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCT 10 0.25 No Hit GCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAAC 9 0.22499999999999998 No Hit CCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATCCCATGCTA 9 0.22499999999999998 No Hit CAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTC 9 0.22499999999999998 No Hit GTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCAT 9 0.22499999999999998 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 9 0.22499999999999998 No Hit CTCCAATGGATCCTCGTTAAGGGATTTAGATTGTACTCATTCCAATTACC 9 0.22499999999999998 No Hit CCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATT 9 0.22499999999999998 No Hit CCGGAATCGAACCCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCT 8 0.2 No Hit CAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGC 8 0.2 No Hit CCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTC 8 0.2 No Hit CAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGG 8 0.2 No Hit CTCAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATAG 8 0.2 No Hit CAAATTTCTGCCCTATCAACTTTCGATGGTAGGATAGAGGCCTACCATGG 7 0.17500000000000002 No Hit CGTCGAGTTATCATGAATCATCAGAGCAACGGGCAGAGCCCGCGTCGACC 7 0.17500000000000002 No Hit CTTTGGGTTGGGTCGGCCGGTCCGCCTCAGGTGTGCACCGGTCGCCTCGT 7 0.17500000000000002 No Hit GTTTGTTTGATGGTATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCT 7 0.17500000000000002 No Hit GTACAATCTAAATCCCTTAACGAGGATCCATTGGAGGGCAAGTCTGGTGC 7 0.17500000000000002 No Hit CTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTT 7 0.17500000000000002 No Hit CTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAAC 7 0.17500000000000002 No Hit CTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACC 7 0.17500000000000002 No Hit CGATCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACA 6 0.15 No Hit GTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGGTGTGCACCGGTCG 6 0.15 No Hit CTCCGTCACCCGTCACCACCATGGTAGGCCTCTATCCTACCATCGAAAGT 6 0.15 No Hit CTCCGGAATCGAACCCTAATTCTCCGTCACCCGTCACCACCATGGTAGGC 6 0.15 No Hit CCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTTTGAAGAA 6 0.15 No Hit CGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCA 6 0.15 No Hit GTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCT 6 0.15 No Hit ATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCT 6 0.15 No Hit GTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGC 6 0.15 No Hit CGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCT 6 0.15 No Hit CCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCA 6 0.15 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 6 0.15 No Hit ATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAG 6 0.15 No Hit CTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTC 6 0.15 No Hit CCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCT 5 0.125 No Hit GTGCGATCCGTCGAGTTATCATGAATCATCAGAGCAACGGGCAGAGCCCG 5 0.125 No Hit CACGGCCTTCGTGCTGGCGACGCATCATTCAAATTTCTGCCCTATCAACT 5 0.125 No Hit CACGTATTAGCTCTAGAATTACTACGGTTATCCGAGTAGCAAATACCATC 5 0.125 No Hit CTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATGAACTAATTCAGAC 5 0.125 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCA 5 0.125 