Starting /dee2/code/volunteer_pipeline.sh SRR8846491 current disk space = 1501801598976 free memory = 1404932456 SRR8846491 SRAfilesize 59db116d42344399fd117d6f81a90d18 SRR8846491.sra SRR8846491.sra file validated SRR8846491 is single end SRR8846491 is conventional basespace SRR8846491 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR8846491_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 46 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.24025 34.0 33.0 34.0 31.0 34.0 2 32.86 34.0 33.0 34.0 31.0 34.0 3 32.993 34.0 33.0 34.0 32.0 34.0 4 33.16575 34.0 33.0 34.0 32.0 34.0 5 33.163 34.0 33.0 34.0 32.0 34.0 6 36.8385 38.0 37.0 38.0 35.0 38.0 7 37.165 38.0 38.0 38.0 36.0 38.0 8 37.333 38.0 38.0 38.0 37.0 38.0 9 37.3645 38.0 38.0 38.0 37.0 38.0 10-11 37.467 38.0 38.0 38.0 37.0 38.0 12-13 37.534625000000005 38.0 38.0 38.0 37.5 38.0 14-15 37.432125 38.0 38.0 38.0 37.0 38.0 16-17 37.438625 38.0 38.0 38.0 37.0 38.0 18-19 37.466625 38.0 38.0 38.0 37.0 38.0 20-21 37.42425 38.0 38.0 38.0 37.0 38.0 22-23 37.418875 38.0 38.0 38.0 37.0 38.0 24-25 37.449625 38.0 38.0 38.0 37.0 38.0 26-27 37.408125 38.0 38.0 38.0 37.0 38.0 28-29 37.381625 38.0 38.0 38.0 37.0 38.0 30-31 37.428625 38.0 38.0 38.0 37.0 38.0 32-33 37.328875 38.0 38.0 38.0 37.0 38.0 34-35 37.105875 38.0 38.0 38.0 36.0 38.0 36-37 37.053125 38.0 38.0 38.0 36.0 38.0 38-39 36.911625 38.0 38.0 38.0 35.5 38.0 40-41 37.178875 38.0 38.0 38.0 36.0 38.0 42-43 37.094875 38.0 38.0 38.0 36.0 38.0 44-45 37.0805 38.0 38.0 38.0 36.0 38.0 46-47 37.0005 38.0 38.0 38.0 36.0 38.0 48-49 37.089375000000004 38.0 38.0 38.0 36.0 38.0 50-51 37.12575 38.0 38.0 38.0 36.5 38.0 52-53 37.13975 38.0 38.0 38.0 36.0 38.0 54-55 36.989375 38.0 38.0 38.0 35.5 38.0 56-57 36.923500000000004 38.0 38.0 38.0 36.0 38.0 58-59 36.78625 38.0 38.0 38.0 35.0 38.0 60-61 36.679500000000004 38.0 38.0 38.0 34.0 38.0 62-63 36.176874999999995 38.0 37.0 38.0 32.0 38.0 64-65 36.040625 38.0 37.0 38.0 31.0 38.0 66-67 35.822500000000005 38.0 37.0 38.0 30.0 38.0 68-69 35.693875 38.0 37.0 38.0 29.0 38.0 70-71 35.6445 38.0 37.0 38.0 29.0 38.0 72-73 35.568875000000006 38.0 37.0 38.0 29.5 38.0 74-75 35.3215 38.0 36.5 38.0 28.5 38.0 76-77 35.181250000000006 38.0 36.0 38.0 28.0 38.0 78-79 35.10375 38.0 36.0 38.0 28.0 38.0 80-81 34.6415 38.0 35.5 38.0 27.0 38.0 82-83 34.861375 38.0 36.0 38.0 27.0 38.0 84-85 34.672375 38.0 36.0 38.0 27.0 38.0 86-87 34.845625 38.0 36.0 38.0 27.5 38.0 88-89 34.772875 38.0 36.0 38.0 27.0 38.0 90-91 34.278875 38.0 35.0 38.0 25.5 38.0 92-93 33.945875 38.0 35.0 38.0 24.0 38.0 94-95 32.921625 38.0 34.5 38.0 14.5 38.0 96-97 30.5415 38.0 31.0 38.0 2.0 38.0 98-99 27.43175 37.0 13.5 38.0 2.0 38.0 100-101 24.43275 35.0 2.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 0.0 20 1.0 21 6.0 22 2.0 23 6.0 24 13.0 25 24.0 26 33.0 27 22.0 28 27.0 29 32.0 30 47.0 31 86.0 32 131.0 33 192.0 34 355.0 35 564.0 36 1007.0 37 1451.