Starting /dee2/code/volunteer_pipeline.sh SRR6127926 current disk space = 1526343606272 free memory = 1562969776 SRR6127926 SRAfilesize fe82d3f10b2df87705ec4bdc1430fc3b SRR6127926.sra SRR6127926.sra file validated SRR6127926 is paired end SRR6127926 is conventional basespace SRR6127926 read1 length is 100 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6127926_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 100 %GC 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.23575 33.0 33.0 33.0 33.0 33.0 2 32.39325 33.0 33.0 33.0 33.0 33.0 3 32.69375 33.0 33.0 33.0 33.0 33.0 4 36.71925 37.0 37.0 37.0 37.0 37.0 5 36.726 37.0 37.0 37.0 37.0 37.0 6 36.61675 37.0 37.0 37.0 37.0 37.0 7 36.628 37.0 37.0 37.0 37.0 37.0 8 36.6345 37.0 37.0 37.0 37.0 37.0 9 36.628 37.0 37.0 37.0 37.0 37.0 10-11 36.614875 37.0 37.0 37.0 37.0 37.0 12-13 36.593 37.0 37.0 37.0 37.0 37.0 14-15 38.912499999999994 40.0 40.0 40.0 37.0 40.0 16-17 38.915125 40.0 40.0 40.0 37.0 40.0 18-19 38.864374999999995 40.0 40.0 40.0 37.0 40.0 20-21 38.8575 40.0 40.0 40.0 37.0 40.0 22-23 38.733625 40.0 38.5 40.0 37.0 40.0 24-25 38.574124999999995 40.0 37.0 40.0 37.0 40.0 26-27 38.534625000000005 40.0 37.0 40.0 37.0 40.0 28-29 38.5095 40.0 37.0 40.0 37.0 40.0 30-31 38.438500000000005 40.0 37.0 40.0 37.0 40.0 32-33 38.419375 40.0 37.0 40.0 37.0 40.0 34-35 38.343625 40.0 37.0 40.0 37.0 40.0 36-37 38.244125 40.0 37.0 40.0 37.0 40.0 38-39 38.028875 40.0 37.0 40.0 37.0 40.0 40-41 37.897 40.0 37.0 40.0 35.0 40.0 42-43 37.547375 40.0 37.0 40.0 33.0 40.0 44-45 37.488875 40.0 37.0 40.0 33.0 40.0 46-47 37.294375 40.0 37.0 40.0 33.0 40.0 48-49 37.254000000000005 40.0 37.0 40.0 33.0 40.0 50-51 37.014375 40.0 37.0 40.0 33.0 40.0 52-53 36.7315 37.0 37.0 40.0 33.0 40.0 54-55 36.15275 37.0 37.0 40.0 33.0 40.0 56-57 36.16675 37.0 37.0 40.0 33.0 40.0 58-59 35.87975 37.0 37.0 40.0 33.0 40.0 60-61 35.589875 37.0 37.0 40.0 33.0 40.0 62-63 35.434875000000005 37.0 37.0 40.0 33.0 40.0 64-65 35.258250000000004 37.0 35.0 37.0 33.0 40.0 66-67 34.843 37.0 33.0 37.0 27.0 40.0 68-69 34.611 37.0 33.0 37.0 27.0 40.0 70-71 34.332 37.0 33.0 37.0 27.0 40.0 72-73 34.039375 37.0 33.0 37.0 27.0 38.5 74-75 33.573125000000005 37.0 33.0 37.0 27.0 37.0 76-77 30.9055 33.0 30.0 35.0 22.0 37.0 78-79 32.650125 37.0 33.0 37.0 27.0 37.0 80-81 32.85825 37.0 33.0 37.0 27.0 37.0 82-83 32.961124999999996 37.0 33.0 37.0 27.0 37.0 84-85 32.954 37.0 33.0 37.0 27.0 37.0 86-87 32.780874999999995 37.0 33.0 37.0 27.0 37.0 88-89 32.599875 37.0 33.0 37.0 24.5 37.0 90-91 32.695 37.0 33.0 37.0 27.0 37.0 92-93 32.349125 37.0 33.0 37.0 22.0 37.0 94-95 32.18475 37.0 33.0 37.0 22.0 37.0 96-97 31.87125 37.0 33.0 37.0 22.0 37.0 98-99 31.4805 37.0 33.0 37.0 15.0 37.0 100 27.63825 33.0 27.0 33.0 2.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 2.0 9 3.0 10 5.0 11 9.0 12 3.0 13 3.0 14 5.0 15 7.0 16 8.0 17 5.0 18 10.0 19 15.0 20 18.0 21 11.0 22 18.0 23 16.0 24 16.0 25 32.0 26 38.0 27 43.0 28 35.0 29 36.0 30 69.0 31 79.0 32 107.0 33 112.0 34 175.0 35 284.0 36 573.0 37 1383.0 38 880.