Starting /dee2/code/volunteer_pipeline.sh ERR3450062 current disk space = 1543071436800 free memory = 1602355560 ERR3450062 SRAfilesize 2f25f1708ee6d912246c733ebfcfb37d ERR3450062.sra ERR3450062.sra file validated ERR3450062 is paired end ERR3450062 is conventional basespace ERR3450062 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450062_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 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.082 37.0 37.0 37.0 37.0 37.0 2 36.38 37.0 37.0 37.0 37.0 37.0 3 36.3735 37.0 37.0 37.0 37.0 37.0 4 36.487 37.0 37.0 37.0 37.0 37.0 5 36.588 37.0 37.0 37.0 37.0 37.0 6 36.5895 37.0 37.0 37.0 37.0 37.0 7 36.388 37.0 37.0 37.0 37.0 37.0 8 36.4985 37.0 37.0 37.0 37.0 37.0 9 36.4855 37.0 37.0 37.0 37.0 37.0 10-11 36.519999999999996 37.0 37.0 37.0 37.0 37.0 12-13 36.480000000000004 37.0 37.0 37.0 37.0 37.0 14-15 36.486999999999995 37.0 37.0 37.0 37.0 37.0 16-17 36.45225000000001 37.0 37.0 37.0 37.0 37.0 18-19 36.494 37.0 37.0 37.0 37.0 37.0 20-21 36.512249999999995 37.0 37.0 37.0 37.0 37.0 22-23 36.40875 37.0 37.0 37.0 37.0 37.0 24-25 36.43175 37.0 37.0 37.0 37.0 37.0 26-27 36.384249999999994 37.0 37.0 37.0 37.0 37.0 28-29 36.402 37.0 37.0 37.0 37.0 37.0 30-31 36.4045 37.0 37.0 37.0 37.0 37.0 32-33 36.32 37.0 37.0 37.0 37.0 37.0 34-35 36.328 37.0 37.0 37.0 37.0 37.0 36-37 36.34525 37.0 37.0 37.0 37.0 37.0 38-39 36.2625 37.0 37.0 37.0 37.0 37.0 40-41 36.366 37.0 37.0 37.0 37.0 37.0 42-43 36.3125 37.0 37.0 37.0 37.0 37.0 44-45 36.203 37.0 37.0 37.0 37.0 37.0 46-47 36.103 37.0 37.0 37.0 37.0 37.0 48-49 36.1785 37.0 37.0 37.0 37.0 37.0 50-51 36.182 37.0 37.0 37.0 37.0 37.0 52-53 36.174 37.0 37.0 37.0 37.0 37.0 54-55 36.12325 37.0 37.0 37.0 37.0 37.0 56-57 36.161500000000004 37.0 37.0 37.0 37.0 37.0 58-59 36.03425 37.0 37.0 37.0 37.0 37.0 60-61 35.98325 37.0 37.0 37.0 37.0 37.0 62-63 35.937250000000006 37.0 37.0 37.0 37.0 37.0 64-65 35.957750000000004 37.0 37.0 37.0 37.0 37.0 66-67 36.0435 37.0 37.0 37.0 37.0 37.0 68-69 35.923249999999996 37.0 37.0 37.0 37.0 37.0 70-71 35.766 37.0 37.0 37.0 37.0 37.0 72-73 35.701 37.0 37.0 37.0 37.0 37.0 74-75 36.0905 37.0 37.0 37.0 37.0 37.0 76-77 36.1385 37.0 37.0 37.0 37.0 37.0 78-79 36.073499999999996 37.0 37.0 37.0 37.0 37.0 80-81 36.080749999999995 37.0 37.0 37.0 37.0 37.0 82-83 36.033500000000004 37.0 37.0 37.0 37.0 37.0 84-85 36.06275 37.0 37.0 37.0 37.0 37.0 86-87 36.02225 37.0 37.0 37.0 37.0 37.0 88-89 35.9765 37.0 37.0 37.0 37.0 37.0 90-91 36.064 37.0 37.0 37.0 37.0 37.0 92-93 35.96875 37.0 37.0 37.0 37.0 37.0 94-95 35.91525 37.0 37.0 37.0 37.0 37.0 96-97 35.8785 37.0 37.0 37.0 37.0 37.0 98-99 35.8545 37.0 37.0 37.0 37.0 37.0 100-101 35.885999999999996 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 2.0 23 2.0 24 5.0 25 10.0 26 12.0 27 13.0 28 22.0 29 32.0 30 48.0 31 55.0 32 67.0 33 76.0 34 126.0 35 196.0 36 1840.0 37 1493.