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 31.893333333333334 26.74666666666667 20.48 20.880000000000003 2 28.1 27.625 17.025000000000002 27.250000000000004 3 29.099999999999998 20.375 17.7 32.824999999999996 4 28.999999999999996 33.475 15.325 22.2 5 27.775 26.6 23.5 22.125 6 25.93148287071768 23.93098274568642 25.681420355088775 24.456114028507127 7 34.525 25.624999999999996 17.1 22.75 8 21.25 22.325 32.95 23.474999999999998 9 24.55 32.65 22.525000000000002 20.275000000000002 10-11 28.962500000000002 23.6625 25.3 22.075 12-13 23.1875 21.925 23.875 31.0125 14-15 24.3625 36.1125 19.8375 19.6875 16-17 23.95 27.35 29.675 19.025 18-19 32.3625 24.7375 20.2875 22.6125 20-21 22.75 27.762500000000003 25.924999999999997 23.5625 22-23 28.599999999999998 28.1875 27.875 15.3375 24-25 28.8875 26.125 26.9625 18.025 26-27 29.562500000000004 28.525 24.325 17.5875 28-29 23.05 25.374999999999996 28.0875 23.4875 30-31 27.200000000000003 18.224999999999998 34.8125 19.7625 32-33 26.137500000000003 18.1125 32.5625 23.1875 34-35 33.7125 14.2125 30.175 21.9 36-37 36.6875 16.75 26.150000000000002 20.4125 38-39 33.800000000000004 18.825 26.05 21.325 40-41 31.05 19.2 22.175 27.575 42-43 32.074999999999996 25.4375 19.0125 23.474999999999998 44-45 37.675 22.8 13.325000000000001 26.200000000000003 46-47 29.462500000000002 30.175 15.299999999999999 25.0625 48-49 26.237500000000004 25.337500000000002 16.6875 31.7375 50-51 21.3875 28.7 15.287500000000001 34.625 52-53 23.525 31.275 13.6625 31.5375 54-55 18.987499999999997 31.275 17.1 32.6375 56-57 18.912499999999998 29.525000000000002 19.4375 32.125 58-59 15.412500000000001 27.075 22.35 35.1625 60-61 13.0625 26.2625 26.700000000000003 33.975 62-63 13.475000000000001 22.425 25.924999999999997 38.175 64-65 11.725 23.8875 31.674999999999997 32.7125 66-67 13.2875 20.2125 31.15 35.35 68-69 16.525000000000002 19.9125 32.7125 30.85 70-71 16.2625 17.4625 34.0625 32.2125 72-73 19.787499999999998 14.0625 34.0375 32.1125 74-75 15.725 12.662499999999998 33.5125 38.1 76-77 20.775 9.45 39.925 29.849999999999998 78-79 17.7375 8.575000000000001 39.35 34.3375 80-81 20.724999999999998 9.3625 38.75 31.162499999999998 82-83 19.8125 10.2625 41.712500000000006 28.212500000000002 84-85 20.474999999999998 14.0375 37.5375 27.950000000000003 86-87 19.3875 22.95 35.0875 22.575 88-89 13.7625 37.974999999999994 30.7 17.5625 90-91 13.025 47.3 26.174999999999997 13.5 92-93 10.7125 58.3875 18.9 12.0 94-95 9.725 66.725 16.4375 7.112499999999999 96-97 6.3 76.5 11.837499999999999 5.3625 98-99 5.2 83.25 7.3 4.25 100-101 2.9375 87.275 5.3374999999999995 4.45 >>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 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 0.0 31 0.0 32 1.5 33 4.0 34 4.5 35 4.0 36 6.0 37 13.0 38 18.0 39 38.5 40 68.5 41 117.5 42 180.5 43 231.5 44 292.5 45 328.5 46 414.0 47 457.0 48 365.5 49 331.0 50 333.5 51 257.5 52 145.0 53 85.0 54 77.0 55 101.0 56 74.5 57 20.0 58 11.0 59 9.0 60 7.0 61 2.0 62 0.5 63 0.5 64 0.5 65 0.0 66 0.0 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 