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.11704834605598 13.231552162849871 8.040712468193384 40.61068702290076 2 23.05 16.5 35.65 24.8 3 21.175 21.325 24.95 32.550000000000004 4 27.375 28.675 21.349999999999998 22.6 5 26.1 31.3 23.849999999999998 18.75 6 19.45 33.074999999999996 25.775 21.7 7 16.225 20.1 42.275 21.4 8 20.225 19.2 29.799999999999997 30.775000000000002 9 20.125 19.6 31.874999999999996 28.4 10-11 24.0625 28.812500000000004 22.075 25.05 12-13 23.5375 22.3125 27.5875 26.5625 14-15 21.475 25.624999999999996 27.425 25.474999999999998 16-17 23.0125 24.587500000000002 25.9625 26.437500000000004 18-19 23.9 23.95 27.075 25.074999999999996 20-21 23.200000000000003 24.712500000000002 26.487500000000004 25.6 22-23 23.75 23.9 26.387500000000003 25.9625 24-25 23.200000000000003 24.4375 25.662499999999998 26.700000000000003 26-27 23.175 24.925 26.5875 25.3125 28-29 22.6875 23.9 27.187499999999996 26.224999999999998 30-31 22.6875 24.975 26.5 25.837500000000002 32-33 22.9875 25.2375 25.412499999999998 26.3625 34-35 22.8875 23.9125 26.887499999999996 26.3125 36-37 23.375 24.8625 25.7375 26.025 38-39 23.225 23.3125 26.025 27.437499999999996 40-41 24.8 24.224999999999998 25.624999999999996 25.35 42-43 25.05 24.5375 25.7125 24.7 44-45 24.1875 24.925 26.387500000000003 24.5 46-47 23.9125 24.4375 24.9875 26.6625 48-49 23.625 23.400000000000002 26.8625 26.1125 50-51 23.1875 24.5 26.087500000000002 26.224999999999998 52-53 23.9875 23.7625 26.137500000000003 26.1125 54-55 24.0 23.75 26.2625 25.9875 56-57 21.8125 24.9 26.3625 26.924999999999997 58-59 23.5625 24.6 26.525 25.3125 60-61 22.8 24.5 26.5 26.200000000000003 62-63 22.6375 24.1375 27.200000000000003 26.025 64-65 23.3375 25.424999999999997 25.4375 25.8 66-67 23.025000000000002 24.275 25.474999999999998 27.224999999999998 68-69 23.175 24.462500000000002 25.412499999999998 26.950000000000003 70-71 24.3 24.55 25.1875 25.9625 72-73 24.087500000000002 23.8375 25.75 26.325 74-75 24.2 23.8625 25.55 26.387500000000003 76-77 24.625 23.849999999999998 25.112499999999997 26.4125 78-79 23.4875 24.725 25.837500000000002 25.95 80-81 23.150000000000002 23.925 26.5 26.424999999999997 82-83 23.775 23.825 25.5625 26.8375 84-85 24.075 22.95 25.275 27.700000000000003 86-87 23.875 23.2125 26.224999999999998 26.687499999999996 88-89 23.925 23.799999999999997 25.900000000000002 26.375 90-91 24.224999999999998 23.8375 25.7125 26.224999999999998 92-93 23.1125 24.8125 26.224999999999998 25.85 94-95 23.6625 24.625 25.525 26.187500000000004 96-97 22.0 25.337500000000002 25.7125 26.950000000000003 98-99 24.025 24.0125 25.5375 26.424999999999997 100 24.975 24.349999999999998 23.775 26.900000000000002 >>END_MODULE >>Per sequence GC content fail #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 0.5 21 0.5 22 0.0 23 0.5 24 1.0 25 1.0 26 0.5 27 2.0 28 3.5 29 8.0 30 13.0 31 15.0 32 17.5 33 22.0 34 31.5 35 49.0 36 67.0 37 77.5 38 83.5 39 84.0 40 86.0 41 87.0 42 98.5 43 104.0 44 125.0 45 151.0 46 164.0 47 182.5 48 181.0 49 167.0 50 163.5 51 176.0 52 186.5 53 182.5 54 193.5 55 215.5 56 193.0 57 155.5 58 131.0 59 106.0 60 90.0 61 76.0 62 53.0 63 42.0 64 39.0 65 32.5 66 26.5 67 21.5 68 20.5 69 13.0 70 6.5 71 7.0 72 6.0 73 5.5 74 6.5 75 8.0 76 7.0 77 3.5 78 1.5 79 2.0 80 2.5 81 1.5 82 0.0 83 0.5 84 1.0 85 0.5 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 1.7500000000000002 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 