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 5 0.125 No Hit CCCGTCACCACCATGGTAGGCCTCTATCCTACCATCGAAAGTTGATAGGG 5 0.125 No Hit CTGCTAACTAGCTATGCGGAGGTGACCCTCCGCGGCCAGCTTCTTAGAGG 5 0.125 No Hit CTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCT 5 0.125 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAA 5 0.125 No Hit ATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAA 5 0.125 No Hit CAACTTTCGATGGTAGGATAGAGGCCTACCATGGTGGTGACGGGTGACGG 5 0.125 No Hit CGGAAACCTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAGTGG 5 0.125 No Hit GTCGTGCCTCCGGTGCTGTTACTTTGAAGAAATTAGAGTGCTCAAAGCAA 5 0.125 No Hit CTGGAAGGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTCTGCCCGT 5 0.125 No Hit CGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCA 5 0.125 No Hit CGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCT 5 0.125 No Hit CTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCTCTATCCTACCATC 5 0.125 No Hit TAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGG 5 0.125 No Hit CGCAAATTACCCAATCCTGACACGGGGAGGTAGTGACAATAAATAACAAT 5 0.125 No Hit CGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCC 5 0.125 No Hit CTAATGTATCCAGAGCGTAGGCTTGCTTTGAGCACTCTAATTTCTTCAAA 5 0.125 No Hit CTCATTCCAATTACCAGACTCGAAGAGCCCGGTATTGTTATTTATTGTCA 5 0.125 No Hit GTTAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCA 5 0.125 No Hit GGCCGGTCCGCCTCAGGTGTGCACCGGTCGCCTCGTCCCTTCTACCGGCG 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 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.0625 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.0875 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.1375 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 82-83 0.15 0.0 0.0 0.0 0.0 84-85 0.175 0.0 0.0 0.0 0.0 86-87 0.1875 0.0 0.0 0.0 0.0 88-89 0.225 0.0 0.0 0.0 0.0 90-91 0.2875 0.0 0.0 0.0 0.0 92-93 0.3875 0.0 0.0 0.0 0.0 94-95 0.425 0.0 0.0 0.0 0.0 96-97 0.48750000000000004 0.0 0.0 0.0 0.0 98-99 0.625 0.0 0.0 0.0 0.0 100-101 0.7625 0.0 0.0 0.0 0.0 102-103 0.9375 0.0 0.0 0.0 0.0 104-105 1.0875 0.0 0.0 0.0 0.0 106-107 1.45 0.0 0.0 0.0 0.0 108-109 1.8125 0.0 0.0 0.0 0.0 110-111 2.2125000000000004 0.0 0.0 0.0 0.0 112-113 2.825 0.0 0.0 0.0 0.0 114-115 3.2249999999999996 0.0 0.0 0.0 0.0 116-117 3.7125 0.0 0.0 0.0 0.0 118-119 4.1875 0.0 0.0 0.0 0.0 120-121 4.85 0.0 0.0 0.0 0.0 122-123 5.8125 0.0 0.0 0.0 0.0 124-125 6.6875 0.0 0.0 0.0 0.0 126-127 7.6 0.0 0.0 0.0 0.0 128-129 8.8875 0.0 0.0 0.0 0.0 130-131 10.1125 0.0 0.0 0.0 0.0 132-133 11.625 0.0 0.0 0.0 0.0 134-135 12.875 0.0 0.0 0.0 0.0 136-137 14.3125 0.0 0.0 0.0 0.0 138-139 15.6875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111066 READS because READLEN < 1 Read 2111066 spots for SRR6793149.sra Written 2111066 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra Rejected 2111056 READS because READLEN < 1 Read 2111056 spots for SRR6793149.sra Written 2111056 spots for SRR6793149.sra SRR ids: ['SRR6793149.