6.25 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 61.625 #Duplication Level Percentage of deduplicated Percentage of total 1 86.36916835699797 53.225 2 6.206896551724138 7.6499999999999995 3 2.434077079107505 4.5 4 1.5821501014198782 3.9 5 0.8519269776876268 2.625 6 0.5273833671399595 1.95 7 0.2839756592292089 1.225 8 0.2839756592292089 1.4000000000000001 9 0.2434077079107505 1.35 >10 1.0141987829614605 12.35 >50 0.16227180527383367 7.249999999999999 >100 0.04056795131845842 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 GGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 103 2.5749999999999997 No Hit GGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 83 2.075 RNA PCR Primer, Index 1 (100% over 22bp) TCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 78 1.95 RNA PCR Primer, Index 1 (100% over 29bp) AGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 65 1.625 No Hit TCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 64 1.6 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTGGAATTCTCGGGTGCC 49 1.225 No Hit GACACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAA 44 1.0999999999999999 RNA PCR Primer, Index 1 (100% over 23bp) GACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAAC 38 0.95 RNA PCR Primer, Index 1 (100% over 24bp) AGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGG 27 0.675 Illumina Small RNA Adapter 2 (100% over 21bp) TGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAA 25 0.625 No Hit GCCCACCCCAAGATGAGTGCTCTCTCTGGAATTCTCGGGTGCCAAGGAAC 24 0.6 RNA PCR Primer, Index 1 (100% over 24bp) GGGATTGTAGTTCAATTGGTCAGAGCACCTGGAATTCTCGGGTGCCAAGG 23 0.575 Illumina Small RNA Adapter 2 (100% over 21bp) GACACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACT 22 0.5499999999999999 RNA PCR Primer, Index 1 (100% over 25bp) GCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCC 21 0.525 No Hit TTCGGACCAGGCTTCATTCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 20 0.5 RNA PCR Primer, Index 1 (100% over 29bp) CTCTGATGATGATCAAACTAATACTTTCGTTCTTCTGGAATTCTCGGGTG 20 0.5 No Hit CACGACTCTCGGCAACGGATATCTCGGCTCTCGCATCGATGATGGAATTC 19 0.475 No Hit CTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCCGTCTTC 16 0.4 RNA PCR Primer, Index 14 (100% over 50bp) CATCGAGTAGACCTTGTTATTGTGAGAATATGGAATTCTCGGGTGCCAAG 16 0.4 No Hit GAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAG 15 0.375 No Hit GAAGTCCTCGTGTTGCATTCCTTGGAATTCTCGGGTGCCAAGGAACTCCA 14 0.35000000000000003 RNA PCR Primer, Index 1 (100% over 28bp) CATCGAGTAGACCTTGTTATTGTGAGAATTTGGAATTCTCGGGTGCCAAG 13 0.325 No Hit GACACGACTCTCGGCAACGTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 12 0.3 RNA PCR Primer, Index 1 (100% over 31bp) CACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGAAC 12 0.3 RNA PCR Primer, Index 1 (100% over 24bp) GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCCTGGAATTCTCGGGTGC 11 0.27499999999999997 No Hit TCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCCGTCTT 11 0.27499999999999997 RNA PCR Primer, Index 14 (100% over 50bp) TCCGTCGTAGTCTAGGTGGTTAGGATATGGAATTCTCGGGTGCCAAGGAA 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 23bp) ATATATTTCAAGTTATTTCGGATCTTGGAATTCTCGGGTGCCAAGGAACT 11 0.27499999999999997 RNA PCR Primer, Index 1 (100% over 25bp) AATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCCGT 10 0.25 RNA PCR Primer, Index 14 (100% over 50bp) GACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGGA 10 0.25 RNA PCR Primer, Index 1 (100% over 22bp) TCCGTCGTAGTCTAGGTGGTTAGGATACTCTGGAATTCTCGGGTGCCAAG 9 0.22499999999999998 No Hit CTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCA 9 0.22499999999999998 RNA PCR Primer, Index 1 (100% over 28bp) ATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCCGTC 9 0.22499999999999998 RNA PCR Primer, Index 14 (100% over 50bp) NGGATTGTAGTTCAATTGGTCAGAGCACCGCCTGGAATTCTCGGGTGCCA 9 0.22499999999999998 No Hit ACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGC 9 0.22499999999999998 No Hit CTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCA 9 0.22499999999999998 No Hit CAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTG 8 0.2 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTGGAATTCTCGGGTGCCAAGG 8 0.2 Illumina Small RNA Adapter 2 (100% over 21bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTGGAATTCTCGGGTGCCA 8 0.2 No Hit GCGAGCGTAGTTCAATGGTAAAACATCTCCTTTGGAATTCTCGGGTGCCA 8 0.2 No Hit ACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCC 8 0.2 No Hit CAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTC 8 0.2 RNA PCR Primer, Index 1 (100% over 26bp) CAGGGTTCGTTTCCCTGGATGCGCACCATGGAATTCTCGGGTGCCAAGGA 8 0.2 RNA PCR Primer, Index 1 (100% over 22bp) CACGACTCTCGGCAACGGATATCTCTGGAATTCTCGGGTGCCAAGGAACT 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 25bp) CGACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAA 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 23bp) GCACCAGTGGTCTAGTGGTAGAATAGTACCTGGAATTCTCGGGTGCCAAG 7 0.17500000000000002 No Hit NCGGACCAGGCTTCATTCCCCTGGAATTCTCGGGTGCCAAGGAACTCCAG 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 29bp) CACGACTCTCGGCAACGGATATCTGGAATTCTCGGGTGCCAAGGAACTCC 7 0.17500000000000002 RNA PCR Primer, Index 1 (100% over 27bp) CCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGG 7 0.17500000000000002 No Hit GCCTTGATGGTGAAATGGTAGACACGCGAGACTCATGGAATTCTCGGGTG 7 0.17500000000000002 No Hit NCCACTGAGATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGT 6 0.15 No Hit CGGATAACCGTAGTAATTCTAGAGCTAATACGTGGAATTCTCGGGTGCCA 6 0.15 No Hit GGCGGATGTAGCCAAGTGGATCAAGGCAGTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) CAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGG 6 0.15 No Hit ACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAG 6 0.15 RNA PCR Primer, Index 2 (97% over 35bp) AGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) GACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTG 6 0.15 No Hit