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.89473684210527 10.501253132832082 10.952380952380953 40.65162907268171 2 20.825 12.925 31.075000000000003 35.175 3 21.25 16.875 25.724999999999998 36.15 4 28.475 23.225 18.15 30.15 5 27.55 27.55 20.65 24.25 6 23.45 30.95 24.349999999999998 21.25 7 20.325 22.45 37.625 19.6 8 22.05 20.200000000000003 29.849999999999998 27.900000000000002 9 23.25 19.975 31.474999999999998 25.3 10-11 23.275000000000002 27.875 21.925 26.924999999999997 12-13 23.2625 22.650000000000002 26.5125 27.575 14-15 23.2875 24.462500000000002 25.825 26.424999999999997 16-17 23.7625 23.9 25.387500000000003 26.950000000000003 18-19 24.887500000000003 24.462500000000002 24.8125 25.837500000000002 20-21 24.3125 25.35 23.7875 26.55 22-23 24.887500000000003 23.65 25.124999999999996 26.337500000000002 24-25 23.7 24.25 23.875 28.175 26-27 24.8 23.2875 23.8625 28.050000000000004 28-29 25.0375 24.5375 23.2375 27.187499999999996 30-31 25.3 22.9375 24.0 27.762500000000003 32-33 23.0 24.55 24.762500000000003 27.6875 34-35 24.587500000000002 23.5375 24.3 27.575 36-37 24.8125 23.7375 24.4875 26.9625 38-39 24.099999999999998 23.2375 24.2 28.462500000000002 40-41 24.55 24.1375 23.962500000000002 27.35 42-43 24.4125 23.5875 24.5625 27.437499999999996 44-45 23.925 23.6875 24.8125 27.575 46-47 24.9125 23.225 25.025 26.8375 48-49 23.974999999999998 23.1125 23.8125 29.099999999999998 50-51 23.95 22.725 25.662499999999998 27.6625 52-53 25.575 23.4875 23.9875 26.950000000000003 54-55 24.587500000000002 23.925 24.325 27.1625 56-57 24.349999999999998 23.325000000000003 25.0125 27.3125 58-59 24.4875 24.2375 23.775 27.500000000000004 60-61 25.650000000000002 23.825 24.8125 25.7125 62-63 25.35 22.1 24.275 28.275 64-65 23.962500000000002 23.925 24.2875 27.825 66-67 24.8125 22.475 24.9125 27.800000000000004 68-69 24.55 23.8625 24.4 27.187499999999996 70-71 25.937500000000004 24.887500000000003 23.325000000000003 25.85 72-73 25.362499999999997 24.775 23.8375 26.025 74-75 25.424999999999997 22.925 23.7625 27.8875 76-77 26.05 24.2875 23.275000000000002 26.387500000000003 78-79 25.4875 23.4375 22.9625 28.1125 80-81 25.224999999999998 23.875 22.7375 28.1625 82-83 25.75 23.9375 23.2625 27.05 84-85 26.237500000000004 23.5875 22.475 27.700000000000003 86-87 24.55 24.5 23.1125 27.8375 88-89 26.25 24.0 22.95 26.8 90-91 25.662499999999998 24.2 23.400000000000002 26.737499999999997 92-93 25.25 23.8375 23.3125 27.6 94-95 25.900000000000002 24.9 22.912499999999998 26.2875 96-97 25.2 24.1875 23.225 27.3875 98-99 24.9 23.875 23.75 27.474999999999998 100-101 26.237500000000004 24.5 22.3625 26.900000000000002 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 4.0 1 2.5 2 0.5 3 0.5 4 1.0 5 0.5 6 0.5 7 1.0 8 1.0 9 1.0 10 0.5 11 1.0 12 1.0 13 0.0 14 0.0 15 0.5 16 1.0 17 0.5 18 0.0 19 0.0 20 0.0 21 0.0 22 1.0 23 1.0 24 0.0 25 0.0 26 1.5 27 5.0 28 4.0 29 0.5 30 1.5 31 4.5 32 5.0 33 8.0 34 13.5 35 16.5 36 26.0 37 35.5 38 41.0 39 51.5 40 71.5 41 86.5 42 105.5 43 133.5 44 143.5 45 156.5 46 