Starting /dee2/code/volunteer_pipeline.sh SRR7472592 current disk space = 3088090419200 free memory = 1438721536 SRR7472592 SRAfilesize 6cf0e0eae9836432bb3c112756f9b8e6 SRR7472592.sra SRR7472592.sra file validated SRR7472592 is single end SRR7472592 is conventional basespace SRR7472592 read1 length is 51 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7472592_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 51 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.91475 32.0 32.0 32.0 27.0 32.0 2 31.31175 32.0 32.0 32.0 32.0 32.0 3 31.20725 32.0 32.0 32.0 32.0 32.0 4 31.424 32.0 32.0 32.0 32.0 32.0 5 31.16475 32.0 32.0 32.0 32.0 32.0 6 35.20125 37.0 37.0 37.0 32.0 37.0 7 35.614 37.0 37.0 37.0 32.0 37.0 8 35.15325 37.0 37.0 37.0 32.0 37.0 9 35.194 37.0 37.0 37.0 32.0 37.0 10 35.52525 37.0 37.0 37.0 32.0 37.0 11 35.3725 37.0 37.0 37.0 32.0 37.0 12 35.4945 37.0 37.0 37.0 32.0 37.0 13 35.41225 37.0 37.0 37.0 32.0 37.0 14 35.28225 37.0 37.0 37.0 32.0 37.0 15 35.4755 37.0 37.0 37.0 32.0 37.0 16 35.48825 37.0 37.0 37.0 32.0 37.0 17 35.51825 37.0 37.0 37.0 32.0 37.0 18 35.3345 37.0 37.0 37.0 32.0 37.0 19 35.03875 37.0 37.0 37.0 32.0 37.0 20 34.88475 37.0 37.0 37.0 32.0 37.0 21 34.9375 37.0 37.0 37.0 32.0 37.0 22 34.9235 37.0 37.0 37.0 27.0 37.0 23 35.23675 37.0 37.0 37.0 32.0 37.0 24 35.119 37.0 37.0 37.0 32.0 37.0 25 35.23575 37.0 37.0 37.0 32.0 37.0 26 35.673 37.0 37.0 37.0 32.0 37.0 27 35.64475 37.0 37.0 37.0 32.0 37.0 28 35.51475 37.0 37.0 37.0 32.0 37.0 29 35.6765 37.0 37.0 37.0 32.0 37.0 30 35.27975 37.0 37.0 37.0 32.0 37.0 31 35.45025 37.0 37.0 37.0 32.0 37.0 32 35.40125 37.0 37.0 37.0 32.0 37.0 33 35.346 37.0 37.0 37.0 32.0 37.0 34 35.55825 37.0 37.0 37.0 32.0 37.0 35 35.56475 37.0 37.0 37.0 37.0 37.0 36 35.86375 37.0 37.0 37.0 37.0 37.0 37 35.7425 37.0 37.0 37.0 37.0 37.0 38 35.588 37.0 37.0 37.0 32.0 37.0 39 35.55975 37.0 37.0 37.0 32.0 37.0 40 35.309 37.0 37.0 37.0 32.0 37.0 41 35.423 37.0 37.0 37.0 32.0 37.0 42 35.48475 37.0 37.0 37.0 32.0 37.0 43 35.32375 37.0 37.0 37.0 32.0 37.0 44 35.44525 37.0 37.0 37.0 32.0 37.0 45 35.54125 37.0 37.0 37.0 32.0 37.0 46 35.29625 37.0 37.0 37.0 32.0 37.0 47 35.003 37.0 37.0 37.0 32.0 37.0 48 35.474 37.0 37.0 37.0 32.0 37.0 49 35.0 37.0 37.0 37.0 32.0 37.0 50 35.196 37.0 37.0 37.0 32.0 37.0 51 34.72175 37.0 37.0 37.0 27.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 1.0 19 4.0 20 1.0 21 4.0 22 6.0 23 8.0 24 15.0 25 21.0 26 35.0 27 31.0 28 46.0 29 50.0 30 62.0 31 83.0 32 120.0 33 190.0 34 418.0 35 1198.0 36 1706.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 19.925 30.5 28.549999999999997 21.025 2 25.324999999999996 24.675 22.95 27.05 3 28.849999999999998 27.575 21.875 21.7 4 31.85 26.474999999999998 19.7 21.975 5 26.950000000000003 34.8 18.4 19.85 6 27.921092564491655 25.67020738492666 17.071320182094084 29.337379868487606 7 27.900000000000002 25.4 21.9 24.8 8 26.650000000000002 30.375000000000004 19.8 23.175 9 31.025000000000002 28.375 19.425 21.175 10 35.8 24.4 18.575 21.224999999999998 11 31.624999999999996 23.075000000000003 22.0 23.3 12 28.875 23.150000000000002 25.074999999999996 22.900000000000002 13 24.95 22.8 27.55 24.7 14 23.125 29.325000000000003 22.475 25.074999999999996 15 28.799999999999997 33.85 19.475 17.875 16 25.874999999999996 26.325 25.074999999999996 22.725 17 22.650000000000002 27.400000000000002 30.599999999999998 19.35 18 26.450000000000003 23.599999999999998 22.45 27.500000000000004 19 25.0 22.775000000000002 28.825 23.400000000000002 20 