CGACACGACTCTCGGCAACGGATATCTCGTGGAATTCTCGGGTGCCAAGG 6 0.15 Illumina Small RNA Adapter 2 (100% over 21bp) CGACACGACTCTCGGCAACGGATGGAATTCTCGGGTGCCAAGGAACTCCA 6 0.15 RNA PCR Primer, Index 1 (100% over 28bp) GCGACCCCAGGTCAGGCGGGACTTGGAATTCTCGGGTGCCAAGGAACTCC 6 0.15 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGATGGAATTCTCGGGTGCCAAGGAA 6 0.15 RNA PCR Primer, Index 1 (100% over 23bp) GCGAGCGTAGTTCAATGGTAAAACATCTCCTTGCCAAGGATGGAATTCTC 6 0.15 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTGGAATTCTCGGGTGC 6 0.15 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTTTACACTGGAATTCTCG 5 0.125 No Hit NGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGA 5 0.125 RNA PCR Primer, Index 1 (100% over 22bp) GCAGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGT 5 0.125 No Hit GCTATGAGATCCGAGGGACTGGAATTCTCGGGTGCCAAGGAACTCCAGTC 5 0.125 RNA PCR Primer, Index 1 (100% over 31bp) ATAACCGTAGTAATTCTAGAGCTAATTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) CATAGCAAGGATTGACAGACTGAGAGCTCTTTCTGGAATTCTCGGGTGCC 5 0.125 No Hit TCCTGTGGATGAGAAGGCATTTATATTCTGATGATATGGAATTCTCGGGT 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) ATATATTTCAAGTTATTTCGGATCTGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) TCGTGACCCTGACCTGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGT 5 0.125 RNA PCR Primer, Index 8 (97% over 36bp) GATAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) ACACGACTCTCGGCAACGGATATCTTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) ATGCAGTTACTAATTCATGATCTGGCTGGAATTCTCGGGTGCCAAGGAAC 5 0.125 RNA PCR Primer, Index 1 (100% over 24bp) NGCTGAGGCATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGC 5 0.125 No Hit GGGGATATAGCTCAGTTGGTAGATGGAATTCTCGGGTGCCAAGGAACTCC 5 0.125 RNA PCR Primer, Index 1 (100% over 27bp) CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATGGAATTCTCGGGTG 5 0.125 No Hit ATCCTAACGAACGAACGATTTGAACTGGAATTCTCGGGTGCCAAGGAACT 5 0.125 RNA PCR Primer, Index 1 (100% over 25bp) ATCCAGCCCCACGTCGCACGGATTCGTTGGAATTCTCGGGTGCCAAGGAA 5 0.125 RNA PCR Primer, Index 1 (100% over 23bp) TAACCGTAGTAATTCTAGAGCTAATGGAATTCTCGGGTGCCAAGGAACTC 5 0.125 RNA PCR Primer, Index 1 (100% over 26bp) GCCTTGATGGTGAAATGGTAGACACGCGAGACTCAAAATCTGGAATTCTC 5 0.125 No Hit GGGATTGTAGTTCAATTGGTCAGAGCACCGCCCTTGGAATTCTCGGGTGC 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 0.025 0.0 0.0 0.0 2 0.0 0.025 0.0 0.0 0.0 3 0.0 0.025 0.0 0.0 0.0 4 0.0 0.025 0.0 0.0 0.0 5 0.0 0.05 0.0 0.0 0.0 6 0.0 0.05 0.0 0.0 0.0 7 0.0 0.075 0.0 0.0 0.0 8 0.0 0.075 0.0 0.0 0.0 9 0.0 0.1 0.0 0.0 0.0 10-11 0.0 0.15 0.0 0.0 0.0 12-13 0.0 0.1875 0.0 0.0 0.0 14-15 0.0 0.6625 0.0 0.0 0.0 16-17 0.0 1.8 0.0 0.0 0.0 18-19 0.0 3.6625 0.0 0.0 0.0 20-21 0.0 7.2875 0.0 0.0 0.0 22-23 0.0 16.9375 0.0 0.0 0.0 24-25 0.0 28.425 0.0 0.0 0.0 26-27 0.0 40.849999999999994 0.0 0.0 0.0 28-29 0.0 51.537499999999994 0.0 0.0 0.0 30-31 0.0 61.65 0.0 0.0 0.0 32-33 0.0 70.5625 0.0 0.0 0.0 34-35 0.0 80.38749999999999 0.0 0.0 0.0 36-37 0.0 87.5625 0.0 0.0 0.0 38-39 0.0 91.05 