94-95 0.0 96-97 0.0 98-99 0.0 100 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 100 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 84.425 #Duplication Level Percentage of deduplicated Percentage of total 1 88.77702102457803 74.95 2 7.373408350607049 12.45 3 2.132069884512881 5.4 4 0.8587503701510216 2.9000000000000004 5 0.3849570624814925 1.625 6 0.32573289902280134 1.6500000000000001 7 0.029612081729345572 0.17500000000000002 8 0.059224163458691144 0.4 9 0.059224163458691144 0.44999999999999996 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GTTGATACCGTCTGCGATAGGCTAGTTCATAAACGAGGGGCGATGCCCGG 9 0.22499999999999998 No Hit CTCGTTCTCGCCCGCTTTGCAAAAATATCTAATATCAATTGCGTGCGGTC 9 0.22499999999999998 No Hit CGGGGAACAGTCGCATGACGAGGCAGTTTCCAGAAACGTGTATCACATCT 8 0.2 No Hit GGAAGATCCTGAATAAATCCTACTGTATCTGAAAGAAGAACACTGTAGCC 8 0.2 No Hit CCGGGATCGGGCAAAGGGGCAACTCGAGCTAATCTCCCCAGCGGCTAGCA 7 0.17500000000000002 No Hit GTTGATTTCATGAATGCGATTTCTGATATGGCGGCGGTCGGTTTCCAGTT 6 0.15 No Hit GTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGA 6 0.15 No Hit CTTCACTTCAATTGCTGTTGCCAATGACTTCAGCTGACTTGGCGACAGTT 6 0.15 No Hit GTGGAAAGCTGTGTGTTGATTTCATGAATGCGATTTCTGATATGGCGGCG 6 0.15 No Hit GTAAAGGCTCCCACTTATCCTACACCTCTCAAGTCATTTCACAAAGTCGG 6 0.15 No Hit CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 6 0.15 No Hit CTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATTGAAGTA 6 0.15 No Hit GGTCAATCATCTTCACTTCAATTGCTGTTGCCAATGACTTCAGCTGACTT 6 0.15 No Hit GGGGTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATGG 6 0.15 No Hit GGAAGCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATTG 6 0.15 No Hit GGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTT 6 0.15 No Hit CAATCATCTTCACTTCAATTGCTGTTGCCAATGACTTCAGCTGACTTGGC 5 0.125 No Hit GTTCAGGGTTCCAAACTCATAGTGGCAACTAAACACGAGGGTTGCGCTCG 5 0.125 No Hit GGGCTTACTACTTATATGCTTTCAGCAGTTATCCTCTCCGCACTTGGCTA 5 0.125 No Hit CAGGGTTCCAAACTCATAGTGGCAACTAAACACGAGGGTTGCGCTCGTTG 5 0.125 No Hit GGCAGGTTCATTTTAAACGCGGTGACTAGGATGCTCATTTGAATGTCCCC 5 0.125 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 5 0.125 No Hit GCCTCACTTAGTTACAGTTTTATGGATAATTGGGATATTCTTTGGTATAG 5 0.125 No Hit GTCGGAAGATCCTGAATAAATCCTACTGTATCTGAAAGAAGAACACTGTA 5 0.125 No Hit GGACAACTGATGGACCCACGTTGCGAGTCCAGTAAATCAGGACGGGGATA 5 0.125 No Hit GTCGTCATTGCGCCAGCTCGTCAGCGCTGGTCGTCTACCAGCTCGATAAT 5 0.125 No Hit GGGATATTCTTTGGTATAGTTGGGATTTTAATATCATTAATAGCATGATG 5 0.125 No Hit GGATATTCTTTGGTATAGTTGGGATTTTAATATCATTAATAGCATGATGG 5 0.125 No Hit CCCAGCTCACGTACCGCATTAATGGGCGAACAGCCCAACCCTTGGAACCA 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 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.037500000000000006 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.23750000000000002 0.0 0.0 0.0 0.0 70-71 0.3375 0.0 0.0 0.0 0.0 72-73 0.4 0.0 0.0 0.0 0.0 74-75 0.5375 0.0 0.0 0.0 0.0 76-77 0.6 0.0 0.0 0.0 0.0 78-79 0.7 0.0 0.0 0.0 0.0 80-81 0.8999999999999999 0.0 0.0 0.0 0.0 82-83 1.1 0.0 0.0 0.0 0.0 84-85 1.4625 0.0 0.0 0.0 0.0 86-87 1.7875 0.0 0.0 0.0 0.0 88 2.