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_bqu6wnwa SRR6793149.sra spots: 42221130 blocks: [[1, 2111056], [2111057, 4222112], [4222113, 6333168], [6333169, 8444224], [8444225, 10555280], [10555281, 12666336], [12666337, 14777392], [14777393, 16888448], [16888449, 18999504], [18999505, 21110560], [21110561, 23221616], [23221617, 25332672], [25332673, 27443728], [27443729, 29554784], [29554785, 31665840], [31665841, 33776896], [33776897, 35887952], [35887953, 37999008], [37999009, 40110064], [40110065, 42221130]] SRR6793149 file size 14285655 SRR6793149 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 SRR6793149 SRR6793149_1.fastq Input file: SRR6793149_1.fastq trimmed: SRR6793149-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 Thu Feb 13 14:49:56 2025 >> started Thu Feb 13 14:50:20 2025 >> done (24.312s) 42221130 reads processed; of these: 3440 ( 0.01%) short reads filtered out after trimming by size control 102 ( 0.00%) empty reads filtered out after trimming by size control 42217588 (99.99%) reads available; of these: 2070404 ( 4.90%) trimmed reads available after processing 40147184 (95.10%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 240 0.00% 19 231 0.00% 20 240 0.00% 21 230 0.00% 22 308 0.00% 23 326 0.00% 24 338 0.00% 25 417 0.00% 26 559 0.00% 27 546 0.00% 28 655 0.00% 29 705 0.00% 30 694 0.00% 31 747 0.00% 32 824 0.00% 33 786 0.00% 34 824 0.00% 35 892 0.00% 36 952 0.00% 37 920 0.00% 38 987 0.00% 39 906 0.00% 40 1000 0.00% 41 1088 0.00% 42 1000 0.00% 43 1043 0.00% 44 1117 0.00% 45 1116 0.00% 46 1146 0.00% 47 1125 0.00% 48 1263 0.00% 49 1220 0.00% 50 1212 0.00% 51 1227 0.00% 52 1227 0.00% 53 1270 0.00% 54 1327 0.00% 55 1431 0.00% 56 1366 0.00% 57 1482 0.00% 58 1456 0.00% 59 1651 0.00% 60 1813 0.00% 61 1657 0.00% 62 1718 0.00% 63 1724 0.00% 64 1555 0.00% 65 1588 0.00% 66 1703 0.00% 67 1784 0.00% 68 1841 0.00% 69 1776 0.00% 70 1911 0.00% 71 2295 0.01% 72 2106 0.00% 73 2367 0.01% 74 2381 0.01% 75 2818 0.01% 76 2908 0.01% 77 2768 0.01% 78 3359 0.01% 79 3423 0.01% 80 3669 0.01% 81 4602 0.01% 82 4635 0.01% 83 5075 0.01% 84 5583 0.01% 85 6203 0.01% 86 7200 0.02% 87 7237 0.02% 88 7565 0.02% 89 8653 0.02% 90 9972 0.02% 91 11495 0.03% 92 13766 0.03% 93 15353 0.04% 94 16261 0.04% 95 18196 0.04% 96 19859 0.05% 97 22655 0.05% 98 25093 0.06% 99 29884 0.07% 100 29172 0.07% 101 34586 0.08% 102 40394 0.10% 103 42950 0.10% 104 49271 0.12% 105 51962 0.12% 106 55640 0.13% 107 62696 0.15% 108 67005 0.16% 109 77144 0.18% 110 79033 0.19% 111 100854 0.24% 112 104376 0.25% 113 108274 0.26% 114 119165 0.28% 115 127439 0.30% 116 149552 0.35% 117 141831 0.34% 118 142519 0.34% 119 154954 0.37% 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 68 0.00% 131 208 0.00% 132 103 0.00% 133 137 0.00% 134 226 0.00% 135 189 0.00% 136 105 0.00% 137 18 0.00% 138 68 0.00% 139 4 0.00% 140 0 0.00% 141 26 0.00% 142 15 0.00% 143 491 0.00% 144 320 0.00% 145 37 0.00% 146 46 0.00% 147 215 0.00% 148 1047 0.00% 149 738 0.00% 150 2981 0.01% 151 40147184 95.10% 42217588 reads passed initial QC criterion=sequence-density sequence-density=11.36 sequence-density-rank=1 fanout-score=36.17 fanout-score-rank=2 prefix-density=13.65 prefix-fanout=30.1 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAGAATCTCG criterion=fanout-score sequence-density=0.05 sequence-density-rank=7 fanout-score=52.41 fanout-score-rank=1 prefix-density=2.17 prefix-fanout=1.2 