Starting /dee2/code/volunteer_pipeline.sh SRR8846554 current disk space = 1527907024896 free memory = 1395988988 SRR8846554 SRAfilesize af04474e7514a49b8053b85a80e67c23 SRR8846554.sra SRR8846554.sra file validated SRR8846554 is single end SRR8846554 is conventional basespace SRR8846554 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846554_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 48 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.70425 34.0 33.0 34.0 25.0 34.0 2 32.80625 34.0 33.0 34.0 28.0 34.0 3 32.99525 34.0 33.0 34.0 32.0 34.0 4 33.1665 34.0 33.0 34.0 32.0 34.0 5 33.2475 34.0 33.0 34.0 32.0 34.0 6 36.994 38.0 37.0 38.0 36.0 38.0 7 37.25775 38.0 38.0 38.0 36.0 38.0 8 37.4605 38.0 38.0 38.0 37.0 38.0 9 37.51625 38.0 38.0 38.0 37.0 38.0 10-11 37.51875 38.0 38.0 38.0 38.0 38.0 12-13 37.559375 38.0 38.0 38.0 38.0 38.0 14-15 37.487625 38.0 38.0 38.0 37.0 38.0 16-17 37.46575 38.0 38.0 38.0 37.5 38.0 18-19 37.5525 38.0 38.0 38.0 38.0 38.0 20-21 37.45425 38.0 38.0 38.0 37.5 38.0 22-23 37.486 38.0 38.0 38.0 37.5 38.0 24-25 37.560874999999996 38.0 38.0 38.0 38.0 38.0 26-27 37.543125 38.0 38.0 38.0 37.5 38.0 28-29 37.51049999999999 38.0 38.0 38.0 37.5 38.0 30-31 37.432500000000005 38.0 38.0 38.0 37.0 38.0 32-33 37.4225 38.0 38.0 38.0 37.0 38.0 34-35 37.18675 38.0 38.0 38.0 36.5 38.0 36-37 37.107749999999996 38.0 38.0 38.0 36.0 38.0 38-39 37.142250000000004 38.0 38.0 38.0 36.0 38.0 40-41 37.084875 38.0 38.0 38.0 36.0 38.0 42-43 36.991375000000005 38.0 38.0 38.0 35.5 38.0 44-45 37.049 38.0 38.0 38.0 36.0 38.0 46-47 37.078 38.0 38.0 38.0 36.0 38.0 48-49 37.134875 38.0 38.0 38.0 36.0 38.0 50-51 37.116375000000005 38.0 38.0 38.0 36.5 38.0 52-53 37.0805 38.0 38.0 38.0 36.0 38.0 54-55 37.003625 38.0 38.0 38.0 36.0 38.0 56-57 36.8515 38.0 38.0 38.0 35.5 38.0 58-59 36.719375 38.0 38.0 38.0 35.0 38.0 60-61 36.215374999999995 38.0 37.5 38.0 33.0 38.0 62-63 35.89575000000001 38.0 37.0 38.0 30.0 38.0 64-65 35.577375 38.0 36.5 38.0 29.0 38.0 66-67 35.177625 38.0 36.0 38.0 27.0 38.0 68-69 35.157375 38.0 36.0 38.0 27.5 38.0 70-71 35.179249999999996 38.0 36.5 38.0 27.5 38.0 72-73 35.288 38.0 37.0 38.0 28.0 38.0 74-75 34.613375000000005 38.0 35.5 38.0 26.0 38.0 76-77 34.42675 38.0 35.5 38.0 26.0 38.0 78-79 34.072 38.0 34.5 38.0 24.5 38.0 80-81 34.099000000000004 38.0 34.5 38.0 24.5 38.0 82-83 34.015249999999995 38.0 34.5 38.0 24.0 38.0 84-85 34.068749999999994 38.0 34.5 38.0 24.0 38.0 86-87 34.227125 38.0 35.0 38.0 24.5 38.0 88-89 34.7575 38.0 36.0 38.0 27.5 38.0 90-91 34.298125 38.0 35.5 38.0 25.0 38.0 92-93 33.929 38.0 35.5 38.0 20.0 38.0 94-95 32.719875 38.0 34.0 38.0 15.0 38.0 96-97 31.07 38.0 32.0 38.0 2.0 38.0 98-99 28.75675 37.5 23.0 38.0 2.0 38.0 100-101 25.488125 35.5 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 1.0 14 0.0 15 1.0 16 0.0 17 1.0 18 3.0 19 3.0 20 0.0 21 3.0 22 9.0 23 15.0 24 20.0 25 30.0 26 17.0 27 23.0 28 21.0 29 42.0 30 49.0 31 88.0 32 134.0 33 197.0 34 329.0 35 528.0 36 1083.0 37 1402.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.8866090712743 27.699784017278617 19.11447084233261 23.29913606911447 2 25.124999999999996 32.15 18.224999999999998 24.5 3 25.474999999999998 20.549999999999997 21.0 32.975 4 26.55 32.65 17.775 23.025000000000002 5 30.425 26.6 22.25 20.724999999999998 6 25.131282820705174 30.03250812703176 22.330582645661416 22.50562640660165 7 35.6 26.575 18.075 19.75 8 20.925 22.400000000000002 35.275 21.4 9 23.724999999999998 36.1 21.6 18.575 10-11 29.65 27.35 23.200000000000003 