164.0 47 156.5 48 166.0 49 173.5 50 170.5 51 164.5 52 171.0 53 176.5 54 175.0 55 166.5 56 146.5 57 133.5 58 124.5 59 101.5 60 87.0 61 81.0 62 67.5 63 63.0 64 60.5 65 62.5 66 58.5 67 53.0 68 52.0 69 46.5 70 38.0 71 30.0 72 28.0 73 31.5 74 26.5 75 23.5 76 21.5 77 15.5 78 12.5 79 7.0 80 3.5 81 4.5 82 3.0 83 2.0 84 1.5 85 0.5 86 0.5 87 0.5 88 0.5 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 0.25 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 85.125 #Duplication Level Percentage of deduplicated Percentage of total 1 88.01762114537445 74.925 2 8.986784140969164 15.299999999999999 3 1.908957415565345 4.875 4 0.4698972099853157 1.6 5 0.2936857562408223 1.25 6 0.11747430249632893 0.6 7 0.05873715124816446 0.35000000000000003 8 0.0881057268722467 0.6 9 0.0 0.0 >10 0.05873715124816446 0.5 >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 CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 10 0.25 No Hit GCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGC 10 0.25 No Hit CCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCAT 8 0.2 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 8 0.2 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCGGAGAATCTCGGTT 8 0.2 TruSeq Adapter, Index 6 (97% over 36bp) GTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCC 7 0.17500000000000002 No Hit CCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAAT 7 0.17500000000000002 No Hit CCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATCCCATGCTA 6 0.15 No Hit CTCCAATGGATCCTCGTTAAGGGATTTAGATTGTACTCATTCCAATTACC 6 0.15 No Hit CATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACC 6 0.15 No Hit CTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTG 6 0.15 No Hit GTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCT 5 0.125 No Hit CTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAG 5 0.125 No Hit GTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCG 5 0.125 No Hit GGCTAGGAGCGCATCGCCGGCTGAAGGGTCGAGTAGGTCGGTGCTCGCCG 5 0.125 No Hit ACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCGACG 5 0.125 No Hit GCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTCG 5 0.125 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCA 5 0.125 No Hit GTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCAT 5 0.125 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 5 0.125 No Hit TCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATAT 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.037500000000000006 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.1 0.0 0.0 0.0 0.0 28-29 0.1 0.0 0.0 0.0 0.0 30-31 0.1 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.125 0.0 0.0 0.0 0.0 36-37 0.1875 0.0 0.0 0.0 0.0 38-39 0.225 0.0 0.0 0.0 0.0 40-41 0.225 0.0 0.0 0.0 0.0 42-43 0.2375 0.0 0.0 0.0 0.0 44-45 0.2875 0.0 0.0 0.0 0.0 46-47 0.42500000000000004 0.0 0.0 0.0 0.0 48-49 0.5125 0.0 0.0 0.0 0.0 50-51 0.6 0.0 0.0 0.0 0.0 52-53 0.675 0.0 0.0 0.0 0.0 54-55 0.8125 