Starting /dee2/code/volunteer_pipeline.sh ERR3450057 current disk space = 1543082254336 free memory = 1478851976 ERR3450057 SRAfilesize dce3fd15e19cba53b05b11ca1d89d3af ERR3450057.sra ERR3450057.sra file validated ERR3450057 is paired end ERR3450057 is conventional basespace ERR3450057 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450057_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.08125 37.0 37.0 37.0 37.0 37.0 2 36.3715 37.0 37.0 37.0 37.0 37.0 3 36.3775 37.0 37.0 37.0 37.0 37.0 4 36.495 37.0 37.0 37.0 37.0 37.0 5 36.527 37.0 37.0 37.0 37.0 37.0 6 36.471 37.0 37.0 37.0 37.0 37.0 7 36.489 37.0 37.0 37.0 37.0 37.0 8 36.4635 37.0 37.0 37.0 37.0 37.0 9 36.525 37.0 37.0 37.0 37.0 37.0 10-11 36.545 37.0 37.0 37.0 37.0 37.0 12-13 36.560249999999996 37.0 37.0 37.0 37.0 37.0 14-15 36.535250000000005 37.0 37.0 37.0 37.0 37.0 16-17 36.51925 37.0 37.0 37.0 37.0 37.0 18-19 36.4875 37.0 37.0 37.0 37.0 37.0 20-21 36.497 37.0 37.0 37.0 37.0 37.0 22-23 36.4895 37.0 37.0 37.0 37.0 37.0 24-25 36.45375 37.0 37.0 37.0 37.0 37.0 26-27 36.482 37.0 37.0 37.0 37.0 37.0 28-29 36.47 37.0 37.0 37.0 37.0 37.0 30-31 36.412 37.0 37.0 37.0 37.0 37.0 32-33 36.408500000000004 37.0 37.0 37.0 37.0 37.0 34-35 36.379999999999995 37.0 37.0 37.0 37.0 37.0 36-37 36.371 37.0 37.0 37.0 37.0 37.0 38-39 36.3955 37.0 37.0 37.0 37.0 37.0 40-41 36.301 37.0 37.0 37.0 37.0 37.0 42-43 36.346000000000004 37.0 37.0 37.0 37.0 37.0 44-45 36.317750000000004 37.0 37.0 37.0 37.0 37.0 46-47 36.23650000000001 37.0 37.0 37.0 37.0 37.0 48-49 36.26825 37.0 37.0 37.0 37.0 37.0 50-51 36.254999999999995 37.0 37.0 37.0 37.0 37.0 52-53 36.266999999999996 37.0 37.0 37.0 37.0 37.0 54-55 36.16975 37.0 37.0 37.0 37.0 37.0 56-57 36.192499999999995 37.0 37.0 37.0 37.0 37.0 58-59 36.216 37.0 37.0 37.0 37.0 37.0 60-61 36.1485 37.0 37.0 37.0 37.0 37.0 62-63 36.17675 37.0 37.0 37.0 37.0 37.0 64-65 36.130250000000004 37.0 37.0 37.0 37.0 37.0 66-67 36.18 37.0 37.0 37.0 37.0 37.0 68-69 36.1485 37.0 37.0 37.0 37.0 37.0 70-71 36.20525000000001 37.0 37.0 37.0 37.0 37.0 72-73 36.087 37.0 37.0 37.0 37.0 37.0 74-75 36.222 37.0 37.0 37.0 37.0 37.0 76-77 36.2385 37.0 37.0 37.0 37.0 37.0 78-79 36.12375 37.0 37.0 37.0 37.0 37.0 80-81 36.186 37.0 37.0 37.0 37.0 37.0 82-83 36.1525 37.0 37.0 37.0 37.0 37.0 84-85 36.113 37.0 37.0 37.0 37.0 37.0 86-87 36.135 37.0 37.0 37.0 37.0 37.0 88-89 36.16175 37.0 37.0 37.0 37.0 37.0 90-91 36.1055 37.0 37.0 37.0 37.0 37.0 92-93 36.006 37.0 37.0 37.0 37.0 37.0 94-95 36.0845 37.0 37.0 37.0 37.0 37.0 96-97 36.03775 37.0 37.0 37.0 37.0 37.0 98-99 36.004000000000005 37.0 37.0 37.0 37.0 37.0 100-101 35.98125 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 3.0 24 2.0 25 10.0 26 11.0 27 22.0 28 16.0 29 28.0 30 45.0 31 46.0 32 62.0 33 83.0 34 93.0 35 156.0 36 1591.0 37 1831.