0.0 0.0 0.0 40-41 0.0 92.9375 0.0 0.0 0.0 42-43 0.0 94.45 0.0 0.0 0.0 44-45 0.0 95.42500000000001 0.0 0.0 0.0 46-47 0.0 95.575 0.0 0.0 0.0 48-49 0.0 95.6 0.0 0.0 0.0 50-51 0.0 95.6875 0.0 0.0 0.0 52-53 0.0 95.7 0.0 0.0 0.0 54-55 0.0 95.725 0.0 0.0 0.0 56-57 0.0 95.725 0.0 0.0 0.0 58-59 0.0 95.725 0.0 0.0 0.0 60-61 0.0 95.725 0.0 0.0 0.0 62-63 0.0 95.725 0.0 0.0 0.0 64-65 0.0 95.725 0.0 0.0 0.0 66-67 0.0 95.725 0.0 0.0 0.0 68-69 0.0 95.725 0.0 0.0 0.0 70-71 0.0 95.725 0.0 0.0 0.0 72-73 0.0 95.725 0.0 0.0 0.0 74-75 0.0 95.725 0.0 0.0 0.0 76-77 0.0 95.725 0.0 0.0 0.0 78-79 0.0 95.725 0.0 0.0 0.0 80-81 0.0 95.7375 0.0 0.0 0.0 82-83 0.0 95.75 0.0 0.0 0.0 84-85 0.0 95.775 0.0 0.0 0.0 86-87 0.0 95.775 0.0 0.0 0.0 88-89 0.0 95.775 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCGGACC 25 2.3796383E-7 102.62162 1 GACACGA 15 4.4910912E-4 102.62162 1 GGGATTG 25 2.3796383E-7 102.62162 1 ACACGAC 20 1.545283E-5 94.924995 2 TTGTAGT 25 3.8470353E-7 94.924995 5 GGACCAG 25 3.8470353E-7 94.924995 3 GGATTGT 25 3.8470353E-7 94.924995 2 CACGACT 20 1.545283E-5 94.924995 3 CGGACCA 25 3.8470353E-7 94.924995 2 GATTGTA 25 3.8470353E-7 94.924995 3 TAGTTCA 25 3.8470353E-7 94.924995 8 ATTGTAG 25 3.8470353E-7 94.924995 4 AGGCTTC 25 3.8470353E-7 94.924995 8 TGTAGTT 25 3.8470353E-7 94.924995 6 GGCTTCA 25 3.8470353E-7 94.924995 9 CAGGCTT 25 3.8470353E-7 94.924995 7 AGTTCAA 25 3.8470353E-7 94.924995 9 GACCAGG 25 3.8470353E-7 94.924995 4 GTAGTTC 25 3.8470353E-7 94.924995 7 CCAGGCT 25 3.8470353E-7 94.924995 6 >>END_MODULE Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra Rejected 833245 READS because READLEN < 1 Read 833245 spots for SRR8846491.sra Written 833245 spots for SRR8846491.sra SRR ids: ['SRR8846491.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_zpy8cyob SRR8846491.sra spots: 16664900 blocks: [[1, 833245], [833246, 1666490], [1666491, 2499735], [2499736, 3332980], [3332981, 4166225], [4166226, 4999470], [4999471, 5832715], [5832716, 6665960], [6665961, 7499205], [7499206, 8332450], [8332451, 9165695], [9165696, 9998940], [9998941, 10832185], [10832186, 11665430], [11665431, 12498675], [12498676, 13331920], [13331921, 14165165], [14165166, 14998410], [14998411, 15831655], [15831656, 16664900]] SRR8846491 file size 3998055 SRR8846491 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 SRR8846491 SRR8846491_1.fastq Input file: SRR8846491_1.fastq trimmed: SRR8846491-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 Sun Dec 8 21:03:43 2024 >> started Sun Dec 8 21:04:27 2024 >> done (43.708s) 16664900 reads processed; of these: 337 ( 0.00%) short reads filtered out after trimming by size control 45 ( 0.00%) empty reads filtered out after trimming by size control 16664518 (100.00%) reads available; of these: 4271802 (25.63%) trimmed reads available after processing 12392716 (74.37%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 38 0.00% 19 28 0.00% 20 41 0.00% 21 45 0.00% 22 39 0.00% 23 46 0.00% 24 62 0.00% 25 85 0.00% 