26.55 27.224999999999998 22.0 24.224999999999998 21 26.75 28.349999999999998 20.075000000000003 24.825 22 23.075000000000003 26.075 32.0 18.85 23 34.525 24.7 22.45 18.325 24 34.300000000000004 23.175 26.3 16.225 25 25.387693846923458 29.63981990995498 31.89094547273637 13.081540770385192 26 33.074999999999996 30.65 23.7 12.575 27 29.897423067300476 24.293219914936202 31.22341756317238 14.585939454590942 28 18.998748435544428 32.46558197747184 32.340425531914896 16.195244055068837 29 19.914936202151615 25.569176882662 29.321991493620214 25.193895421566175 30 19.46459844883663 15.861896422316738 48.08606454841131 16.587440580435324 31 24.44333249937453 13.284963722792096 34.475856892669505 27.795846885163872 32 33.97548161120841 12.284213159869903 24.718538904178132 29.02176632474356 33 35.90192644483363 13.88541406054541 33.950462847135356 16.262196647485613 34 39.27945959469602 13.460095071303476 23.19239429572179 24.06805103827871 35 41.20590442832124 11.533650237678259 32.624468351263445 14.635976982737054 36 48.3112334250688 12.709532149111835 23.19239429572179 15.786840130097573 37 38.1285964473355 13.835376532399298 19.53965474105579 28.49637227920941 38 25.869402051538653 13.93545158869152 30.172629472104077 30.022516887665752 39 32.89967475606705 24.7935951963973 19.11433575181386 23.19239429572179 40 26.5015015015015 27.87787787787788 15.515515515515515 30.105105105105107 41 37.61261261261261 18.993993993993993 14.68968968968969 28.703703703703702 42 38.63863863863864 27.927927927927925 12.962962962962962 20.47047047047047 43 30.197648236177134 39.27945959469602 12.48436327245434 18.038528896672503 44 39.554665999499626 32.99974981235927 9.457092819614711 17.988491368526393 45 36.05203902927195 23.19239429572179 9.807355516637479 30.94821115836878 46 23.34250688016012 31.17338003502627 21.766324743557668 23.71778834125594 47 20.715536652489366 33.47510632974731 12.509382036527395 33.29997498123593 48 18.11358518889167 25.04378283712785 10.80810607955967 46.03452589442082 49 19.41456092069052 31.998999249437077 18.8141105829372 29.772329246935204 50 28.149261207112446 25.544703230653642 10.693713999499122 35.612321562734785 51 17.325 28.199999999999996 20.150000000000002 34.325 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.5 2 1.0 3 0.5 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.5 12 1.0 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 1.0 21 1.5 22 2.0 23 1.5 24 1.0 25 1.5 26 1.5 27 1.0 28 1.0 29 1.0 30 3.5 31 6.0 32 6.5 33 7.0 34 8.5 35 10.0 36 15.5 37 21.0 38 28.5 39 36.0 40 60.0 41 84.0 42 154.0 43 224.0 44 217.0 45 210.0 46 260.5 47 311.0 48 336.0 49 361.0 50 467.0 51 573.0 52 568.0 53 563.0 54 524.0 55 485.0 56 526.5 57 568.0 58 379.0 59 190.0 60 153.0 61 116.0 62 114.0 63 112.0 64 85.0 65 58.0 66 42.5 67 27.0 68 22.5 69 18.0 70 12.0 71 6.0 72 4.5 73 3.0 74 1.5 75 0.0 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 0.5 90 1.0 91 0.5 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 1.15 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 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.05 26 0.0 27 0.075 28 0.125 29 0.075 30 0.075 31 0.075 32 0.075 33 0.075 34 0.075 35 0.075 36 0.075 37 0.075 38 0.075 39 0.075 40 0.1 41 0.1 42 0.1 43 0.075 44 0.075 45 0.075 46 0.075 47 0.075 48 0.075 49 0.075 50 0.17500000000000002 51 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 51 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 67.9 #Duplication Level Percentage of deduplicated