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.849435382685066 9.786700125470514 10.564617314930992 39.799247176913426 2 21.125 13.025 29.725 36.125 3 20.8 16.950000000000003 25.025 37.225 4 28.275 23.474999999999998 18.375 29.875 5 25.75 28.175 20.974999999999998 25.1 6 22.425 32.225 24.4 20.95 7 19.8 22.5 36.7 21.0 8 21.675 20.075000000000003 29.349999999999998 28.9 9 21.175 22.375 31.1 25.35 10-11 23.8875 27.8625 22.825 25.424999999999997 12-13 23.1625 22.5875 26.325 27.925 14-15 23.0625 24.4375 26.075 26.424999999999997 16-17 23.200000000000003 24.825 26.55 25.424999999999997 18-19 24.9 24.9 24.175 26.025 20-21 23.1625 24.9 25.424999999999997 26.5125 22-23 24.625 25.5625 24.837500000000002 24.975 24-25 24.337500000000002 24.775 24.4375 26.450000000000003 26-27 23.95 23.875 24.212500000000002 27.962500000000002 28-29 25.275 24.4 23.8375 26.487500000000004 30-31 24.2875 23.2625 25.45 27.0 32-33 23.9125 23.849999999999998 25.2 27.037499999999998 34-35 24.025 23.6625 25.137500000000003 27.175 36-37 25.0125 24.7875 24.075 26.125 38-39 24.1125 24.6 24.85 26.437500000000004 40-41 23.9375 24.325 24.9875 26.75 42-43 24.275 23.7 25.174999999999997 26.85 44-45 23.6875 23.575 25.15 27.5875 46-47 24.3 24.125 24.55 27.025 48-49 24.6125 23.95 24.474999999999998 26.9625 50-51 25.3 24.5375 23.0 27.1625 52-53 25.474999999999998 23.925 24.4875 26.1125 54-55 24.8 24.1375 24.025 27.037499999999998 56-57 24.0 24.0 24.325 27.675 58-59 24.525 24.2375 23.6125 27.625 60-61 24.0375 24.425 24.5125 27.025 62-63 25.2625 23.225 24.075 27.437499999999996 64-65 24.625 23.9 23.6625 27.8125 66-67 24.9 24.224999999999998 23.6375 27.237499999999997 68-69 24.212500000000002 24.55 23.7375 27.500000000000004 70-71 24.875 23.849999999999998 24.5 26.775 72-73 25.4875 24.099999999999998 24.3625 26.05 74-75 24.6 23.825 24.1375 27.437499999999996 76-77 25.0 24.075 23.6625 27.2625 78-79 24.825 24.4875 22.95 27.737499999999997 80-81 24.425 24.95 23.3875 27.237499999999997 82-83 25.650000000000002 24.15 23.4125 26.787499999999998 84-85 25.162499999999998 24.462500000000002 23.4875 26.887499999999996 86-87 24.525 24.075 24.15 27.250000000000004 88-89 25.75 23.8375 23.9125 26.5 90-91 24.9375 24.1875 23.8125 27.0625 92-93 25.2625 24.525 23.599999999999998 26.6125 94-95 24.7 23.875 23.575 27.85 96-97 25.374999999999996 23.5 24.1125 27.0125 98-99 24.975 24.7 23.575 26.75 100-101 24.775 25.624999999999996 23.125 26.474999999999998 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 7.0 1 4.0 2 1.0 3 0.5 4 1.0 5 2.5 6 2.5 7 2.0 8 1.5 9 2.0 10 1.5 11 0.0 12 1.5 13 1.5 14 0.5 15 0.5 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 1.5 26 2.0 27 2.0 28 1.5 29 0.5 30 3.0 31 7.5 32 7.5 33 6.0 34 11.0 35 14.5 36 28.5 37 44.0 38 48.5 39 57.5 40 78.5 41 102.0 42 120.5 43 138.5 44 147.0 45 159.0 46 175.5 47 188.0 48 195.0 49 176.5 50 162.5 51 163.0 52 163.5 53 154.0 54 155.5 55 159.5 56 136.5 57 114.0 58 105.0 59 96.5 60 83.0 61 70.5 62 66.0 63 60.5 64 58.0 65 55.5 66 54.5 67 54.5 68 39.0 69 38.5 70 43.0 71 36.5 72 38.5 73 36.0 74 25.5 75 20.0 76 13.5 77 17.5 78 16.0 79 6.0 80 5.0 81 4.5 82 2.5 83 2.0 84 0.5 85 0.0 86 0.5 87 0.5 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.375 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 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 87.55 #Duplication Level Percentage of deduplicated Percentage of total 1 89.46316390633923 78.325 2 8.366647629925756 14.649999999999999 3 1.4563106796116505 3.8249999999999997 4 0.2569960022844089 0.8999999999999999 5 0.2284408909194746 1.0 6 0.1427755568246716 0.75 