26 139 0.00% 27 194 0.00% 28 268 0.00% 29 299 0.00% 30 261 0.00% 31 207 0.00% 32 204 0.00% 33 172 0.00% 34 196 0.00% 35 140 0.00% 36 172 0.00% 37 156 0.00% 38 183 0.00% 39 160 0.00% 40 167 0.00% 41 155 0.00% 42 143 0.00% 43 141 0.00% 44 147 0.00% 45 145 0.00% 46 137 0.00% 47 127 0.00% 48 104 0.00% 49 106 0.00% 50 106 0.00% 51 124 0.00% 52 109 0.00% 53 164 0.00% 54 158 0.00% 55 163 0.00% 56 212 0.00% 57 215 0.00% 58 300 0.00% 59 365 0.00% 60 503 0.00% 61 939 0.01% 62 1354 0.01% 63 1656 0.01% 64 2591 0.02% 65 3847 0.02% 66 7892 0.05% 67 38188 0.23% 68 41453 0.25% 69 30134 0.18% 70 26919 0.16% 71 33287 0.20% 72 14904 0.09% 73 5132 0.03% 74 5299 0.03% 75 3488 0.02% 76 3145 0.02% 77 3341 0.02% 78 3836 0.02% 79 4334 0.03% 80 5049 0.03% 81 5979 0.04% 82 8617 0.05% 83 8963 0.05% 84 10594 0.06% 85 13402 0.08% 86 16575 0.10% 87 23852 0.14% 88 45562 0.27% 89 67880 0.41% 90 89056 0.53% 91 103814 0.62% 92 132369 0.79% 93 187613 1.13% 94 244407 1.47% 95 407707 2.45% 96 482261 2.89% 97 498878 2.99% 98 664497 3.99% 99 640093 3.84% 100 375969 2.26% 101 12392716 74.37% 16664518 reads passed initial QC criterion=sequence-density sequence-density=94.99 sequence-density-rank=1 fanout-score=32.60 fanout-score-rank=2 prefix-density=95.39 prefix-fanout=32.5 sequence=TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=1.39 sequence-density-rank=6 fanout-score=71.13 fanout-score-rank=1 prefix-density=98.44 prefix-fanout=1.0 sequence=CACAGTTCCATATCGTATGCCGT 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 TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR8846491 - Input file: STDIN trimmed: SRR8846491-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): TGGAATTCTCGGGTGCCAAGGAACTCCAGTCACAGTTCCATCTCGTATGCCGTCTTCTGCTTGA -- 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 Sun Dec 8 21:07:20 2024 >> started Sun Dec 8 21:08:38 2024 >> done (77.980s) 16313686 reads processed; of these: 515218 ( 3.16%) short reads filtered out after trimming by size control 9000 ( 0.06%) empty reads filtered out after trimming by size control 15789468 (96.79%) reads available; of these: 15366270 (97.32%) trimmed reads available after processing 423198 ( 2.68%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 185978 1.18% 19 308069 1.95% 20 327493 2.07% 21 945186 5.99% 22 589677 3.73% 23 709944 4.50% 24 1691147 10.71% 25 765677 4.85% 26 918474 5.82% 27 825170 5.23% 28 995039 6.30% 29 785306 4.97% 30 728940 4.62% 31 575604 3.65% 32 1007581 6.38% 33 832724 5.27% 34 775129 4.91% 35 548180 3.47% 36 618388 3.92% 37 262700 1.66% 38 207733 1.32% 39 169802 1.08% 40 140139 0.89% 41 156836 0.99% 42 143612 0.91% 43 52189 0.33% 44 42566 0.27% 45 19882 0.13% 46 10020 0.06% 47 5077 0.03% 48 4048 0.03% 49 2321 0.01% 50 1590 0.01% 51 1340 0.01% 52 761 0.00% 53 613 0.00% 54 730 0.00% 55 308 0.00% 56 369 0.00% 57 265 0.00% 58 282 0.00% 59 345 0.00% 60 459 0.00% 61 912 0.01% 62 1250 0.01% 63 1530 0.01% 64 2393 0.02% 65 3585 0.02% 66 7497 0.05% 67 37063 0.23% 