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR6127926 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6127926_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.76125 33.0 33.0 33.0 27.0 33.0 2 31.87175 33.0 33.0 33.0 33.0 33.0 3 31.99275 33.0 33.0 33.0 33.0 33.0 4 35.55125 37.0 37.0 37.0 33.0 37.0 5 35.52025 37.0 37.0 37.0 33.0 37.0 6 35.46925 37.0 37.0 37.0 33.0 37.0 7 35.51375 37.0 37.0 37.0 33.0 37.0 8 35.62575 37.0 37.0 37.0 33.0 37.0 9 35.78775 37.0 37.0 37.0 37.0 37.0 10-11 35.8735 37.0 37.0 37.0 37.0 37.0 12-13 35.82575 37.0 37.0 37.0 37.0 37.0 14-15 38.09462499999999 40.0 37.0 40.0 37.0 40.0 16-17 38.062749999999994 40.0 37.0 40.0 37.0 40.0 18-19 38.0535 40.0 37.0 40.0 37.0 40.0 20-21 38.024375 40.0 37.0 40.0 37.0 40.0 22-23 37.2545 40.0 37.0 40.0 33.0 40.0 24-25 37.75475 40.0 37.0 40.0 35.0 40.0 26-27 37.854749999999996 40.0 37.0 40.0 37.0 40.0 28-29 37.758250000000004 40.0 37.0 40.0 37.0 40.0 30-31 37.71925 40.0 37.0 40.0 37.0 40.0 32-33 37.627125 40.0 37.0 40.0 33.0 40.0 34-35 37.650625 40.0 37.0 40.0 33.0 40.0 36-37 37.4995 40.0 37.0 40.0 33.0 40.0 38-39 37.40325 40.0 37.0 40.0 33.0 40.0 40-41 37.35225 40.0 37.0 40.0 33.0 40.0 42-43 37.204125000000005 40.0 37.0 40.0 33.0 40.0 44-45 36.982375 40.0 37.0 40.0 33.0 40.0 46-47 36.82025 40.0 37.0 40.0 33.0 40.0 48-49 36.69925 38.5 37.0 40.0 33.0 40.0 50-51 34.9985 37.0 35.0 38.5 30.0 40.0 52-53 35.267125 37.0 35.0 38.5 30.0 40.0 54-55 36.007374999999996 37.0 37.0 40.0 33.0 40.0 56-57 35.880250000000004 37.0 37.0 40.0 33.0 40.0 58-59 35.623999999999995 37.0 37.0 40.0 33.0 40.0 60-61 35.334 37.0 37.0 40.0 33.0 40.0 62-63 35.172625 37.0 37.0 37.0 33.0 40.0 64-65 34.961875 37.0 37.0 37.0 33.0 40.0 66-67 34.7775 37.0 33.0 37.0 33.0 40.0 68-69 34.539 37.0 33.0 37.0 27.0 40.0 70-71 34.389125 37.0 33.0 37.0 27.0 40.0 72-73 34.229749999999996 37.0 33.0 37.0 27.0 37.0 74-75 34.047625 37.0 33.0 37.0 27.0 37.0 76-77 33.767375 37.0 33.0 37.0 27.0 37.0 78-79 33.469125000000005 37.0 33.0 37.0 27.0 37.0 80-81 33.28775 37.0 33.0 37.0 27.0 37.0 82-83 33.166875000000005 37.0 33.0 37.0 27.0 37.0 84-85 33.254625000000004 37.0 33.0 37.0 27.0 37.0 86-87 33.243125000000006 37.0 33.0 37.0 27.0 37.0 88-89 33.0965 37.0 33.0 37.0 27.0 37.0 90-91 33.109 37.0 33.0 37.0 27.0 37.0 92-93 32.963 37.0 33.0 37.0 27.0 37.0 94-95 32.784625000000005 37.0 33.0 37.0 27.0 37.0 96-97 32.369375000000005 37.0 33.0 37.0 22.0 37.0 98-99 32.408625 37.0 33.0 37.0 22.0 37.0 100-101 30.818125000000002 35.0 30.0 37.0 18.5 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 60.0 3 7.0 4 3.0 5 2.0 6 5.0 7 4.0 8 1.0 9 2.0 10 6.0 11 5.0 12 6.0 13 4.0 14 7.0 15 7.0 16 5.0 17 5.0 18 8.0 19 11.0 20 6.0 21 6.0 22 14.0 23 9.0 24 19.0 25 12.0 26 16.0 27 27.0 28 30.0 29 48.0 30 55.0 31 60.0 32 81.0 33 131.0 34 160.0 35 242.0 36 521.0 37 1519.0 38 896.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.625 16.75 10.35 33.275 2 30.275000000000002 23.525 28.775000000000002 17.424999999999997 3 23.0 25.624999999999996 26.55 24.825 4 26.625 33.225 19.05 21.099999999999998 5 27.525 35.775 18.55 18.15 6 24.075 35.125 19.650000000000002 21.15 7 21.0 18.975 35.975 24.05 8 23.1 23.325000000000003 24.0 29.575000000000003 9 25.874999999999996 22.900000000000002 26.375 24.85 10-11 27.250000000000004 29.362500000000004 18.975 24.4125 12-13 26.8125 23.175 23.5625 26.450000000000003 14-15 25.137500000000003 27.025 23.9375 23.9 16-17 