7 0.05711022272986865 0.35000000000000003 8 0.028555111364934323 0.2 9 0.0 0.0 >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 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 8 0.2 No Hit CTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACT 7 0.17500000000000002 No Hit GGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCT 7 0.17500000000000002 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTG 6 0.15 No Hit GCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCA 6 0.15 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 6 0.15 No Hit GGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGA 6 0.15 No Hit GCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGC 6 0.15 No Hit CGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTC 5 0.125 No Hit GTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAG 5 0.125 No Hit CCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTAT 5 0.125 No Hit CCACCGTCCTGCTGTCTTAATCGACCAACACCCTTTGTGGGTTCTAGGTT 5 0.125 No Hit CTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGG 5 0.125 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 5 0.125 No Hit GTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCT 5 0.125 No Hit GAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCTTTTATCTAATAAA 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 0.0625 0.0 0.0 0.0 0.0 42-43 0.1125 0.0 0.0 0.0 0.0 44-45 0.1375 0.0 0.0 0.0 0.0 46-47 0.15 0.0 0.0 0.0 0.0 48-49 0.225 0.0 0.0 0.0 0.0 50-51 0.2625 0.0 0.0 0.0 0.0 52-53 0.3875 0.0 0.0 0.0 0.0 54-55 0.45 0.0 0.0 0.0 0.0 56-57 0.525 0.0 0.0 0.0 0.0 58-59 0.625 0.0 0.0 0.0 0.0 60-61 0.7 0.0 0.0 0.0 0.0 62-63 0.8125 0.0 0.0 0.0 0.0 64-65 0.9375 0.0 0.0 0.0 0.0 66-67 1.15 0.0 0.0 0.0 0.0 68-69 1.2999999999999998 0.0 0.0 0.0 0.0 70-71 1.4375 0.0 0.0 0.0 0.0 72-73 1.55 0.0 0.0 0.0 0.0 74-75 1.7875 0.0 0.0 0.0 0.0 76-77 2.1375 0.0 0.0 0.0 0.0 78-79 2.5999999999999996 0.0 0.0 0.0 0.0 80-81 2.925 0.0 0.0 0.0 0.0 82-83 3.25 0.0 0.0 0.0 0.0 84-85 3.675 0.0 0.0 0.0 0.0 86-87 4.1625 0.0 0.0 0.0 0.0 88-89 4.5875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGTACCT 15 0.009957196 47.5 54-55 >>END_MODULE ERR3450057 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450057_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.8945 37.0 37.0 37.0 37.0 37.0 2 35.8845 37.0 37.0 37.0 37.0 37.0 3 35.8595 37.0 37.0 37.0 37.0 37.0 4 36.1845 37.0 37.0 37.0 37.0 37.0 5 36.1175 37.0 37.0 37.0 37.0 37.0 6 36.1515 37.0 37.0 37.0 37.0 37.0 7 36.057 37.0 37.0 37.0 37.0 37.0 8 36.0135 37.0 37.0 37.0 37.0 37.0 9 36.1665 37.0 37.0 37.0 37.0 37.0 10-11 36.1095 37.0 37.0 37.0 37.0 37.0 12-13 36.13175 37.0 37.0 37.0 37.0 37.0 14-15 36.023 37.0 37.0 37.0 37.0 37.0 16-17 36.1 37.0 37.0 37.0 37.0 37.0 18-19 36.16275 37.0 37.0 37.0 37.0 37.0 20-21 36.059 37.0 37.0 37.0 37.0 37.0 22-23 36.093500000000006 37.0 37.0 37.0 37.0 37.0 24-25 36.0225 37.0 37.0 37.0 37.0 37.0 26-27 35.95575 37.0 37.0 37.0 37.0 37.0 28-29 35.9225 37.0 37.0 37.0 37.0 37.0 30-31 35.914249999999996 37.0 37.0 37.0 37.0 37.0 32-33 35.883250000000004 37.0 37.0 37.0 37.0 37.0 34-35 35.83425 37.0 37.0 37.0 37.0 37.0 36-37 35.861000000000004 37.0 37.0 37.0 37.0 37.0 38-39 35.84575 