Starting /dee2/code/volunteer_pipeline.sh ERR6133338 current disk space = 1548084326400 free memory = 1412591696 ERR6133338 SRAfilesize 01dc1175c1378febcb7d029621238952 ERR6133338.sra ERR6133338.sra file validated ERR6133338 is single end ERR6133338 is conventional basespace ERR6133338 read1 length is 70-93 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR6133338_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70-93 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.47075 37.0 37.0 37.0 37.0 37.0 2 36.6105 37.0 37.0 37.0 37.0 37.0 3 36.43525 37.0 37.0 37.0 37.0 37.0 4 36.40075 37.0 37.0 37.0 37.0 37.0 5 36.4225 37.0 37.0 37.0 37.0 37.0 6 36.51725 37.0 37.0 37.0 37.0 37.0 7 38.631 40.0 37.0 40.0 37.0 40.0 8 38.742 40.0 37.0 40.0 37.0 40.0 9 38.7105 40.0 37.0 40.0 37.0 40.0 10-11 38.7495 40.0 37.0 40.0 37.0 40.0 12-13 38.7565 40.0 37.0 40.0 37.0 40.0 14-15 38.642875000000004 40.0 37.0 40.0 37.0 40.0 16-17 38.638374999999996 40.0 37.0 40.0 37.0 40.0 18-19 38.720875 40.0 37.0 40.0 37.0 40.0 20-21 38.404624999999996 40.0 37.0 40.0 37.0 40.0 22-23 38.544 40.0 37.0 40.0 37.0 40.0 24-25 38.54875 40.0 37.0 40.0 37.0 40.0 26-27 38.44775 40.0 37.0 40.0 37.0 40.0 28-29 38.453625 40.0 37.0 40.0 37.0 40.0 30-31 38.41325 40.0 37.0 40.0 37.0 40.0 32-33 38.367000000000004 40.0 37.0 40.0 37.0 40.0 34-35 38.33725 40.0 37.0 40.0 37.0 40.0 36-37 38.1825 40.0 37.0 40.0 37.0 40.0 38-39 37.9525 40.0 37.0 40.0 37.0 40.0 40-41 37.880875 40.0 37.0 40.0 37.0 40.0 42-43 37.836749999999995 37.0 37.0 40.0 37.0 40.0 44-45 37.677375 37.0 37.0 40.0 35.0 40.0 46-47 37.424875 37.0 37.0 40.0 33.0 40.0 48-49 37.322125 37.0 37.0 40.0 33.0 40.0 50-51 37.078875 37.0 37.0 40.0 33.0 40.0 52-53 36.939875 37.0 37.0 40.0 33.0 40.0 54-55 36.786875 37.0 37.0 37.0 33.0 40.0 56-57 36.532875000000004 37.0 37.0 37.0 33.0 40.0 58-59 36.21125 37.0 37.0 37.0 33.0 40.0 60-61 36.053749999999994 37.0 37.0 37.0 33.0 40.0 62-63 35.539 37.0 33.0 37.0 33.0 37.0 64-65 35.308125000000004 37.0 33.0 37.0 33.0 37.0 66-67 35.210125000000005 37.0 33.0 37.0 33.0 37.0 68-69 33.729125 35.0 33.0 37.0 30.0 37.0 70-71 33.61211727581009 33.0 33.0 37.0 30.0 37.0 72-73 34.05481724776823 33.0 33.0 37.0 33.0 37.0 74-75 34.03685061354032 33.0 33.0 37.0 33.0 37.0 76-77 33.733100555660506 33.0 33.0 37.0 33.0 37.0 78-79 33.41654819026898 33.0 33.0 37.0 27.0 37.0 80-81 33.024980430872255 33.0 33.0 37.0 27.0 37.0 82-83 32.88875952436216 33.0 33.0 37.0 27.0 37.0 84-85 32.23725139167074 33.0 33.0 35.0 27.0 37.0 86-87 31.989745011086477 33.0 33.0 33.0 27.0 37.0 88-89 32.1399667405765 33.0 33.0 33.0 27.0 37.0 90-91 31.4160199556541 33.0 30.0 33.0 27.0 37.0 92-93 30.581069844789354 33.0 27.0 33.0 22.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 3.0 21 1.0 22 3.0 23 6.0 24 3.0 25 6.0 26 10.0 27 15.0 28 12.0 29 21.0 30 33.0 31 52.0 32 67.0 33 91.0 34 233.0 35 619.0 36 1019.0 37 1494.0 38 299.0 39 13.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 62.925 9.55 9.775 17.75 2 46.800000000000004 26.150000000000002 15.9 11.15 3 29.375 36.625 19.125 14.875 4 29.225 27.400000000000002 22.425 20.95 5 23.200000000000003 28.799999999999997 28.65 19.35 6 19.45 34.35 27.875 18.325 7 32.025 26.700000000000003 24.05 17.224999999999998 8 27.775 26.775 26.424999999999997 19.025 9 23.549999999999997 27.025 30.175 19.25 10-11 23.9125 28.512500000000003 28.475 19.1 12-13 23.9875 27.800000000000004 28.875 19.3375 14-15 22.225 28.712500000000002 30.862499999999997 