27.790973871733964 25.95324415551944 22.877859732466558 23.377922240280036 18-19 26.703337917239654 26.003250406300786 23.665458182272783 23.627953494186773 20-21 26.672502188320617 25.959734900587723 23.48380642741028 23.88395648368138 22-23 25.965745718214777 26.653331666458307 23.790473809226153 23.590448806100763 24-25 26.765845730716343 26.22827853481685 22.86535816977122 24.14051756469559 26-27 26.487500000000004 26.150000000000002 23.599999999999998 23.7625 28-29 27.400000000000002 26.0625 24.0625 22.475 30-31 26.1 26.387500000000003 23.799999999999997 23.7125 32-33 26.8125 26.825 23.1625 23.200000000000003 34-35 26.325 27.825 22.9875 22.8625 36-37 26.825 26.25 22.8375 24.087500000000002 38-39 26.325 25.85 24.6875 23.1375 40-41 26.55 26.674999999999997 23.9 22.875 42-43 26.775 26.3125 23.95 22.9625 44-45 26.3625 26.2125 23.75 23.674999999999997 46-47 26.650000000000002 26.25 23.35 23.75 48-49 25.87823477934742 25.128141017627204 25.003125390673837 23.990498812351543 50-51 25.687500000000004 26.6 24.625 23.0875 52-53 26.174999999999997 26.150000000000002 23.925 23.75 54-55 27.29091136392049 25.415676959619955 24.04050506313289 23.252906613326665 56-57 26.35329416177022 26.828353544193025 24.415551943992998 22.402800350043755 58-59 25.575 25.324999999999996 24.712500000000002 24.3875 60-61 26.900000000000002 25.5375 23.962500000000002 23.599999999999998 62-63 26.2875 25.45 24.5375 23.724999999999998 64-65 26.303287910988875 27.353419177397175 23.090386298287285 23.252906613326665 66-67 25.912499999999998 26.3625 24.575 23.150000000000002 68-69 26.415801975246904 25.66570821352669 24.065508188523566 23.85298162270284 70-71 25.0375 25.2625 24.6 25.1 72-73 25.678209776222026 25.528191023877984 24.440555069383674 24.353044130516317 74-75 25.2125 26.525 24.4 23.8625 76-77 25.650000000000002 25.95 24.65 23.75 78-79 26.294073518379594 26.619154788697173 23.355838959739934 23.730932733183295 80-81 26.2875 27.275 23.7 22.7375 82-83 26.638319159579787 25.887943971985994 23.84942471235618 23.62431215607804 84-85 26.413913913913913 26.676676676676674 23.623623623623622 23.285785785785787 86-87 26.59082385298162 26.365795724465556 23.865483185398176 23.177897237154642 88-89 27.737499999999997 26.4125 23.6625 22.1875 90-91 25.162499999999998 27.150000000000002 24.425 23.2625 92-93 26.803350418802353 26.503312914114264 24.14051756469559 22.552819102387797 94-95 27.0625 26.6625 24.05 22.225 96-97 27.325 26.3625 24.2875 22.025 98-99 27.3125 27.037499999999998 23.3125 22.3375 100-101 27.1625 27.0 23.7375 22.1 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.5 11 0.5 12 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.5 18 1.0 19 0.5 20 0.0 21 0.5 22 1.0 23 0.5 24 0.0 25 0.0 26 1.0 27 3.5 28 4.5 29 5.0 30 11.0 31 21.5 32 26.0 33 21.5 34 30.5 35 44.5 36 53.0 37 63.0 38 85.5 39 105.0 40 103.0 41 89.0 42 86.5 43 99.0 44 117.5 45 126.5 46 138.5 47 175.5 48 195.5 49 187.0 50 171.5 51 156.0 52 157.0 53 174.0 54 181.5 55 196.0 56 204.5 57 170.0 58 136.0 59 125.5 60 101.5 61 74.0 62 58.5 63 52.0 64 37.0 65 27.0 66 28.5 67 29.0 68 27.5 69 20.0 70 16.5 71 15.0 72 10.0 73 7.5 74 7.0 75 5.0 76 4.0 77 2.0 78 1.0 79 0.5 80 0.5 81 1.0 82 1.0 83 0.5 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 