0.0 0.0 0.0 0.0 56-57 0.925 0.0 0.0 0.0 0.0 58-59 1.1 0.0 0.0 0.0 0.0 60-61 1.35 0.0 0.0 0.0 0.0 62-63 1.65 0.0 0.0 0.0 0.0 64-65 1.9749999999999999 0.0 0.0 0.0 0.0 66-67 2.3 0.0 0.0 0.0 0.0 68-69 2.5 0.0 0.0 0.0 0.0 70-71 2.8499999999999996 0.0 0.0 0.0 0.0 72-73 3.1375 0.0 0.0 0.0 0.0 74-75 3.4749999999999996 0.0 0.0 0.0 0.0 76-77 3.9 0.0 0.0 0.0 0.0 78-79 4.425000000000001 0.0 0.0 0.0 0.0 80-81 5.1875 0.0 0.0 0.0 0.0 82-83 5.925 0.0 0.0 0.0 0.0 84-85 6.675 0.0 0.0 0.0 0.0 86-87 7.1375 0.0 0.0 0.0 0.0 88-89 7.6875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TAGATCG 15 0.009957196 47.5 94-95 >>END_MODULE ERR3450062 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450062_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 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.175 37.0 37.0 37.0 37.0 37.0 2 35.86325 37.0 37.0 37.0 37.0 37.0 3 35.958 37.0 37.0 37.0 37.0 37.0 4 36.0535 37.0 37.0 37.0 37.0 37.0 5 36.1115 37.0 37.0 37.0 37.0 37.0 6 36.16775 37.0 37.0 37.0 37.0 37.0 7 36.0265 37.0 37.0 37.0 37.0 37.0 8 35.9435 37.0 37.0 37.0 37.0 37.0 9 36.0525 37.0 37.0 37.0 37.0 37.0 10-11 36.025999999999996 37.0 37.0 37.0 37.0 37.0 12-13 36.051 37.0 37.0 37.0 37.0 37.0 14-15 35.9945 37.0 37.0 37.0 37.0 37.0 16-17 35.994249999999994 37.0 37.0 37.0 37.0 37.0 18-19 35.961875 37.0 37.0 37.0 37.0 37.0 20-21 35.88175 37.0 37.0 37.0 37.0 37.0 22-23 35.96025 37.0 37.0 37.0 37.0 37.0 24-25 35.83475 37.0 37.0 37.0 37.0 37.0 26-27 35.6955 37.0 37.0 37.0 37.0 37.0 28-29 35.652 37.0 37.0 37.0 37.0 37.0 30-31 35.593500000000006 37.0 37.0 37.0 37.0 37.0 32-33 35.68475 37.0 37.0 37.0 37.0 37.0 34-35 35.488249999999994 37.0 37.0 37.0 37.0 37.0 36-37 35.42175 37.0 37.0 37.0 37.0 37.0 38-39 35.475750000000005 37.0 37.0 37.0 37.0 37.0 40-41 35.43275 37.0 37.0 37.0 37.0 37.0 42-43 35.523624999999996 37.0 37.0 37.0 37.0 37.0 44-45 35.539874999999995 37.0 37.0 37.0 37.0 37.0 46-47 35.457750000000004 37.0 37.0 37.0 37.0 37.0 48-49 35.63725 37.0 37.0 37.0 37.0 37.0 50-51 35.4155 37.0 37.0 37.0 37.0 37.0 52-53 35.557500000000005 37.0 37.0 37.0 37.0 37.0 54-55 35.65325 37.0 37.0 37.0 37.0 37.0 56-57 35.485 37.0 37.0 37.0 37.0 37.0 58-59 35.50625 37.0 37.0 37.0 37.0 37.0 60-61 35.6445 37.0 37.0 37.0 37.0 37.0 62-63 35.668 37.0 37.0 37.0 37.0 37.0 64-65 35.70925 37.0 37.0 37.0 37.0 37.0 66-67 35.58725 37.0 37.0 37.0 37.0 37.0 68-69 35.53275 37.0 37.0 37.0 37.0 37.0 70-71 35.484875 37.0 37.0 37.0 37.0 37.0 72-73 35.455 37.0 37.0 37.0 37.0 37.0 74-75 35.359125 37.0 37.0 37.0 37.0 37.0 76-77 35.382999999999996 37.0 37.0 37.0 37.0 37.0 78-79 35.3315 37.0 37.0 37.0 37.0 37.0 80-81 35.2945 37.0 37.0 37.0 31.0 37.0 82-83 35.281875 37.0 37.0 37.0 37.0 37.0 84-85 35.3505 37.0 37.0 37.0 37.0 37.0 86-87 35.3905 37.0 37.0 37.0 37.0 37.0 88-89 35.327749999999995 37.0 37.0 37.0 37.0 37.0 90-91 35.393 37.0 37.0 37.0 37.0 37.0 92-93 35.373875 37.0 37.0 37.0 37.0 37.0 94-95 35.383250000000004 37.0 37.0 37.0 37.0 37.0 96-97 35.29925 37.0 37.0 37.0 37.0 37.0 98-99 35.370625 37.0 37.0 37.0 37.0 37.0 100-101 35.277874999999995 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 1.0 15 2.0 16 2.0 17 2.0 18 7.0 19 8.0 20 12.0 21 14.0 22 12.0 23 10.0 24 8.0 25 13.0 26 14.0 27 20.0 28 32.0 29 30.0 30 43.0 31 55.0 32 88.0 33 104.0 34 179.0 35 456.0 36 2288.0 37 600.