37.0 37.0 37.0 37.0 37.0 40-41 35.8985 37.0 37.0 37.0 37.0 37.0 42-43 35.82825 37.0 37.0 37.0 37.0 37.0 44-45 35.7485 37.0 37.0 37.0 37.0 37.0 46-47 35.81675 37.0 37.0 37.0 37.0 37.0 48-49 35.77475 37.0 37.0 37.0 37.0 37.0 50-51 35.798 37.0 37.0 37.0 37.0 37.0 52-53 35.8245 37.0 37.0 37.0 37.0 37.0 54-55 35.78075 37.0 37.0 37.0 37.0 37.0 56-57 35.713 37.0 37.0 37.0 37.0 37.0 58-59 35.77675 37.0 37.0 37.0 37.0 37.0 60-61 35.687 37.0 37.0 37.0 37.0 37.0 62-63 35.6255 37.0 37.0 37.0 37.0 37.0 64-65 35.7295 37.0 37.0 37.0 37.0 37.0 66-67 35.678 37.0 37.0 37.0 37.0 37.0 68-69 35.686 37.0 37.0 37.0 37.0 37.0 70-71 35.70075 37.0 37.0 37.0 37.0 37.0 72-73 35.666250000000005 37.0 37.0 37.0 37.0 37.0 74-75 35.596000000000004 37.0 37.0 37.0 37.0 37.0 76-77 35.69325 37.0 37.0 37.0 37.0 37.0 78-79 35.66875 37.0 37.0 37.0 37.0 37.0 80-81 35.6295 37.0 37.0 37.0 37.0 37.0 82-83 35.681749999999994 37.0 37.0 37.0 37.0 37.0 84-85 35.6315 37.0 37.0 37.0 37.0 37.0 86-87 35.686 37.0 37.0 37.0 37.0 37.0 88-89 35.70975 37.0 37.0 37.0 37.0 37.0 90-91 35.67075 37.0 37.0 37.0 37.0 37.0 92-93 35.69225 37.0 37.0 37.0 37.0 37.0 94-95 35.6495 37.0 37.0 37.0 37.0 37.0 96-97 35.5925 37.0 37.0 37.0 37.0 37.0 98-99 35.70775 37.0 37.0 37.0 37.0 37.0 100-101 35.61425 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 3.0 15 2.0 16 5.0 17 5.0 18 6.0 19 3.0 20 7.0 21 14.0 22 11.0 23 14.0 24 20.0 25 13.0 26 19.0 27 28.0 28 22.0 29 25.0 30 31.0 31 29.0 32 52.0 33 75.0 34 119.0 35 299.0 36 2162.0 37 1036.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.0 15.174999999999999 12.375 29.45 2 29.275000000000002 21.85 25.15 23.724999999999998 3 24.625 23.925 26.5 24.95 4 30.325000000000003 28.375 17.1 24.2 5 29.625 29.549999999999997 18.825 22.0 6 24.375 33.025 19.8 22.8 7 24.45 19.8 32.525 23.225 8 26.450000000000003 20.25 25.124999999999996 28.175 9 26.174999999999997 21.025 25.25 27.55 10-11 27.474999999999998 27.8125 19.8375 24.875 12-13 28.3625 22.287499999999998 22.4375 26.9125 14-15 27.3625 24.4375 23.5875 24.6125 16-17 28.237499999999997 24.075 22.375 25.3125 18-19 27.9125 25.8 22.725 23.5625 20-21 26.987499999999997 25.825 22.675 24.5125 22-23 27.975 25.087500000000002 22.037499999999998 24.9 24-25 27.35 25.412499999999998 22.912499999999998 24.325 26-27 27.85 24.8 22.4375 24.9125 28-29 27.575 25.15 23.0125 24.2625 30-31 26.85 25.35 22.912499999999998 24.887500000000003 32-33 26.325 25.337500000000002 23.6625 24.675 34-35 26.887499999999996 25.575 23.25 24.2875 36-37 27.3 24.4875 22.55 25.662499999999998 38-39 27.675 24.637500000000003 22.9875 24.7 40-41 26.337500000000002 25.6 22.3125 25.75 42-43 26.9125 24.65 23.3125 25.124999999999996 44-45 26.200000000000003 24.4 24.125 25.275 46-47 26.575 25.4875 22.7625 25.174999999999997 48-49 26.937499999999996 25.174999999999997 23.3375 24.55 50-51 27.0625 25.5375 22.4625 24.9375 52-53 27.3375 24.6 23.6375 24.425 54-55 27.05 24.4125 23.3 25.2375 56-57 27.0125 24.75 23.875 24.3625 58-59 26.924999999999997 24.525 24.4875 24.0625 60-61 28.0875 24.712500000000002 22.325 24.875 62-63 27.962500000000002 23.9125 23.1625 24.962500000000002 64-65 27.450000000000003 24.8 22.6 25.15 66-67 27.275 25.137500000000003 