1.0 91 1.0 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 0.0125 18-19 0.0125 20-21 0.0375 22-23 0.0125 24-25 0.0125 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 0.0125 50-51 0.0 52-53 0.0 54-55 0.0125 56-57 0.0125 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0125 66-67 0.0 68-69 0.0125 70-71 0.0 72-73 0.0125 74-75 0.0 76-77 0.0 78-79 0.025 80-81 0.0 82-83 0.05 84-85 0.1 86-87 0.0125 88-89 0.0 90-91 0.0 92-93 0.0125 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 pass #Total Deduplicated Percentage 86.275 #Duplication Level Percentage of deduplicated Percentage of total 1 89.4523326572008 77.17500000000001 2 7.476093885830195 12.9 3 1.883512025499855 4.875 4 0.5795421616922631 2.0 5 0.34772529701535787 1.5 6 0.11590843233845263 0.6 7 0.08693132425383947 0.525 8 0.028977108084613158 0.2 9 0.028977108084613158 0.22499999999999998 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source GAAAATTCTATGGAAGAGCTAGCATCTCTGACGAAAACAGCAGACGGAAA 9 0.22499999999999998 No Hit GCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCC 8 0.2 No Hit CTTCAATATAAGCCTTGGTAGGGATAGATAGCCACCTATATAGTATAGCT 7 0.17500000000000002 No Hit GTCTGACATGCGTGCGAGTCGACGGGTTCTGAAACCTGGGATGCGCAAGG 7 0.17500000000000002 No Hit GCAAACTTCAAATTGAGCTGGCTCAGCTGCAATATGCACTGCCGCGTCTG 7 0.17500000000000002 No Hit GAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCC 6 0.15 No Hit CCTCGATCCATCGCGTATAGGGACGCCCCCTGCTCGCGTTACTGCCAAGC 6 0.15 No Hit TGAAAATTCTATGGAAGAGCTAGCATCTCTGACGAAAACAGCAGACGGAA 6 0.15 No Hit GTTGGTTTATGCTCATCCCTACTCATAACCCCAGCACTTAGATATTTTAA 6 0.15 No Hit CTGTAACTAAGTGAGGCTCTCTCATTGGTTTATACTTCAATATAAGCCTT 5 0.125 No Hit GGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTC 5 0.125 No Hit GGCCGATTGTCGCAGCCCGGGTCGATTATAACAACGGTGCAATCTCAGCT 5 0.125 No Hit GAAAAACGGTGTGCTTCAAATTGCGCTTGTCGGCTATACAAACGCAGGGA 5 0.125 No Hit CGTGAAACCGTGCTGAGCTCCCAAGCAGTGGGAGGGGAAAGTGATCTCTG 5 0.125 No Hit GGAAGGTAGAAGAGCTGAAGGCACTCGTGGAAGAGCTTGAAGCTGATCTC 5 0.125 No Hit GAAAAGTTACCACAGGGATAACTGGCTTGTGGCAGCCAAGCGTTCATAGC 5 0.125 No Hit GGCAAACTTCAAATTGAGCTGGCTCAGCTGCAATATGCACTGCCGCGTCT 5 0.125 No Hit GCTGAAGGCACTCGTGGAAGAGCTTGAAGCTGATCTCCTCATCTTTAATG 5 0.125 No Hit CAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGATTC 5 0.125 No Hit GTGAAATAGAACGTGAAACCGTGCTGAGCTCCCAAGCAGTGGGAGGGGAA 5 0.125 No Hit CGAATAGCTCGTAACCAAACATGCACAGCGGTCAAACAGTATGTCCCAAG 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 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.037500000000000006 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.23750000000000002 0.0 0.0 0.0 0.0 70-71 0.3375 0.0 0.0 0.0 0.0 72-73 0.4 0.0 0.0 0.0 0.0 74-75 0.5375 0.0 0.0 0.0 0.0 76-77 0.6125 0.0 0.0 0.0 0.0 78-79 0.7250000000000001 0.0 0.0 0.0 0.0 80-81 0.925 0.0 0.0 0.0 0.0 82-83 1.125 0.0 0.0 0.0 0.0 84-85 1.4625 0.0 0.0 0.0 0.0 86-87 1.7875 0.0 0.0 0.0 0.0 88-89 2.1875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507053 spots for SRR6127926.sra Written 1507053 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra Read 1507052 spots for SRR6127926.sra Written 1507052 spots for SRR6127926.sra SRR ids: ['SRR6127926.