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.075 16.875 11.600000000000001 31.45 2 26.9567391847962 21.85546386596649 27.45686421605401 23.730932733183295 3 24.975 23.35 26.700000000000003 24.975 4 30.7 28.275 17.150000000000002 23.875 5 30.25 28.875 18.15 22.725 6 24.60615153788447 31.58289572393098 20.330082520630157 23.48087021755439 7 25.4 19.25 31.0 24.349999999999998 8 26.700000000000003 20.025000000000002 22.975 30.3 9 27.150000000000002 22.7 24.725 25.424999999999997 10-11 28.6625 27.437499999999996 19.6875 24.212500000000002 12-13 29.025000000000002 22.412499999999998 22.4875 26.075 14-15 28.487499999999997 23.75 23.4625 24.3 16-17 27.0875 24.7 22.5 25.7125 18-19 27.303412926615827 25.315664458057256 22.940367545943243 24.440555069383674 20-21 27.762500000000003 25.7 22.287499999999998 24.25 22-23 28.349999999999998 24.224999999999998 21.925 25.5 24-25 28.525 24.8625 21.9375 24.675 26-27 28.712500000000002 24.2 22.375 24.712500000000002 28-29 29.175 24.175 21.6625 24.9875 30-31 27.575 24.887500000000003 22.35 25.1875 32-33 29.15 23.7625 22.7625 24.325 34-35 28.4 24.675 22.375 24.55 36-37 28.275 25.174999999999997 21.5625 24.9875 38-39 27.625 24.575 22.2 25.6 40-41 27.525 24.6125 21.975 25.887500000000003 42-43 27.315914489311165 25.55319414926866 23.002875359419928 24.128016002000248 44-45 28.34104263032879 23.29041130141268 22.327790973871732 26.040755094386796 46-47 28.199999999999996 24.925 21.85 25.025 48-49 27.775 25.0 22.2 25.025 50-51 28.000000000000004 25.025 21.6875 25.2875 52-53 28.6125 23.775 22.662499999999998 24.95 54-55 27.975 24.212500000000002 21.9625 25.85 56-57 28.7 25.087500000000002 22.425 23.7875 58-59 28.525 23.5875 22.975 24.9125 60-61 28.712500000000002 24.474999999999998 22.2 24.6125 62-63 28.212500000000002 24.2 22.6875 24.9 64-65 28.575 24.099999999999998 22.400000000000002 24.925 66-67 28.8875 24.2875 22.537499999999998 24.2875 68-69 28.7 24.887500000000003 22.5125 23.9 70-71 29.066133266658333 24.978122265283158 22.315289411176398 23.64045505688211 72-73 28.49462365591398 23.93098274568642 23.380845211302827 24.193548387096776 74-75 29.25365670708839 24.128016002000248 21.552694086760845 25.065633204150515 76-77 28.9 24.5125 22.412499999999998 24.175 78-79 29.6375 23.125 22.0 25.2375 80-81 29.3875 24.8 22.575 23.2375 82-83 29.678709838729837 24.34054256782098 21.527690961370173 24.453056632079008 84-85 29.675 24.1375 22.3875 23.799999999999997 86-87 28.9875 24.1375 22.425 24.45 88-89 29.799999999999997 25.25 21.475 23.474999999999998 90-91 29.4125 25.087500000000002 21.95 23.549999999999997 92-93 