19.8 12-13 24.0625 24.474999999999998 21.75 29.7125 14-15 22.3125 35.75 24.2625 17.675 16-17 24.125 28.425 29.725 17.724999999999998 18-19 29.212500000000002 27.287499999999998 23.125 20.375 20-21 22.35 30.412499999999998 26.924999999999997 20.3125 22-23 27.500000000000004 29.575000000000003 28.599999999999998 14.325 24-25 26.875 26.575 27.237499999999997 19.3125 26-27 33.1625 28.000000000000004 23.45 15.387500000000001 28-29 22.625 30.625000000000004 26.125 20.625 30-31 25.587500000000002 20.125 36.7 17.5875 32-33 24.087500000000002 18.512500000000003 33.925 23.474999999999998 34-35 28.475 16.975 31.374999999999996 23.175 36-37 37.9 15.325 27.9125 18.862499999999997 38-39 34.112500000000004 19.25 28.025 18.6125 40-41 30.162499999999998 17.9875 23.8875 27.962500000000002 42-43 28.675 26.8375 21.85 22.6375 44-45 38.65 20.8 15.787499999999998 24.762500000000003 46-47 30.3875 30.2125 16.0875 23.3125 48-49 27.875 23.525 18.9375 29.6625 50-51 23.599999999999998 23.6875 15.512500000000001 37.2 52-53 25.974999999999998 31.55 11.200000000000001 31.275 54-55 22.2 26.375 16.4375 34.9875 56-57 21.349999999999998 32.9875 11.1 34.5625 58-59 18.5375 30.162499999999998 12.237499999999999 39.0625 60-61 28.1375 27.037499999999998 11.15 33.675 62-63 25.937500000000004 23.5625 13.9625 36.5375 64-65 22.525000000000002 26.974999999999998 19.5625 30.9375 66-67 21.5625 19.6125 22.4875 36.3375 68-69 24.975 21.6625 19.35 34.0125 70-71 25.7 20.8 24.775 28.725 72-73 29.775000000000002 16.3875 25.887500000000003 27.950000000000003 74-75 22.75 13.700000000000001 26.375 37.175000000000004 76-77 24.1625 11.5 36.162499999999994 28.175 78-79 20.8 7.925 37.0 34.275 80-81 20.45 9.6875 38.45 31.412499999999998 82-83 22.3125 9.7875 41.85 26.05 84-85 20.4375 11.55 37.0375 30.975 86-87 22.2625 16.8875 37.05 23.799999999999997 88-89 15.812499999999998 33.1625 31.837500000000002 19.1875 90-91 12.662499999999998 41.6625 28.849999999999998 16.825000000000003 92-93 12.4875 51.3625 22.1875 13.9625 94-95 9.8 60.1375 19.5125 10.549999999999999 96-97 8.6375 68.22500000000001 16.35 6.7875000000000005 98-99 6.6875 76.5625 11.4875 5.2625 100-101 5.65 82.5125 7.187499999999999 4.65 >>END_MODULE >>Per sequence GC content pass #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 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.5 31 0.5 32 0.0 33 0.0 34 1.0 35 2.5 36 4.0 37 6.5 38 8.0 39 9.0 40 17.5 41 46.0 42 70.5 43 122.0 44 193.5 45 245.0 46 332.0 47 400.0 48 446.0 49 441.5 50 362.5 51 318.5 52 292.5 53 229.5 54 136.0 55 75.0 56 70.0 57 79.5 58 52.0 59 12.5 60 10.0 61 9.0 62 2.5 63 2.5 64 1.0 65 0.5 66 0.5 67 0.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 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 0.0 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 warn #Base N-Count 1 7.3999999999999995 2 0.0 3 0.0 4 0.0 5 0.0 6 0.025 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 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels warn #Total Deduplicated Percentage 58.525000000000006 #Duplication Level Percentage of deduplicated Percentage of total 1 84.9209739427595 49.7 2 7.048269970098249 8.25 3 2.3067065356685177 4.05 4 1.452370781717215 3.4000000000000004 5 0.9397693293464331 2.75 6 0.6834686031610423 2.4 7 0.5126014523707817 2.1 8 0.17086715079026057 0.8 9 0.25630072618539085 1.35 >10 1.5805211448099103 19.400000000000002 >50 0.08543357539513029 3.225 >100 0.042716787697565144 2.5749999999999997 >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 GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 103 2.5749999999999997 RNA PCR Primer, Index 1 (100% over 22bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 70 1.7500000000000002 No Hit TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 59 1.4749999999999999 RNA PCR Primer, Index 1 (100% over 29bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 48 1.2 No Hit GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 42 1.05 RNA PCR Primer, Index 1 (100% over 24bp) TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 40 1.0 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 38 0.95 RNA PCR Primer, Index 1 (100% over 23bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 37 0.9249999999999999 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 35 0.8750000000000001 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 31 0.775 No Hit GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 29 0.7250000000000001 RNA PCR Primer, Index 1 (100% over 25bp) CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 29 0.7250000000000001 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 25 0.625 No Hit AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 25 0.625 Illumina Small RNA Adapter 2 (100% over 21bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 24 0.6 Illumina Small RNA Adapter 2 (100% over 21bp) TCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCCGTCTT 23 0.575 RNA PCR Primer, Index 33 (100% over 50bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 22 0.5499999999999999 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTTGGAATTCT 21 0.525 No Hit ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 21 0.525 RNA PCR Primer, Index 1 (100% over 25bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 21 0.525 No Hit CTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCCGTCTTC 19 0.475 RNA PCR Primer, Index 33 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 19 0.475 Illumina Small RNA Adapter 2 (100% over 21bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 18 0.44999999999999996 No Hit TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 18 0.44999999999999996 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 15 0.375 No Hit GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 14 0.35000000000000003 No Hit CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 14 0.35000000000000003 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAATGGAATTCTCGGGTGCCA 13 0.325 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACACTGGAATTCTCGGGTGCCAA 13 0.325 No Hit GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 13 0.325 RNA PCR Primer, Index 1 (100% over 24bp) TGCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGG 13 0.325 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 12 0.3 RNA PCR Primer, Index 1 (100% over 29bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTG 12 0.3 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 10 0.25 No Hit AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGT 10 0.25 No Hit TTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCCGTCT 10 0.25 RNA PCR Primer, Index 33 (100% over 50bp) GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 10 0.25 RNA PCR Primer, Index 1 (100% over 24bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGG 10 0.25 No Hit NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 22bp) GGAGAGATGGCTGAGTGGACTAAAGCGGCGGATTGCTAATCTGGAATTCT 9 0.22499999999999998 No Hit ATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAAC 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 24bp) TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 9 0.22499999999999998 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGG 9 0.22499999999999998 No Hit CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTCGGGT 9 0.22499999999999998 No Hit CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 8 0.2 No Hit TCGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCC 8 0.2 No Hit TCTCGGACCAGGCTTCATTCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 8 0.2 RNA PCR Primer, Index 1 (100% over 29bp) AGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGT 8 0.2 No Hit GTCAGGATAGCTCAGTTGGTAGAGCAGAGGACTTGGAATTCTCGGGTGCC 7 0.17500000000000002 No Hit AAGGGTGCTGAGAATACTTTGAATCTGACATGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAAAATGGAATTCTCGGG 7 0.17500000000000002 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 28bp) ATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCCA 7 0.17500000000000002 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 7 0.17500000000000002 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAAAATGGAATTCTCGGG 7 0.17500000000000002 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGC 7 0.17500000000000002 No Hit CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTCGGGTGC 7 0.17500000000000002 No Hit AGATGAGCTCAACGAGAACAGAAATCTCGTGTGGAATTCTCGGGTGCCAA 7 0.17500000000000002 No Hit NACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 24bp) NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 6 0.15 No Hit NGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 6 0.15 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCG 6 0.15 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 6 0.15 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGCC 6 0.15 No Hit CGGTCGAGGGCACGCCTGCCTGGGCGTCACGCTGGAATTCTCGGGTGCCA 6 0.15 No Hit TCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCG 6 0.15 No Hit GGGGATGTAGCTCAGATGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGAATAAAAAAATGGAATTCTCGGGT 6 0.15 No Hit ACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 6 0.15 RNA PCR Primer, Index 1 (100% over 31bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTGGAATTCTCGGGTGCCA 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 6 0.15 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACTGGAATTCTCGGGTGCCAA 6 0.15 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 6 0.15 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 6 0.15 No Hit GTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTC 5 0.125 No Hit GATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) GATGAGCTCAACGAGAACAGAAATCTCGTGTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit AGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) GGGATTGTAGTTCAATTGGTCAGAGCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) ATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGAATTCTCGGGTGCCA 5 0.125 No Hit TCCGTCGTAGTCTAGGTGGTTAGGATACTCGTGGAATTCTCGGGTGCCAA 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAAATGGAATTCTCGGGTGCCAAGG 5 0.125 Illumina Small RNA Adapter 2 (100% over 21bp) CACGACTCTCGGCAATGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCA 5 0.125 RNA PCR Primer, Index 7 (100% over 35bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTTGGAATTCTCGGGTGCC 5 0.125 No Hit TCCGTCGTAGTCTAGGTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACC 5 0.125 RNA PCR Primer, Index 2 (100% over 