Percentage of total 1 91.08983799705449 61.85000000000001 2 4.9337260677466865 6.7 3 1.1045655375552283 2.25 4 0.5522827687776142 1.5 5 0.3681885125184094 1.25 6 0.40500736377025043 1.6500000000000001 7 0.29455081001472755 1.4000000000000001 8 0.22091310751104565 1.2 9 0.11045655375552282 0.675 >10 0.7731958762886598 11.425 >50 0.11045655375552282 4.8500000000000005 >100 0.036818851251840944 5.25 >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 TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT 210 5.25 RNA PCR Primer, Index 1 (100% over 30bp) TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAGT 75 1.875 RNA PCR Primer, Index 1 (100% over 30bp) CTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 65 1.625 RNA PCR Primer, Index 1 (100% over 28bp) GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGGA 54 1.35 RNA PCR Primer, Index 1 (100% over 22bp) AGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCAG 50 1.25 RNA PCR Primer, Index 1 (100% over 29bp) CCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCC 37 0.9249999999999999 RNA PCR Primer, Index 1 (100% over 27bp) ATCCGGTTAGGATCGATCTAAACCAGCCCTGGAATTCTCGGGTGCCAAGGA 37 0.9249999999999999 RNA PCR Primer, Index 1 (100% over 22bp) CGATTGGGGGAGTAAGAATAGTATTTAATTGCTGGAATTCTCGGGTGCCAA 36 0.8999999999999999 No Hit TCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTC 30 0.75 RNA PCR Primer, Index 1 (100% over 26bp) TAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAG 29 0.7250000000000001 RNA PCR Primer, Index 1 (100% over 29bp) ATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACT 28 0.7000000000000001 RNA PCR Primer, Index 1 (100% over 25bp) GCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAA 24 0.6 RNA PCR Primer, Index 1 (100% over 23bp) AGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGG 20 0.5 Illumina Small RNA Adapter 2 (100% over 21bp) AACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGT 19 0.475 RNA PCR Primer, Index 1 (100% over 30bp) ACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 18 0.44999999999999996 RNA PCR Primer, Index 1 (100% over 31bp) TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCC 15 0.375 RNA PCR Primer, Index 33 (100% over 51bp) CGATTGGGGGAGTAAGAATAGTATTTAATTGCTTGGAATTCTCGGGTGCCA 15 0.375 No Hit CGATTGGGGGAGTAAGAATAGTATTTAATTGCTACTGGAATTCTCGGGTGC 15 0.375 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCCA 13 0.325 No Hit CATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAAC 13 0.325 RNA PCR Primer, Index 1 (100% over 24bp) TTTGGATTGAAGGGAGCTCTTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 13 0.325 RNA PCR Primer, Index 1 (100% over 31bp) TGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAA 13 0.325 No Hit ATCCGGTTAGGATCGATCTAAACCAGCCTGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) AACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAGGA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 22bp) TCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 10 0.25 RNA PCR Primer, Index 1 (100% over 26bp) GGTCGAGGGCACGTCTGCCTGGGTGTCACGCTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit CAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 32bp) TAAACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) TAAACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGT 8 0.2 No Hit CAGCTGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTG 8 0.2 No Hit GCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGGAA 8 0.2 RNA PCR Primer, Index 1 (100% over 23bp) GAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAG 8 0.2 No Hit CAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 8 0.2 RNA PCR Primer, Index 1 (100% over 27bp) GCGACCCCAGGTCAGGCGGGACTTGGAATTCTCGGGTGCCAAGGAACTCCA 8 0.2 RNA PCR Primer, Index 1 (100% over 28bp) AGCTGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGC 7 0.17500000000000002 No Hit ACTGAGATTCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit GATTGGGGGAGTAAGAATAGTATTTAATTGCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit AGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 33bp) TCTCATGGAGAGTTCGATCCTGGCTTGGAATTCTCGGGTGCCAAGGAACTC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 26bp) CGATTGGGGGAGTAAGAATAGTATTTAATTGTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit GTCGTTGTAGTATAGTGGTGAGTATTCCCGCCTTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit GGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCCAAGGA 6 0.15 RNA PCR Primer, Index 1 (100% over 22bp) GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) ATTCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGGAAC 6 0.15 RNA PCR Primer, Index 1 (100% over 24bp) AGTTACTAATTCATGATCTGGCCTGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) GTCGTTGTAGTATAGTGGTAAGTATTCCCGCCTTGGAATTCTCGGGTGCCA 6 0.15 No Hit CGATTGGGGGAGTAAGAATAGTATTTAATTGCTATGGAATTCTCGGGTGCC 6 0.15 No Hit AACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAG 6 0.15 No Hit GATTGGGGGAGTAAGAATAGTATTTAATTGCTTGGAATTCTCGGGTGCCAA 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCAA 6 0.15 No Hit AGTTACTAATTCATGATCTGGCATGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) GGTGCGGCTGGATCACCTCCTTGGAATTCTCGGGTGCCAAGGAACTCCAGT 6 0.15 RNA PCR Primer, Index 1 (100% over 30bp) CTGAGATTCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAA 5 0.125 No Hit GGTGGCTGTAGTTTAGTGGTGAGAATTCCACGTTTGGAATTCTCGGGTGCC 5 0.125 No Hit GCTGAGGCATCCTAACAGACCGGTAGACTTGAACTGGAATTCTCGGGTGCC 5 0.125 No Hit CGGAAAAATAGCTCGACGCCAGGATTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) AACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) TAAACGACTCTCGGCAACGGATATCTCGGCTTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit GAGATTCAGCCCCATGTCGCTCCGATTCGTTGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) CCACCCCAAGATGAGTGCTCTCCTTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) ATGAGCTCAACGAGAACAGAAATCTCGTGTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) AGTTACTAATTCATGATCTGGCATTGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) >>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 0.425 0.0 0.0 0.0 2 0.0 0.425 0.0 0.0 0.0 3 0.0 0.425 0.0 0.0 0.0 4 0.0 0.425 0.0 0.0 0.0 5 0.0 0.425 0.0 0.0 0.0 6 0.0 0.425 0.0 0.0 0.0 7 0.0 0.425 0.0 0.0 0.0 8 0.0 0.45 0.0 0.0 0.0 9 0.0 0.475 0.0 0.0 0.0 10 0.0 0.475 0.0 0.0 0.0 11 0.0 0.525 0.0 0.0 0.0 12 0.0 0.575 0.0 0.0 0.0 13 0.0 0.625 0.0 0.0 0.0 14 0.0 0.7 0.0 0.0 0.0 15 0.0 0.875 0.0 0.0 0.0 16 0.0 1.1 0.0 0.0 0.0 17 0.0 1.775 0.0 0.0 0.0 18 0.0 2.575 0.0 0.0 0.0 19 0.0 3.9 0.0 0.0 0.0 20 0.0 5.6 0.0 0.0 0.0 21 0.0 8.975 0.0 0.0 0.0 22 0.0 22.45 0.0 0.0 0.0 23 0.0 28.75 0.0 0.0 0.0 24 0.0 34.15 0.0 0.0 0.0 25 0.0 47.225 0.0 0.0 0.0 26 0.0 52.375 0.0 0.0 0.0 27 0.0 56.825 0.0 0.0 0.0 28 0.0 60.375 0.0 0.0 0.0 29 0.0 64.375 0.0 0.0 0.0 30 0.0 69.95 0.0 0.0 0.0 31 0.0 73.4 0.0 0.0 0.0 32 0.0 76.975 0.0 0.0 0.0 33 0.0 81.625 0.0 0.0 0.0 34 0.0 85.175 0.0 0.0 0.0 35 0.0 87.325 0.0 0.0 0.0 36 0.0 89.325 0.0 0.0 0.0 37 0.0 90.525 0.0 0.0 