sequence=CGCATCGCCGGCCCCCATCCACTTCCCTCCCGACAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGACGGAATTTACCGCCCGATTGGGGCTGCATTCCCAAACAACCCGACTCGCAGACAGCGCCTCGTGGTGCGGCAGGGTCCAGCCACGACGGGGCTCTCACCCTCTCCGGCGCCCCTTTCCAGGGGACTTGGGCCTGGTCCGCCGCTGAGGACGCTTCTCCAGACTACAATTCGGACGCCGCAGGCGCCAGATTCTCAAGCTGGGCATTTCCCGGTTCGCTCGCCGTTACTAGGGGAATCCTTGTAAGTTTCTTTTCCT 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAGAATCTCG -o SRR6793149 - Input file: STDIN trimmed: SRR6793149-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGTCAGAATCTCG -- 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 Thu Feb 13 14:52:11 2025 >> started Thu Feb 13 14:52:53 2025 >> done (41.238s) 35181323 reads processed; of these: 80 ( 0.00%) short reads filtered out after trimming by size control 27 ( 0.00%) empty reads filtered out after trimming by size control 35181216 (100.00%) reads available; of these: 7680061 (21.83%) trimmed reads available after processing 27501155 (78.17%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 195 0.00% 19 196 0.00% 20 204 0.00% 21 190 0.00% 22 245 0.00% 23 268 0.00% 24 312 0.00% 25 347 0.00% 26 476 0.00% 27 453 0.00% 28 535 0.00% 29 592 0.00% 30 586 0.00% 31 625 0.00% 32 681 0.00% 33 659 0.00% 34 683 0.00% 35 741 0.00% 36 798 0.00% 37 778 0.00% 38 787 0.00% 39 745 0.00% 40 834 0.00% 41 898 0.00% 42 825 0.00% 43 848 0.00% 44 956 0.00% 45 926 0.00% 46 974 0.00% 47 926 0.00% 48 1058 0.00% 49 1030 0.00% 50 1028 0.00% 51 1007 0.00% 52 1047 0.00% 53 1051 0.00% 54 1094 0.00% 55 1194 0.00% 56 1159 0.00% 57 1264 0.00% 58 1232 0.00% 59 1392 0.00% 60 1520 0.00% 61 1404 0.00% 62 1434 0.00% 63 1476 0.00% 64 1317 0.00% 65 1361 0.00% 66 1419 0.00% 67 1482 0.00% 68 1548 0.00% 69 1515 0.00% 70 1618 0.00% 71 1908 0.01% 72 1759 0.00% 73 2016 0.01% 74 2000 0.01% 75 2356 0.01% 76 2436 0.01% 77 2327 0.01% 78 2795 0.01% 79 2873 0.01% 80 3100 0.01% 81 3838 0.01% 82 3924 0.01% 83 4218 0.01% 84 4703 0.01% 85 5150 0.01% 86 5963 0.02% 87 6067 0.02% 88 6426 0.02% 89 7267 0.02% 90 8446 0.02% 91 9706 0.03% 92 11434 0.03% 93 12766 0.04% 94 13627 0.04% 95 15145 0.04% 96 16709 0.05% 97 19047 0.05% 98 20979 0.06% 99 25193 0.07% 100 24401 0.07% 101 28925 0.08% 102 33772 0.10% 103 35785 0.10% 104 41337 0.12% 105 43649 0.12% 106 46679 0.13% 107 52810 0.15% 108 56050 0.16% 109 64558 0.18% 110 65723 0.19% 111 84112 0.24% 112 87717 0.25% 113 90579 0.26% 114 99860 0.28% 115 106185 0.30% 116 124564 0.35% 117 117178 0.33% 118 118508 0.34% 119 131654 0.37% 120 151613 0.43% 121 157847 0.45% 122 164926 0.47% 123 176242 0.50% 124 170497 0.48% 125 183009 0.52% 126 206564 0.59% 127 200459 0.57% 128 225447 0.64% 129 215427 0.61% 130 232360 0.66% 131 225580 0.64% 132 240862 0.68% 133 271087 0.77% 134 265642 0.76% 135 281375 0.80% 136 268533 0.76% 137 270125 0.77% 138 267067 0.76% 139 264830 0.75% 140 265868 0.76% 141 276994 0.79% 142 284385 0.81% 143 309120 0.88% 144 311741 0.89% 145 302582 0.86% 146 327265 0.93% 147 405922 1.15% 148 736005 2.09% 149 510 0.00% 150 1974 0.01% 151 25793201 73.32% criterion=sequence-density sequence-density=0.46 sequence-density-rank=1 fanout-score=2.67 fanout-score-rank=17 prefix-density=0.46 prefix-fanout=2.6 