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_65sgkoj0 SRR6127926.sra spots: 30141041 blocks: [[1, 1507052], [1507053, 3014104], [3014105, 4521156], [4521157, 6028208], [6028209, 7535260], [7535261, 9042312], [9042313, 10549364], [10549365, 12056416], [12056417, 13563468], [13563469, 15070520], [15070521, 16577572], [16577573, 18084624], [18084625, 19591676], [19591677, 21098728], [21098729, 22605780], [22605781, 24112832], [24112833, 25619884], [25619885, 27126936], [27126937, 28633988], [28633989, 30141041]] SRR6127926 file size 7189779 SRR6127926 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 SRR6127926 SRR6127926_1.fastq SRR6127926_2.fastq Input file: SRR6127926_1.fastq Paired file: SRR6127926_2.fastq trimmed: SRR6127926-trimmed-pair1.fastq, SRR6127926-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- 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 -- number of concurrent threads (-t): 20 Tue Dec 10 04:26:28 2024 >> started Tue Dec 10 04:26:55 2024 >> done (27.383s) 30141041 read pairs processed; of these: 132619 ( 0.44%) short read pairs filtered out after trimming by size control 437950 ( 1.45%) empty read pairs filtered out after trimming by size control 29570472 (98.11%) read pairs available; of these: 5907829 (19.98%) trimmed read pairs available after processing 23662643 (80.02%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 15 0.00% 19 8 0.00% 20 37 0.00% 21 57 0.00% 22 114 0.00% 23 125 0.00% 24 188 0.00% 25 221 0.00% 26 303 0.00% 27 374 0.00% 28 465 0.00% 29 614 0.00% 30 725 0.00% 31 806 0.00% 32 1007 0.00% 33 1220 0.00% 34 1333 0.00% 35 1572 0.01% 36 1720 0.01% 37 2034 0.01% 38 2241 0.01% 39 2560 0.01% 40 2855 0.01% 41 3227 0.01% 42 3576 0.01% 43 3900 0.01% 44 4353 0.01% 45 4824 0.02% 46 5158 0.02% 47 5727 0.02% 48 6170 0.02% 49 6924 0.02% 50 7324 0.02% 51 8037 0.03% 52 8806 0.03% 53 9480 0.03% 54 10017 0.03% 55 10971 0.04% 56 12012 0.04% 57 12893 0.04% 58 14459 0.05% 59 25838 0.09% 60 26496 0.09% 61 28195 0.10% 62 33666 0.11% 63 34694 0.12% 64 38204 0.13% 65 41290 0.14% 66 40368 0.14% 67 41841 0.14% 68 44486 0.15% 69 53753 0.18% 70 53489 0.18% 71 55225 0.19% 72 61199 0.21% 73 58366 0.20% 74 62545 0.21% 75 60949 0.21% 76 61902 0.21% 77 64454 0.22% 78 69053 0.23% 79 73403 0.25% 80 76167 0.26% 81 82840 0.28% 82 91708 0.31% 83 98916 0.33% 84 109053 0.37% 85 120661 0.41% 86 137182 0.46% 87 136518 0.46% 88 138821 0.47% 89 135911 0.46% 90 159641 0.54% 91 162906 0.55% 92 181360 0.61% 93 202976 0.69% 94 222515 0.75% 95 255796 0.87% 96 306724 1.04% 97 369731 1.25% 98 461255 1.56% 99 573658 1.94% 100 24358265 82.37% 29570472 reads passed initial QC criterion=sequence-density sequence-density=0.85 sequence-density-rank=1 fanout-score=1.95 fanout-score-rank=22 prefix-density=0.85 prefix-fanout=1.9 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=11.61 fanout-score-rank=1 prefix-density=0.02 prefix-fanout=2.9 sequence=AGCAGCTCGAGCAATCCGCCGACAGCCGACGGGTTTGGGGCCGGGACCCCCGAGCCCAGTCCTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTCCCTTGCCTACATTGTTCCATTGGCCAGAGGCTGTTCACCTTGGAGACCTGATGCGGTTATGAGTACGACCGGGCGTGAACGGTACTCGGTCCTCCGGATTTTCATGGGCCGCCGGGGGCGCACCGGACACCGCGCGACGTGCGGTGCTCTTCCGGCCACTGGACCCTACCTCCGGCTGAACCGATTCCAGGGTTGGCAGGCCGTTAAGCAGAAAAGATAACTCTTCCCGAGGCCCCCGCCGGCGTCTCCGGACTTCCTAACGTCGCCGTCAACCGCCACATCCCGGCTCGGGAAATCTTAACCCGATTCCCTTTCGGGGGATACGCGTGATCGCGCTATCTGCCGGGGTTACCCCGTCCCTTAGGATCGGCTTACCCATGTGCAAGTGCCGTTCACATGGA