34bp) ATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCCGTC 5 0.125 RNA PCR Primer, Index 33 (100% over 50bp) ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit AGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCCAAG 5 0.125 No Hit NGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 5 0.125 No Hit TTTGGATTGAAGGGAGCTCTGTGGAATTCTCGGGTGCCAAGGAACTCCAG 5 0.125 RNA PCR Primer, Index 1 (100% over 29bp) TCAAAAGAGGAAAGGCTTGCGGTGGAATTCTCGGGTGCCAAGGAACTCCA 5 0.125 RNA PCR Primer, Index 1 (100% over 28bp) GGGGATATAGCTCAGTTGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTCGGG 5 0.125 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTCTAAAAAATGGAATTCTCGG 5 0.125 No Hit TAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) >>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 0.025 0.0 0.0 0.0 2 0.0 0.05 0.0 0.0 0.0 3 0.0 0.05 0.0 0.0 0.0 4 0.0 0.075 0.0 0.0 0.0 5 0.0 0.075 0.0 0.0 0.0 6 0.0 0.075 0.0 0.0 0.0 7 0.0 0.1 0.0 0.0 0.0 8 0.0 0.1 0.0 0.0 0.0 9 0.0 0.125 0.0 0.0 0.0 10-11 0.0 0.1875 0.0 0.0 0.0 12-13 0.0 0.225 0.0 0.0 0.0 14-15 0.0 0.3125 0.0 0.0 0.0 16-17 0.0 1.2125 0.0 0.0 0.0 18-19 0.0 2.375 0.0 0.0 0.0 20-21 0.0 4.7125 0.0 0.0 0.0 22-23 0.0 11.6125 0.0 0.0 0.0 24-25 0.0 22.0625 0.0 0.0 0.0 26-27 0.0 35.625 0.0 0.0 0.0 28-29 0.0 45.075 0.0 0.0 0.0 30-31 0.0 54.6125 0.0 0.0 0.0 32-33 0.0 62.425 0.0 0.0 0.0 34-35 0.0 71.725 0.0 0.0 0.0 36-37 0.0 80.05000000000001 0.0 0.0 0.0 38-39 0.0 85.475 0.0 0.0 0.0 40-41 0.0 88.175 0.0 0.0 0.0 42-43 0.0 91.2125 0.0 0.0 0.0 44-45 0.0 92.51249999999999 0.0 0.0 0.0 46-47 0.0 92.9625 0.0 0.0 0.0 48-49 0.0 93.1 0.0 0.0 0.0 50-51 0.0 93.175 0.0 0.0 0.0 52-53 0.0 93.175 0.0 0.0 0.0 54-55 0.0 93.1875 0.0 0.0 0.0 56-57 0.0 93.2 0.0 0.0 0.0 58-59 0.0 93.2 0.0 0.0 0.0 60-61 0.0 93.2 0.0 0.0 0.0 62-63 0.0 93.2 0.0 0.0 0.0 64-65 0.0 93.2 0.0 0.0 0.0 66-67 0.0 93.2 0.0 0.0 0.0 68-69 0.0 93.2 0.0 0.0 0.0 70-71 0.0 93.2 0.0 0.0 0.0 72-73 0.0 93.2 0.0 0.0 0.0 74-75 0.0 93.2 0.0 0.0 0.0 76-77 0.0 93.2 0.0 0.0 0.0 78-79 0.0 93.2 0.0 0.0 0.0 80-81 0.0 93.2 0.0 0.0 0.0 82-83 0.0 93.2 0.0 0.0 0.0 84-85 0.0 93.2 0.0 0.0 0.0 86-87 0.0 93.2 0.0 0.0 0.0 88-89 0.0 93.2 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTAGACC 40 5.456968E-12 94.9375 7 ACACGAC 30 9.502401E-9 94.9375 2 AGTAGAC 40 5.456968E-12 94.9375 6 CACGACT 30 9.502401E-9 94.9375 3 GAGTAGA 40 5.456968E-12 94.9375 5 CGAGTAG 40 5.456968E-12 94.9375 4 AGACCTT 40 5.456968E-12 94.9375 9 TCGAGTA 40 5.456968E-12 94.9375 3 TAGACCT 40 5.456968E-12 94.9375 8 GACACGA 30 7.653234E-7 84.388885 1 CTCTCGG 35 2.7721399E-8 81.375 8 ACTCTCG 35 2.7721399E-8 81.375 7 ACGACTC 35 2.7721399E-8 81.375 4 GACTCTC 35 2.7721399E-8 81.375 6 CGACTCT 35 2.7721399E-8 81.375 5 CATCGAG 50 2.1827873E-11 81.013336 1 TCGGACC 20 0.0014869607 75.950005 1 ATCGAGT 50 4.1836756E-11 75.950005 2 CGGACCA 20 0.0019308104 71.203125 2 TCTCGGC 40 7.000381E-8 71.203125 9 >>END_MODULE Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965208 READS because READLEN < 1 Read 965208 spots for SRR8846554.sra Written 965208 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra Rejected 965203 READS because READLEN < 1 Read 965203 spots for SRR8846554.sra Written 965203 spots for SRR8846554.sra SRR ids: ['SRR8846554.