sequence=GTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAAAGCAACATCCGCCAATCCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTCACCTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATCCCATGCTAATGTATCCAGAGCGTAGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACAGCACCGGAGGCACGACCCGGCCAGTTAAGGCCAGGAGCGCATCGCCGGTAGAAGGGACGAGGC criterion=fanout-score sequence-density=0.05 sequence-density-rank=24 fanout-score=57.90 fanout-score-rank=1 prefix-density=2.19 prefix-fanout=1.2 sequence=CGCATCGCCGGCCCCCATCCACTTCCCTCCCGACAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGACGGAATTTACCGCCCGATTGGGGCTGCATTCCCAAACAACCCGACTCGCAGACAGCGCCTCGTGGTGCGGCAGGGTCCAGCCACGACGGGGCTCTCACCCTCTCCGGCGCCCCTTTCCAGGGGACTTGGGCCTGGTCCGCCGCTGAGGACGCTTCTCCAGACTACAATTCGGACGCCGCAGGCGCCAGATTCTCAAGCTGGGCATTTCCCGGTTCGCTCGCCGTTACTAGGGGAATCCTTGTAAGTTTCTTTTCCT Started job on | Feb 13 14:53:37 Started mapping on | Feb 13 14:53:37 Finished on | Feb 13 14:56:07 Mapping speed, Million of reads per hour | 1013.22 Number of input reads | 42217481 Average input read length | 146 UNIQUE READS: Uniquely mapped reads number | 16776594 Uniquely mapped reads % | 39.74% Average mapped length | 145.20 Number of splices: Total | 6534973 Number of splices: Annotated (sjdb) | 6366589 Number of splices: GT/AG | 6402586 Number of splices: GC/AG | 95213 Number of splices: AT/AC | 6207 Number of splices: Non-canonical | 30967 Mismatch rate per base, % | 0.52% Deletion rate per base | 0.03% Deletion average length | 2.79 Insertion rate per base | 0.03% Insertion average length | 2.72 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2450476 % of reads mapped to multiple loci | 5.80% Number of reads mapped to too many loci | 22146617 % of reads mapped to too many loci | 52.46% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.56% % of reads unmapped: other | 0.44% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 22990411 22990411 22990411 N_multimapping 2450476 2450476 2450476 N_noFeature 1616885 9021138 9133198 N_ambiguous 326595 43830 44002 UnstrandedReadsAssigned:14833114 PositiveStrandReadsAssigned:7711626 NegativeStrandReadsAssigned:7599394 Dataset is classified unstranded MeadianReadLen=151 20thPercentileLength=143 echo kmer=139 SRR6793149 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: SRR6793149-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 42,217,481 reads, 33,252,482 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,203 rounds 52401 SRR6793149.ke.tsv 34699 SRR6793149.se.tsv 87100 total ==> SRR6793149.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 2798 58.537 Potri.005G024800.1.v4.1 1035 936 246 10.5516 Potri.004G059700.1.v4.1 961 862 9 0.419173 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 1186.29 16.7463 Potri.016G087400.1.v4.1 270 171 839 196.981 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 1394.85 33.4525 Potri.012G127500.1.v4.1 977 878 672 30.7279 ==> SRR6793149.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 250 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 230 Potri.001G212900.v4.1 9 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 31 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 2 SRR6793149 completed mapping pipeline successfully