18.2 16-17 23.6625 29.475 25.937500000000004 20.925 18-19 22.7125 25.4375 31.7375 20.1125 20-21 23.7 26.8375 28.65 20.8125 22-23 26.437500000000004 24.2625 27.962500000000002 21.337500000000002 24-25 23.849999999999998 26.087500000000002 29.65 20.4125 26-27 23.5125 25.5375 30.4375 20.5125 28-29 23.375 27.5125 28.675 20.4375 30-31 25.324999999999996 27.0875 28.275 19.3125 32-33 24.4875 26.687499999999996 29.2 19.625 34-35 22.375 29.2375 28.075 20.3125 36-37 24.0 26.875 27.9125 21.212500000000002 38-39 25.162499999999998 24.65 29.725 20.4625 40-41 25.4625 25.55 29.1375 19.85 42-43 24.837500000000002 29.2 27.5625 18.4 44-45 22.8 28.349999999999998 29.075 19.775000000000002 46-47 23.6625 27.200000000000003 28.449999999999996 20.6875 48-49 23.5625 25.9875 29.4875 20.962500000000002 50-51 22.45 27.8625 29.262500000000003 20.424999999999997 52-53 24.1625 28.6375 26.8625 20.3375 54-55 23.974999999999998 27.762500000000003 28.5625 19.7 56-57 23.9875 27.762500000000003 28.8625 19.3875 58-59 24.2875 26.887499999999996 29.6625 19.162499999999998 60-61 25.7375 27.2625 28.625 18.375 62-63 22.0875 30.1375 29.2875 18.4875 64-65 22.4375 31.837500000000002 27.575 18.15 66-67 23.425 29.25 28.425 18.9 68-69 22.25 28.275 28.962500000000002 20.5125 70-71 24.01954642275404 28.116777346197217 27.61558701917053 20.248089211878213 72-73 23.56744421906694 27.066430020283978 29.221602434077077 20.14452332657201 74-75 24.219853602157443 28.84294336715038 28.316424810581736 18.62077822011044 76-77 22.541249837599064 26.42588021307003 28.5825646355723 22.450305313758605 78-79 24.029477562837215 27.50361889722332 29.898670877747076 18.568232662192393 80-81 22.848387956301625 30.60218491873168 27.88435917932321 18.665067945643486 82-83 22.698305084745762 27.29491525423729 27.90508474576271 22.10169491525424 84-85 22.458270106221548 25.6863015588357 31.383639122637607 20.471789212305143 86-87 21.577050997782703 29.115853658536583 28.104212860310422 21.20288248337029 88-89 21.25831485587583 30.473946784922397 28.97727272727273 19.290465631929045 90-91 23.170731707317074 30.36308203991131 27.342017738359203 19.124168514412418 92-93 20.717849223946786 32.6219512195122 28.31208425720621 18.34811529933481 >>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 0.0 16 0.0 17 1.0 18 2.0 19 1.5 20 1.0 21 2.0 22 3.0 23 5.0 24 8.5 25 8.0 26 11.0 27 23.0 28 34.5 29 38.0 30 41.5 31 48.5 32 61.5 33 82.5 34 92.0 35 100.0 36 146.0 37 192.5 38 210.5 39 210.0 40 225.5 41 230.5 42 235.0 43 260.0 44 219.0 45 178.5 46 176.0 47 152.0 48 127.5 49 130.0 50 143.0 51 145.0 52 141.5 53 163.0 54 167.0 55 117.5 56 81.0 57 76.0 58 55.5 59 31.5 60 26.5 61 15.0 62 6.5 63 6.5 64 3.0 65 3.0 66 4.0 67 2.0 68 0.5 69 1.5 70 2.0 71 2.0 72 1.0 73 0.0 74 0.0 75 0.5 76 0.5 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 pass #Base N-Count 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 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 70 19.0 71 23.0 72 28.0 73 26.0 74 21.0 75 24.0 76 21.0 77 27.0 78 23.0 79 17.0 80 36.0 81 27.0 82 41.0 83 26.0 84 33.0 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 3608.