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_167mpflm SRR8846554.sra spots: 19304065 blocks: [[1, 965203], [965204, 1930406], [1930407, 2895609], [2895610, 3860812], [3860813, 4826015], [4826016, 5791218], [5791219, 6756421], [6756422, 7721624], [7721625, 8686827], [8686828, 9652030], [9652031, 10617233], [10617234, 11582436], [11582437, 12547639], [12547640, 13512842], [13512843, 14478045], [14478046, 15443248], [15443249, 16408451], [16408452, 17373654], [17373655, 18338857], [18338858, 19304065]] SRR8846554 file size 4634651 SRR8846554 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 SRR8846554 SRR8846554_1.fastq Input file: SRR8846554_1.fastq trimmed: SRR8846554-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 Mon Dec 9 10:45:44 2024 >> started Mon Dec 9 10:46:34 2024 >> done (49.266s) 19304065 reads processed; of these: 392 ( 0.00%) short reads filtered out after trimming by size control 63 ( 0.00%) empty reads filtered out after trimming by size control 19303610 (100.00%) reads available; of these: 4191195 (21.71%) trimmed reads available after processing 15112415 (78.29%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 57 0.00% 19 40 0.00% 20 42 0.00% 21 62 0.00% 22 60 0.00% 23 60 0.00% 24 77 0.00% 25 128 0.00% 26 124 0.00% 27 163 0.00% 28 241 0.00% 29 251 0.00% 30 211 0.00% 31 268 0.00% 32 270 0.00% 33 321 0.00% 34 416 0.00% 35 413 0.00% 36 414 0.00% 37 413 0.00% 38 479 0.00% 39 402 0.00% 40 466 0.00% 41 347 0.00% 42 362 0.00% 43 375 0.00% 44 382 0.00% 45 414 0.00% 46 366 0.00% 47 425 0.00% 48 424 0.00% 49 463 0.00% 50 466 0.00% 51 522 0.00% 52 491 0.00% 53 499 0.00% 54 456 0.00% 55 411 0.00% 56 488 0.00% 57 570 0.00% 58 640 0.00% 59 818 0.00% 60 1283 0.01% 61 1705 0.01% 62 2457 0.01% 63 2944 0.02% 64 5209 0.03% 65 6288 0.03% 66 12788 0.07% 67 56922 0.29% 68 61285 0.32% 69 39977 0.21% 70 25880 0.13% 71 27698 0.14% 72 12229 0.06% 73 5246 0.03% 74 6428 0.03% 75 4758 0.02% 76 3887 0.02% 77 3786 0.02% 78 4285 0.02% 79 4489 0.02% 80 4784 0.02% 81 5709 0.03% 82 9470 0.05% 83 9268 0.05% 84 8511 0.04% 85 9932 0.05% 86 11906 0.06% 87 17117 0.09% 88 28325 0.15% 89 50419 0.26% 90 76657 0.40% 91 86003 0.45% 92 99548 0.52% 93 149369 0.77% 94 196518 1.02% 95 398441 2.06% 96 454354 2.35% 97 491948 2.55% 98 691887 3.58% 99 662430 3.43% 100 424758 2.20% 101 15112415 78.29% 19303610 reads passed initial QC criterion=sequence-density sequence-density=93.24 sequence-density-rank=1 fanout-score=33.86 fanout-score-rank=2 prefix-density=93.72 prefix-fanout=33.7 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=2.31 sequence-density-rank=4 fanout-score=43.19 fanout-score-rank=1 prefix-density=98.77 prefix-fanout=1.0 sequence=CACCAGGCGATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846554 - Input file: STDIN trimmed: SRR8846554-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACCAGGCGATCTCGTATGCCGTCTTCTGCTTGA -- 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 Mon Dec 9 10:48:08 2024 >> started Mon Dec 9 10:49:32 2024 >> done (83.730s) 18892895 reads processed; of these: 349515 ( 1.85%) short reads filtered out after trimming by size control 5913 ( 0.03%) empty reads filtered out after trimming by size control 18537467 (98.12%) reads available; of these: 18046955 (97.35%) trimmed reads available after processing 490512 ( 2.65%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 128743 0.69% 19 205180 1.11% 20 256919 1.39% 21 866854 4.68% 22 493534 2.66% 23 722376 3.90% 24 2190111 11.81% 25 836508 4.51% 26 875103 4.72% 27 819456 4.42% 28 967427 5.22% 29 918119 4.95% 30 1046582 5.65% 31 724403 3.91% 32 754908 4.07% 33 918618 4.96% 34 1043789 5.63% 35 979358 5.28% 36 878733 4.74% 37 516931 2.79% 38 428637 2.31% 39 327778 1.77% 40 272810 1.47% 41 313339 1.69% 42 276187 1.49% 43 101280 