68 40254 0.25% 69 29100 0.18% 70 25971 0.16% 71 31994 0.20% 72 13156 0.08% 73 3575 0.02% 74 2049 0.01% 75 1390 0.01% 76 1631 0.01% 77 3081 0.02% 78 1704 0.01% 79 1893 0.01% 80 2852 0.02% 81 2212 0.01% 82 1999 0.01% 83 2892 0.02% 84 1512 0.01% 85 1274 0.01% 86 1254 0.01% 87 999 0.01% 88 905 0.01% 89 1160 0.01% 90 970 0.01% 91 994 0.01% 92 1085 0.01% 93 1226 0.01% 94 1605 0.01% 95 2392 0.02% 96 2826 0.02% 97 3887 0.02% 98 5688 0.04% 99 6309 0.04% 100 8185 0.05% 101 169521 1.07% criterion=sequence-density sequence-density=2.55 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=18 prefix-density=0.00 prefix-fanout=1.0 sequence=CATCGAGTAGACCTTGTTATTGTGAGAATTCTTAATTCAAGA criterion=fanout-score sequence-density=0.01 sequence-density-rank=38 fanout-score=67.41 fanout-score-rank=1 prefix-density=0.37 prefix-fanout=1.0 sequence=GTAGCCAAGTGCGGAGAGGATAACTGCTGAAAGCATATAAGTAGTAAGCCCACCCCAAGATGAGTGCTCTCTCCTC Started job on | Dec 08 21:10:59 Started mapping on | Dec 08 21:11:00 Finished on | Dec 08 21:17:53 Mapping speed, Million of reads per hour | 140.69 Number of input reads | 16140300 Average input read length | 31 UNIQUE READS: Uniquely mapped reads number | 2268579 Uniquely mapped reads % | 14.06% Average mapped length | 26.35 Number of splices: Total | 36648 Number of splices: Annotated (sjdb) | 23252 Number of splices: GT/AG | 34133 Number of splices: GC/AG | 1961 Number of splices: AT/AC | 21 Number of splices: Non-canonical | 533 Mismatch rate per base, % | 0.16% Deletion rate per base | 0.00% Deletion average length | 1.32 Insertion rate per base | 0.00% Insertion average length | 1.03 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 6259436 % of reads mapped to multiple loci | 38.78% Number of reads mapped to too many loci | 6616143 % of reads mapped to too many loci | 40.99% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.67% % of reads unmapped: other | 0.50% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7612285 7612285 7612285 N_multimapping 6259436 6259436 6259436 N_noFeature 1352223 1502609 2103786 N_ambiguous 36709 21934 490 UnstrandedReadsAssigned:879647 PositiveStrandReadsAssigned:744036 NegativeStrandReadsAssigned:164303 Dataset is classified unstranded MeadianReadLen=28 20thPercentileLength=24 echo kmer=19 SRR8846491 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: SRR8846491-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,140,300 reads, 3,858,361 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,065 rounds 52973 SRR8846491.ke.tsv 35125 SRR8846491.se.tsv 88098 total ==> SRR8846491.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 9 1.73007 PNS24243 293 194 0 0 KQK14069 1603 1504 85.0406 14.9126 KQK14071 474 375 0 0 ==> SRR8846491.se.tsv <== BRADI_1g14170v3 85 BRADI_1g53295v3 2 BRADI_1g59795v3 5 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 42 BRADI_1g74790v3 39 BRADI_1g09890v3 3 BRADI_1g77505v3 3 BRADI_1g48960v3 0 SRR8846491 completed mapping pipeline successfully