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 77.225 #Duplication Level Percentage of deduplicated Percentage of total 1 91.19456134671414 70.42500000000001 2 4.5322110715441895 7.000000000000001 3 1.424409193913888 3.3000000000000003 4 0.809323405632891 2.5 5 0.48559404337973455 1.875 6 0.356102298478472 1.6500000000000001 7 0.29135642602784073 1.575 8 0.19423761735189382 1.2 9 0.03237293622531564 0.22499999999999998 >10 0.6474587245063127 8.85 >50 0.03237293622531564 1.4000000000000001 >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 GGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGC 56 1.4000000000000001 No Hit TACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATGCTT 36 0.8999999999999999 No Hit GGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGG 32 0.8 No Hit CAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCT 25 0.625 No Hit GGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGT 23 0.575 No Hit GGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTC 20 0.5 No Hit GGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAA 19 0.475 No Hit GGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCT 18 0.44999999999999996 No Hit GGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAA 17 0.42500000000000004 No Hit GGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGC 17 0.42500000000000004 No Hit TCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGA 17 0.42500000000000004 No Hit GTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAA 15 0.375 No Hit GGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTG 15 0.375 No Hit CAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATAT 14 0.35000000000000003 No Hit CAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTG 14 0.35000000000000003 No Hit CAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTC 13 0.325 No Hit GAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTCC 13 0.325 No Hit GTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTT 12 0.3 No Hit GTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAG 12 0.3 No Hit GGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCTTT 11 0.27499999999999997 No Hit GGGCTGATATCATCAACCGTGCTAATCTTGGTATGGAAGTAATGCACGAA 11 0.27499999999999997 No Hit GGGGCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTA 9 0.22499999999999998 No Hit CGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTC 8 0.2 No Hit GTATTAGTACTATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCT 8 0.2 No Hit GAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAATACTCCTG 8 0.2 No Hit GGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAAATG 8 0.2 No Hit GGGCGCGATCTTGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAA 8 0.2 No Hit AACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAAGGTCG 8 0.2 No Hit GCAACCAATCTGTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCT 7 0.17500000000000002 No Hit GGCCTGTAGTAGGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCG 7 0.17500000000000002 No Hit GTCAAAAGAGGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGG 7 0.17500000000000002 No Hit ATGGCGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAG 7 0.17500000000000002 No Hit GGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGC 7 0.17500000000000002 No Hit GCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGTATG 7 0.17500000000000002 No Hit CAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAGCAGGCAAGA 7 0.17500000000000002 No Hit GTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATCTTGGT 7 0.17500000000000002 No Hit GGAGGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAA 7 0.17500000000000002 No Hit GGAAAGGCTTGCGGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTA 6 0.15 No Hit