criterion=sequence-density sequence-density=1.07 sequence-density-rank=1 fanout-score=1.98 fanout-score-rank=26 prefix-density=1.05 prefix-fanout=2.0 sequence=GGTGGTGCATGGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=27 fanout-score=8.24 fanout-score-rank=1 prefix-density=0.13 prefix-fanout=1.0 sequence=TAACTTCGGGAGAAGGGGTGCCCCCTCACAAAAGGGGGTCGCAGTGACCAGGCCCGGGCGACTGTTTACCAAAAACACAGGTCTCCGCAAAGTCGTAAGACCATGTATGGGGGCTGACGCCTGCCCAGTGCCGGAAGGTCAAGGAAGTTGGTGAACTGATGACAGGGAAGCCGGCGACCGAAGCCCCGGTGAACGGCGGCCGTAAC SRR6127926 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 04:27:51 Started mapping on | Dec 10 04:27:51 Finished on | Dec 10 04:49:34 Mapping speed, Million of reads per hour | 81.70 Number of input reads | 29570472 Average input read length | 196 UNIQUE READS: Uniquely mapped reads number | 10515141 Uniquely mapped reads % | 35.56% Average mapped length | 196.34 Number of splices: Total | 5480260 Number of splices: Annotated (sjdb) | 5161642 Number of splices: GT/AG | 5394697 Number of splices: GC/AG | 68017 Number of splices: AT/AC | 2406 Number of splices: Non-canonical | 15140 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.02% Deletion average length | 2.19 Insertion rate per base | 0.02% Insertion average length | 1.93 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 3834907 % of reads mapped to multiple loci | 12.97% Number of reads mapped to too many loci | 754831 % of reads mapped to too many loci | 2.55% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 36.52% % of reads unmapped: other | 12.40% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 15229594 15229594 15229594 N_multimapping 3834907 3834907 3834907 N_noFeature 1627449 10226459 1701877 N_ambiguous 248644 1034 34488 UnstrandedReadsAssigned:8639048 PositiveStrandReadsAssigned:287648 NegativeStrandReadsAssigned:8778776 Dataset is classified negative stranded MeadianReadLen=100 20thPercentileLength=100 echo kmer=95 SRR6127926 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [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 paired-end mode [quant] will process pair 1: SRR6127926-trimmed-pair1.fastq SRR6127926-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 29,570,472 reads, 9,495,142 reads pseudoaligned [quant] estimated average fragment length: 155.467 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,127 rounds 52973 SRR6127926.ke.tsv 35125 SRR6127926.se.tsv 88098 total ==> SRR6127926.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 781.666 29.4077 4.59084 PNS24247 1044 889.533 21.7751 2.98711 PNS24249 1928 1773.53 19.8076 1.36284 PNS24246 1044 889.533 21.7751 2.98711 PNS24248 1044 889.533 21.7751 2.98711 PNS24244 1471 1316.53 98.4593 9.12592 PNS24243 293 143.434 0 0 KQK14069 1603 1448.53 837.575 70.5581 KQK14071 474 320.623 36.9885 14.0774 ==> SRR6127926.se.tsv <== BRADI_1g14170v3 976 BRADI_1g53295v3 308 BRADI_1g59795v3 80 BRADI_1g07683v3 0 BRADI_1g00485v3 2 BRADI_1g20270v3 207 BRADI_1g74790v3 61 BRADI_1g09890v3 0 BRADI_1g77505v3 230 BRADI_1g48960v3 0 SRR6127926 completed mapping pipeline successfully