23.75 23.8375 68-69 26.937499999999996 24.75 23.525 24.7875 70-71 28.1375 24.887500000000003 22.475 24.5 72-73 27.6 24.5625 22.7 25.137500000000003 74-75 27.200000000000003 25.3 23.2625 24.2375 76-77 29.062500000000004 23.8125 23.1875 23.9375 78-79 27.875 25.324999999999996 22.425 24.375 80-81 27.1625 24.9875 24.125 23.724999999999998 82-83 27.1 24.2375 23.9 24.762500000000003 84-85 27.962500000000002 24.7 23.05 24.2875 86-87 28.050000000000004 25.324999999999996 22.7125 23.9125 88-89 29.212500000000002 24.837500000000002 21.9625 23.9875 90-91 28.6125 25.337500000000002 22.5125 23.5375 92-93 28.675 26.1 22.225 23.0 94-95 28.65 24.825 22.925 23.599999999999998 96-97 28.8375 24.8 23.1125 23.25 98-99 29.349999999999998 25.374999999999996 22.75 22.525000000000002 100-101 29.75 25.662499999999998 21.5625 23.025000000000002 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.5 2 0.5 3 1.0 4 1.0 5 0.0 6 0.0 7 1.5 8 1.5 9 2.0 10 6.0 11 5.5 12 3.0 13 2.5 14 1.0 15 0.5 16 1.0 17 1.5 18 2.0 19 1.5 20 2.5 21 2.0 22 1.0 23 1.5 24 1.5 25 1.5 26 1.5 27 2.5 28 3.5 29 2.5 30 6.0 31 9.5 32 8.0 33 7.0 34 11.0 35 18.0 36 25.5 37 39.5 38 49.5 39 64.5 40 86.0 41 105.0 42 107.5 43 113.5 44 135.5 45 152.0 46 163.0 47 163.5 48 163.5 49 182.0 50 171.0 51 152.5 52 154.0 53 155.5 54 149.5 55 134.5 56 134.0 57 110.0 58 94.0 59 87.5 60 83.5 61 84.0 62 72.5 63 66.5 64 68.5 65 67.0 66 60.0 67 54.0 68 55.0 69 58.5 70 54.0 71 48.0 72 40.0 73 32.5 74 34.5 75 26.5 76 13.0 77 18.0 78 17.0 79 9.5 80 5.0 81 4.5 82 5.5 83 3.0 84 2.0 85 1.5 86 0.5 87 1.0 88 1.0 89 0.5 90 0.0 91 0.0 92 0.0 93 0.0 94 0.5 95 1.0 96 0.5 97 0.5 98 0.5 99 0.0 100 2.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 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 88.7 #Duplication Level Percentage of deduplicated Percentage of total 1 89.82525366403607 79.675 2 8.370913190529876 14.85 3 1.3810597519729426 3.675 4 0.2536640360766629 0.8999999999999999 5 0.05636978579481398 0.25 6 0.08455467869222097 0.44999999999999996 7 0.0 0.0 8 0.02818489289740699 0.2 9 0.0 0.0 >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 CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 8 0.2 No Hit GCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAAC 6 0.15 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6 0.15 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 6 0.15 No Hit TACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTTGA 5 0.125 No Hit CTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACC 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 0.0625 0.0 0.0 0.0 0.0 42-43 0.1125 0.0 0.0 0.0 0.0 44-45 0.1375 0.0 0.0 0.0 0.0 46-47 0.15 0.0 0.0 0.0 0.0 48-49 0.2 0.0 0.0 0.0 0.0 50-51 0.2375 0.0 0.0 0.0 0.0 52-53 0.3625 0.0 0.0 0.0 0.0 54-55 0.425 0.0 0.0 0.0 0.0 56-57 0.5 0.0 0.0 0.0 0.0 58-59 0.6 0.0 0.0 0.0 0.0 60-61 0.675 0.0 0.0 0.0 0.0 62-63 0.8 0.0 0.0 0.0 0.0 64-65 0.9375 0.0 0.0 0.0 0.0 66-67 1.15 0.0 0.0 0.0 0.0 68-69 1.2999999999999998 0.0 0.0 0.0 0.0 70-71 1.4375 0.0 0.0 0.0 0.0 72-73 1.55 0.0 0.0 0.0 0.0 74-75 1.7875 0.0 0.0 0.0 0.0 76-77 2.1375 0.0 0.0 0.0 0.0 78-79 2.5875 0.0 0.0 0.0 0.0 80-81 2.875 0.0 0.0 0.0 0.0 82-83 3.2 0.0 0.0 0.0 0.0 84-85 3.625 0.0 0.0 0.0 0.0 86-87 4.1125 0.0 0.0 0.0 0.0 88-89 4.5625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGCACCA 15 0.009957196 47.5 82-83 TGCAGTT 15 0.009957196 47.5 16-17 >>END_MODULE Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572437 spots for ERR3450057.sra Written 1572437 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra Read 1572433 spots for ERR3450057.sra Written 1572433 spots for ERR3450057.sra SRR ids: ['ERR3450057.