0.55% 44 93613 0.50% 45 37548 0.20% 46 20478 0.11% 47 10930 0.06% 48 9073 0.05% 49 4674 0.03% 50 3084 0.02% 51 2844 0.02% 52 1464 0.01% 53 1118 0.01% 54 1254 0.01% 55 508 0.00% 56 654 0.00% 57 426 0.00% 58 420 0.00% 59 551 0.00% 60 828 0.00% 61 1279 0.01% 62 1971 0.01% 63 2462 0.01% 64 4625 0.02% 65 5671 0.03% 66 11961 0.06% 67 55058 0.30% 68 59227 0.32% 69 38215 0.21% 70 24329 0.13% 71 25919 0.14% 72 9982 0.05% 73 3222 0.02% 74 3160 0.02% 75 2178 0.01% 76 1713 0.01% 77 1906 0.01% 78 1785 0.01% 79 1791 0.01% 80 2058 0.01% 81 1572 0.01% 82 1393 0.01% 83 1371 0.01% 84 1063 0.01% 85 981 0.01% 86 890 0.00% 87 957 0.01% 88 927 0.01% 89 888 0.00% 90 1023 0.01% 91 1218 0.01% 92 1260 0.01% 93 1454 0.01% 94 1665 0.01% 95 2226 0.01% 96 2955 0.02% 97 4020 0.02% 98 5370 0.03% 99 6551 0.04% 100 8398 0.05% 101 179623 0.97% criterion=sequence-density sequence-density=5.90 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=15 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=110.04 fanout-score-rank=1 prefix-density=0.61 prefix-fanout=1.0 sequence=TAGCCAAGTGCGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTCCGACTTC Started job on | Dec 09 10:52:02 Started mapping on | Dec 09 10:52:03 Finished on | Dec 09 10:58:04 Mapping speed, Million of reads per hour | 188.96 Number of input reads | 18948182 Average input read length | 32 UNIQUE READS: Uniquely mapped reads number | 3185622 Uniquely mapped reads % | 16.81% Average mapped length | 26.89 Number of splices: Total | 35854 Number of splices: Annotated (sjdb) | 22811 Number of splices: GT/AG | 33086 Number of splices: GC/AG | 1952 Number of splices: AT/AC | 31 Number of splices: Non-canonical | 785 Mismatch rate per base, % | 0.14% Deletion rate per base | 0.00% Deletion average length | 1.36 Insertion rate per base | 0.00% Insertion average length | 1.02 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 6399715 % of reads mapped to multiple loci | 33.77% Number of reads mapped to too many loci | 8204442 % of reads mapped to too many loci | 43.30% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.44% % of reads unmapped: other | 0.67% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9362845 9362845 9362845 N_multimapping 6399715 6399715 6399715 N_noFeature 1875905 2047791 2997907 N_ambiguous 55133 38846 599 UnstrandedReadsAssigned:1254584 PositiveStrandReadsAssigned:1098985 NegativeStrandReadsAssigned:187116 Dataset is classified positive stranded MeadianReadLen=29 20thPercentileLength=24 echo kmer=19 SRR8846554 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: 52,972 [index] number of k-mers: 65,492,969 [index] number of equivalence classes: 320,172 [quant] running in single-end mode [quant] will process file 1: SRR8846554-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,948,182 reads, 3,224,492 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 912 rounds 52973 SRR8846554.ke.tsv 35125 SRR8846554.se.tsv 88098 total ==> SRR8846554.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0.5305 0.233225 PNS24249 1928 1829 0 0 PNS24246 1044 945 0.5305 0.233225 PNS24248 1044 945 0.5305 0.233225 PNS24244 1471 1372 9.4085 2.84897 PNS24243 293 194 0 0 KQK14069 1603 1504 229.69 63.4478 KQK14071 474 375 5.10322 5.65372 ==> SRR8846554.se.tsv <== BRADI_1g14170v3 338 BRADI_1g53295v3 2 BRADI_1g59795v3 20 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 53 BRADI_1g74790v3 13 BRADI_1g09890v3 0 BRADI_1g77505v3 9 BRADI_1g48960v3 0 SRR8846554 completed mapping pipeline successfully