GGAATCTGGTTCACTGCTTTAGGTATTAGTACTATGGCGTTCAACCTAAA 6 0.15 No Hit GTAGTTGATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAA 6 0.15 No Hit GTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTA 6 0.15 No Hit CGGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACC 6 0.15 No Hit GAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGC 6 0.15 No Hit CGTTCAACCTAAATGGATTCAATTTCAACCAATCTGTAGTTGATAGTCAA 6 0.15 No Hit GGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGT 6 0.15 No Hit GCACGTGGAATCCCGTGTGAATCAGCAAGGACCACCTTGCAAGGCTAAAT 6 0.15 No Hit GGAGATTCCCAAATAGGTCAACCTTTTAAACTGCCTGCTGAATCCATGAG 6 0.15 No Hit CACGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGT 6 0.15 No Hit GGAGTTTGGCTGGGGCGGCACATCTGTTAAAAGATAACGCAGGTGTCCTA 5 0.125 No Hit GGGAATGCAGCCCAAATCGGGCGGTAGACTCCGTCCAAGGCTAAATACAG 5 0.125 No Hit CACCCTAGATGGCTAAAGTCCAGTAGCCGAAAGCATCACTAGCTTACGCT 5 0.125 No Hit GGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTT 5 0.125 No Hit GATAGTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGC 5 0.125 No Hit CGAACGTAATGCTCACAACTTCCCTCTAGATCTAGCTGCTCTTGAAGTTC 5 0.125 No Hit GGGGTTGTGGGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTG 5 0.125 No Hit GGAGAGCAATACAAGCGTTGTGCTGCTAGGCGAAGCGGTTGAGTGCCGCA 5 0.125 No Hit GTCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAAT 5 0.125 No Hit GGGGAGTTGAAAATAAGCATAGATCCGGAGATTCCCAAATAGGTCAACCT 5 0.125 No Hit GGTGGATACCTAGGCACCCAGAGACGAGGAAGGGCGTAGCAAGCGACGAA 5 0.125 No Hit GCAAGGTCGCGTTATTAATACTTGGGCTGATATCATCAACCGTGCTAATC 5 0.125 No Hit GGAAGGGCGTAGCAAGCGACGAAATGCTTCGGGGAGTTGAAAATAAGCAT 5 0.125 No Hit CAACGAGTCGGGTTGTTTGGGAATGCAGCCCAAATCGGGCGGTAGACTCC 5 0.125 No Hit GGAAAAGAAAGCAAAAGCGATTCCCGTAGTAGCGGCGAGCGAAATGGGAG 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0125 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122404 READS because READLEN < 1 Read 122404 spots for ERR6133338.sra Written 122404 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra Rejected 122396 READS because READLEN < 1 Read 122396 spots for ERR6133338.sra Written 122396 spots for ERR6133338.sra SRR ids: ['ERR6133338.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_mhc7bmyn ERR6133338.sra spots: 2447928 blocks: [[1, 122396], [122397, 244792], [244793, 367188], [367189, 489584], [489585, 611980], [611981, 734376], [734377, 856772], [856773, 979168], [979169, 1101564], [1101565, 1223960], [1223961, 1346356], [1346357, 1468752], [1468753, 1591148], [1591149, 1713544], [1713545, 1835940], [1835941, 1958336], [1958337, 2080732], [2080733, 2203128], [2203129, 2325524], [2325525, 2447928]] ERR6133338 file size 536064 ERR6133338 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 ERR6133338 ERR6133338_1.fastq Input file: ERR6133338_1.fastq trimmed: ERR6133338-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 Sat Dec 7 00:59:21 2024 >> started Sat Dec 7 00:59:23 2024 >> done (1.623s) 2447928 reads processed; of these: 495 ( 0.02%) short reads filtered out after trimming by size control 15 ( 0.00%) empty reads filtered out after trimming by size control 2447418 (99.98%) reads available; of these: 36251 ( 1.48%) trimmed reads available after processing 2411167 (98.52%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 38 0.00% 19 43 0.00% 20 30 0.00% 21 31 0.00% 22 28 0.00% 23 23 0.00% 24 28 0.00% 25 20 0.00% 26 19 0.00% 27 23 0.00% 28 37 0.00% 29 32 0.00% 30 18 0.00% 31 21 0.00% 32 47 0.00% 33 27 0.00% 34 19 0.00% 35 52 0.00% 36 