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ajbn7kzs ERR3450057.sra spots: 31448664 blocks: [[1, 1572433], [1572434, 3144866], [3144867, 4717299], [4717300, 6289732], [6289733, 7862165], [7862166, 9434598], [9434599, 11007031], [11007032, 12579464], [12579465, 14151897], [14151898, 15724330], [15724331, 17296763], [17296764, 18869196], [18869197, 20441629], [20441630, 22014062], [22014063, 23586495], [23586496, 25158928], [25158929, 26731361], [26731362, 28303794], [28303795, 29876227], [29876228, 31448664]] ERR3450057 file size 7564061 ERR3450057 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 ERR3450057 ERR3450057_1.fastq ERR3450057_2.fastq Input file: ERR3450057_1.fastq Paired file: ERR3450057_2.fastq trimmed: ERR3450057-trimmed-pair1.fastq, ERR3450057-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 Sat Dec 7 14:14:26 2024 >> started Sat Dec 7 14:18:23 2024 >> done (236.674s) 31448664 read pairs processed; of these: 205 ( 0.00%) short read pairs filtered out after trimming by size control 30622 ( 0.10%) empty read pairs filtered out after trimming by size control 31417837 (99.90%) read pairs available; of these: 2430899 ( 7.74%) trimmed read pairs available after processing 28986938 (92.26%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 21 0.00% 19 52 0.00% 20 150 0.00% 21 385 0.00% 22 447 0.00% 23 246 0.00% 24 249 0.00% 25 282 0.00% 26 405 0.00% 27 641 0.00% 28 997 0.00% 29 1337 0.00% 30 1567 0.00% 31 1892 0.01% 32 2040 0.01% 33 1767 0.01% 34 1839 0.01% 35 1938 0.01% 36 2155 0.01% 37 2352 0.01% 38 2806 0.01% 39 3220 0.01% 40 3793 0.01% 41 4440 0.01% 42 4977 0.02% 43 5184 0.02% 44 4866 0.02% 45 4662 0.01% 46 5110 0.02% 47 5615 0.02% 48 6188 0.02% 49 6844 0.02% 50 7661 0.02% 51 8579 0.03% 52 9374 0.03% 53 9798 0.03% 54 10409 0.03% 55 10700 0.03% 56 11479 0.04% 57 11945 0.04% 58 13294 0.04% 59 14577 0.05% 60 15671 0.05% 61 17065 0.05% 62 19062 0.06% 63 20606 0.07% 64 21217 0.07% 65 22370 0.07% 66 23157 0.07% 67 24387 0.08% 68 25533 0.08% 69 27195 0.09% 70 28389 0.09% 71 30993 0.10% 72 33218 0.11% 73 35571 0.11% 74 37504 0.12% 75 39090 0.12% 76 40751 0.13% 77 42165 0.13% 78 44044 0.14% 79 46786 0.15% 80 48984 0.16% 81 51091 0.16% 82 54342 0.17% 83 56557 0.18% 84 59715 0.19% 85 63086 0.20% 86 63673 0.20% 87 67233 0.21% 88 69551 0.22% 89 73070 0.23% 90 76161 0.24% 91 80517 0.26% 92 84700 0.27% 93 87387 0.28% 94 90775 0.29% 95 93898 0.30% 96 96727 0.31% 97 100600 0.32% 98 102757 0.33% 99 104459 0.33% 100 124559 0.40% 101 28986938 92.26% 31417837 reads passed initial QC criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=2.47 fanout-score-rank=32 prefix-density=0.22 prefix-fanout=2.5 