0.0 38 0.0 91.25 0.0 0.0 0.0 39 0.0 91.8 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCCCCT 20 6.222983E-4 45.0 16 CCCCTGG 20 6.222983E-4 45.0 18 ATTCCCC 25 3.236105E-5 45.0 15 TCCCCTG 20 6.222983E-4 45.0 17 CTTCATT 35 4.8309703E-6 38.571426 11 GGACCAG 35 4.8309703E-6 38.571426 3 CGGACCA 35 4.8309703E-6 38.571426 2 TCGGACC 35 4.8309703E-6 38.571426 1 AGGCTTC 35 4.8309703E-6 38.571426 8 CCCTGGA 35 4.8309703E-6 38.571426 19 GGCTTCA 35 4.8309703E-6 38.571426 9 CAGGCTT 35 4.8309703E-6 38.571426 7 GCTTCAT 35 4.8309703E-6 38.571426 10 GACCAGG 35 4.8309703E-6 38.571426 4 TTCATTC 30 9.4943156E-5 37.499996 12 CATTCCC 30 9.4943156E-5 37.499996 14 TCATTCC 30 9.4943156E-5 37.499996 13 CCAGGCT 40 1.2085775E-5 33.75 6 ACCAGGC 45 2.707939E-5 30.000002 5 CTCCAGT 100 5.3034273E-7 20.25 45 >>END_MODULE Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012038 READS because READLEN < 1 Read 1012038 spots for SRR7472592.sra Written 1012038 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra Rejected 1012032 READS because READLEN < 1 Read 1012032 spots for SRR7472592.sra Written 1012032 spots for SRR7472592.sra SRR ids: ['SRR7472592.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9rx0ngfu SRR7472592.sra spots: 20240646 blocks: [[1, 1012032], [1012033, 2024064], [2024065, 3036096], [3036097, 4048128], [4048129, 5060160], [5060161, 6072192], [6072193, 7084224], [7084225, 8096256], [8096257, 9108288], [9108289, 10120320], [10120321, 11132352], [11132353, 12144384], [12144385, 13156416], [13156417, 14168448], [14168449, 15180480], [15180481, 16192512], [16192513, 17204544], [17204545, 18216576], [18216577, 19228608], [19228609, 20240646]] SRR7472592 file size 2864172 SRR7472592 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 SRR7472592 SRR7472592_1.fastq Input file: SRR7472592_1.fastq trimmed: SRR7472592-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 18:22:35 2025 >> started Thu Feb 13 18:22:43 2025 >> done (8.057s) 20240646 reads processed; of these: 0 ( 0.00%) short reads filtered out after trimming by size control 0 ( 0.00%) empty reads filtered out after trimming by size control 20240646 (100.00%) reads available; of these: 307018 ( 1.52%) trimmed reads available after processing 19933628 (98.48%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 36 1 0.00% 37 0 0.00% 38 1 0.00% 39 1 0.00% 40 5 0.00% 41 10 0.00% 42 22 0.00% 43 51 0.00% 44 145 0.00% 45 374 0.00% 46 1204 0.01% 47 3796 0.02% 48 11411 0.06% 49 40832 0.20% 50 249165 1.23% 51 19933628 98.48% 20240646 reads passed initial QC criterion=sequence-density sequence-density=93.02 sequence-density-rank=1 fanout-score=27.02 fanout-score-rank=2 prefix-density=94.06 prefix-fanout=26.7 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCC criterion=fanout-score sequence-density=1.43 sequence-density-rank=2 fanout-score=28.29 fanout-score-rank=1 prefix-density=1.42 prefix-fanout=28.3 sequence=GACTGGAATTCT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCC -o SRR7472592 - Input file: STDIN trimmed: SRR7472592-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCC -- 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 18:23:12 2025 >> started Thu Feb 13 18:23:26 2025 >> done (13.610s) 19809994 reads processed; of these: 480802 ( 2.43%) short reads filtered out after trimming by size control 57153 ( 0.29%) empty reads filtered out after trimming by size control 19272039 (97.28%) reads available; of these: 18825744 (97.68%) trimmed reads available after processing 