17 0.00% 37 14 0.00% 38 30 0.00% 39 37 0.00% 40 51 0.00% 41 19 0.00% 42 18 0.00% 43 16 0.00% 44 20 0.00% 45 17 0.00% 46 18 0.00% 47 10 0.00% 48 9 0.00% 49 11 0.00% 50 12 0.00% 51 39 0.00% 52 18 0.00% 53 14 0.00% 54 15 0.00% 55 13 0.00% 56 10 0.00% 57 20 0.00% 58 10 0.00% 59 14 0.00% 60 17 0.00% 61 19 0.00% 62 0 0.00% 63 2 0.00% 64 3 0.00% 65 4 0.00% 66 5 0.00% 67 7 0.00% 68 25 0.00% 69 63 0.00% 70 13732 0.56% 71 13243 0.54% 72 14223 0.58% 73 13748 0.56% 74 12843 0.52% 75 12690 0.52% 76 12513 0.51% 77 13797 0.56% 78 13866 0.57% 79 14845 0.61% 80 14791 0.60% 81 18556 0.76% 82 19626 0.80% 83 16726 0.68% 84 19933 0.81% 85 41 0.00% 86 62 0.00% 87 113 0.00% 88 206 0.01% 89 527 0.02% 90 1269 0.05% 91 4374 0.18% 92 26834 1.10% 93 2187727 89.39% 2447418 reads passed initial QC criterion=sequence-density sequence-density=4.06 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=31 prefix-density=4.09 prefix-fanout=2.0 sequence=CAAGGCTAAATAC criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=39.87 fanout-score-rank=1 prefix-density=0.07 prefix-fanout=5.5 sequence=TTTATTTTCTTAGACTTAGACCCTGCAAGATAATAATTTTTCGCTATTTACGATTTTATATTCTTGTTACTAGATACTCTATAGGAATAAGAATAAATCGCAACTCCTTTCCACTACACATAAAAATTGATTTCGAAAGTCTTTTTTTTTAA 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: 0 (0.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 1 (100.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Dec 07 00:59:42 Started mapping on | Dec 07 00:59:42 Finished on | Dec 07 00:59:49 Mapping speed, Million of reads per hour | 1258.67 Number of input reads | 2447418 Average input read length | 91 UNIQUE READS: Uniquely mapped reads number | 1312670 Uniquely mapped reads % | 53.63% Average mapped length | 90.61 Number of splices: Total | 61627 Number of splices: Annotated (sjdb) | 50897 Number of splices: GT/AG | 59040 Number of splices: GC/AG | 1109 Number of splices: AT/AC | 71 Number of splices: Non-canonical | 1407 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.04% Deletion average length | 1.62 Insertion rate per base | 0.02% Insertion average length | 1.65 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 997759 % of reads mapped to multiple loci | 40.77% Number of reads mapped to too many loci | 88743 % of reads mapped to too many loci | 3.63% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.81% % of reads unmapped: other | 0.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 136989 136989 136989 N_multimapping 997759 997759 997759 N_noFeature 110227 123356 1257836 N_ambiguous 49252 7520 236 UnstrandedReadsAssigned:1153191 PositiveStrandReadsAssigned:1181794 NegativeStrandReadsAssigned:54598 Dataset is classified positive stranded MeadianReadLen=93 20thPercentileLength=93 echo kmer=89 ERR6133338 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: ERR6133338-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 2,447,418 reads, 1,754,169 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 923 rounds 52973 ERR6133338.ke.tsv 35125 ERR6133338.se.tsv 88098 total ==> ERR6133338.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 22 12.0584 PNS24243 293 194 0 0 KQK14069 1603 1504 14 7.00008 KQK14071 474 375 0 0 ==> ERR6133338.se.tsv <== BRADI_1g14170v3 14 BRADI_1g53295v3 29 BRADI_1g59795v3 16 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 13 BRADI_1g74790v3 8 BRADI_1g09890v3 0 BRADI_1g77505v3 32 BRADI_1g48960v3 0 ERR6133338 completed mapping pipeline successfully