sequence=GTCAAATTAAGCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATAAGCAACATCCGCCGATCCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTCACCTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATCCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGATGCCGGAGGCACGACCCGGCCAATTAAGGCTAGGAGCGCATCGCCGGCTGAAGGGTCGAGTA criterion=fanout-score sequence-density=0.06 sequence-density-rank=22 fanout-score=239.77 fanout-score-rank=1 prefix-density=0.59 prefix-fanout=23.6 sequence=GCCGCCGCCGCG criterion=sequence-density sequence-density=0.22 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=29 prefix-density=0.21 prefix-fanout=2.0 sequence=CAAGTGTTGGATT criterion=fanout-score sequence-density=0.07 sequence-density-rank=24 fanout-score=227.90 fanout-score-rank=1 prefix-density=1.31 prefix-fanout=12.4 sequence=CGCCGCCGCCGTC ERR3450057 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:23:17 Started mapping on | Dec 07 14:23:19 Finished on | Dec 07 14:56:51 Mapping speed, Million of reads per hour | 56.21 Number of input reads | 31417837 Average input read length | 199 UNIQUE READS: Uniquely mapped reads number | 22631263 Uniquely mapped reads % | 72.03% Average mapped length | 198.76 Number of splices: Total | 14177315 Number of splices: Annotated (sjdb) | 13427859 Number of splices: GT/AG | 13996839 Number of splices: GC/AG | 155039 Number of splices: AT/AC | 9099 Number of splices: Non-canonical | 16338 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.01% Deletion average length | 2.09 Insertion rate per base | 0.01% Insertion average length | 1.93 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1389201 % of reads mapped to multiple loci | 4.42% Number of reads mapped to too many loci | 1227058 % of reads mapped to too many loci | 3.91% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.23% % of reads unmapped: other | 16.41% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7397373 7397373 7397373 N_multimapping 1389201 1389201 1389201 N_noFeature 710078 21833492 1180868 N_ambiguous 391889 3274 67364 UnstrandedReadsAssigned:21529296 PositiveStrandReadsAssigned:794497 NegativeStrandReadsAssigned:21383031 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450057 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: ERR3450057-trimmed-pair1.fastq ERR3450057-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 31,417,837 reads, 22,506,311 reads pseudoaligned [quant] estimated average fragment length: 192.376 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,204 rounds 52973 ERR3450057.ke.tsv 35125 ERR3450057.se.tsv 88098 total ==> ERR3450057.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 744.857 0 0 PNS24247 1044 852.624 53.9975 4.14242 PNS24249 1928 1736.62 306.208 11.5331 PNS24246 1044 852.624 53.9975 4.14242 PNS24248 1044 852.624 53.9975 4.14242 PNS24244 1471 1279.62 35.7997 1.82993 PNS24243 293 125.352 1 0.521803 KQK14069 1603 1411.62 3127.68 144.924 KQK14071 474 287.15 188.159 42.8601 ==> ERR3450057.se.tsv <== BRADI_1g14170v3 3383 BRADI_1g53295v3 19 BRADI_1g59795v3 199 BRADI_1g07683v3 0 BRADI_1g00485v3 70 BRADI_1g20270v3 3656 BRADI_1g74790v3 233 BRADI_1g09890v3 53 BRADI_1g77505v3 283 BRADI_1g48960v3 2 ERR3450057 completed mapping pipeline successfully