446295 ( 2.32%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 300279 1.56% 19 381188 1.98% 20 631115 3.27% 21 2739965 14.22% 22 1422941 7.38% 23 1281290 6.65% 24 2742811 14.23% 25 1079992 5.60% 26 794642 4.12% 27 768061 3.99% 28 803036 4.17% 29 1212703 6.29% 30 710109 3.68% 31 728576 3.78% 32 930233 4.83% 33 704965 3.66% 34 453514 2.35% 35 378581 1.96% 36 249253 1.29% 37 159413 0.83% 38 115601 0.60% 39 81389 0.42% 40 51633 0.27% 41 29406 0.15% 42 29386 0.15% 43 15889 0.08% 44 10360 0.05% 45 7544 0.04% 46 5565 0.03% 47 5594 0.03% 48 9445 0.05% 49 15107 0.08% 50 39852 0.21% 51 382601 1.99% criterion=sequence-density sequence-density=2.21 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=17 prefix-density=0.00 prefix-fanout=1.0 sequence=TCTCGGACCAGGCTTCATTCCCCTGGAATTCT criterion=fanout-score sequence-density=0.05 sequence-density-rank=21 fanout-score=59.27 fanout-score-rank=1 prefix-density=3.06 prefix-fanout=1.0 sequence=TCCTAACAGACAGGTAGACTTGA Started job on | Feb 13 18:23:44 Started mapping on | Feb 13 18:23:44 Finished on | Feb 13 18:24:25 Mapping speed, Million of reads per hour | 1729.99 Number of input reads | 19702691 Average input read length | 27 UNIQUE READS: Uniquely mapped reads number | 6289951 Uniquely mapped reads % | 31.92% Average mapped length | 26.18 Number of splices: Total | 79436 Number of splices: Annotated (sjdb) | 32484 Number of splices: GT/AG | 77754 Number of splices: GC/AG | 945 Number of splices: AT/AC | 76 Number of splices: Non-canonical | 661 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.00% Deletion average length | 1.18 Insertion rate per base | 0.00% Insertion average length | 1.05 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3467363 % of reads mapped to multiple loci | 17.60% Number of reads mapped to too many loci | 8813212 % of reads mapped to too many loci | 44.73% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.44% % of reads unmapped: other | 1.31% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9945377 9945377 9945377 N_multimapping 3467363 3467363 3467363 N_noFeature 2776028 2899039 4982340 N_ambiguous 1188578 2998 1010 UnstrandedReadsAssigned:2325345 PositiveStrandReadsAssigned:3387914 NegativeStrandReadsAssigned:1306601 Dataset is classified unstranded MeadianReadLen=25 20thPercentileLength=21 echo kmer=19 SRR7472592 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 19 [index] number of targets: 52,400 [index] number of k-mers: 59,590,899 [index] number of equivalence classes: 293,668 [quant] running in single-end mode [quant] will process file 1: SRR7472592-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 19,702,691 reads, 10,526,910 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,187 rounds 52401 SRR7472592.ke.tsv 34699 SRR7472592.se.tsv 87100 total ==> SRR7472592.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 29.7137 1.10202 Potri.005G024800.1.v4.1 1035 936 7.03149 0.534662 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 23.1993 0.580567 Potri.016G087400.1.v4.1 270 171 3 1.24863 Potri.015G069301.1.v4.1 564 465 4 0.61223 Potri.010G195200.1.v4.1 1773 1674 0 0 Potri.012G127500.1.v4.1 977 878 20 1.62123 ==> SRR7472592.se.tsv <== Potri.001G166300.v4.1 2 Potri.001G448400.v4.1 5 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 10 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 5 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 4 Potri.001G452600.v4.1 1 SRR7472592 completed mapping pipeline successfully