30.428803600450056 25.153144143017876 22.290286285785722 22.127765970746342 94-95 29.912499999999998 25.224999999999998 21.1875 23.674999999999997 96-97 29.275000000000002 24.962500000000002 22.975 22.787499999999998 98-99 29.541192649081133 24.40305038129766 22.615326915864483 23.44043005375672 100-101 31.403925490686333 24.778097262157768 21.852731591448933 21.965245655706962 >>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 0.5 7 1.0 8 0.5 9 0.5 10 1.0 11 1.0 12 1.0 13 1.0 14 0.5 15 2.0 16 2.0 17 0.0 18 0.5 19 1.5 20 1.0 21 1.0 22 1.0 23 0.5 24 1.0 25 1.0 26 2.0 27 3.0 28 3.0 29 2.0 30 1.0 31 0.5 32 2.0 33 3.5 34 7.5 35 15.0 36 19.5 37 33.5 38 52.5 39 68.0 40 74.5 41 79.5 42 102.0 43 114.0 44 124.0 45 145.5 46 154.5 47 155.0 48 163.5 49 173.0 50 170.5 51 159.5 52 160.0 53 158.0 54 157.0 55 163.5 56 156.5 57 130.0 58 98.5 59 91.0 60 86.0 61 82.0 62 79.0 63 71.0 64 73.5 65 67.5 66 58.5 67 56.5 68 68.5 69 69.5 70 50.5 71 45.5 72 38.0 73 30.5 74 26.0 75 13.5 76 15.0 77 18.0 78 11.0 79 10.5 80 7.5 81 6.5 82 5.0 83 2.0 84 3.0 85 4.0 86 2.5 87 2.0 88 2.0 89 1.0 90 1.5 91 1.5 92 0.5 93 0.5 94 1.0 95 1.0 96 1.5 97 2.0 98 2.0 99 4.0 100 10.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.025 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 0.0125 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 0.0125 44-45 0.0125 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 0.0125 72-73 0.025 74-75 0.0125 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0125 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0125 94-95 0.0 96-97 0.0 98-99 0.0125 100-101 0.0125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 86.9 #Duplication Level Percentage of deduplicated Percentage of total 1 88.86651323360184 77.225 2 8.918296892980438 15.5 3 1.668584579976985 4.35 4 0.2589182968929804 0.8999999999999999 5 0.05753739930955121 0.25 6 0.05753739930955121 0.3 7 0.05753739930955121 0.35000000000000003 8 0.05753739930955121 0.4 9 0.0 0.0 >10 0.05753739930955121 0.7250000000000001 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 18 0.44999999999999996 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 11 0.27499999999999997 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 8 0.2 No Hit CTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACC 8 0.2 No Hit GTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCAC 7 0.17500000000000002 No Hit AGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAA 7 0.17500000000000002 No Hit CAAACCCCGACTTCTGGGAGGGGCGCATTTATTAGATAAAAGGCTGACGC 6 0.15 No Hit GTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTATATAGCC 6 0.15 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAAG 5 0.125 No Hit AAGCCATGCATGTGCAAGTATGAACTAATTTGAACTGTGAAACTGCGAAT 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.037500000000000006 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.075 0.0 0.0 0.0 0.0 26-27 0.1 0.0 0.0 0.0 0.0 28-29 0.1 0.0 0.0 0.0 0.0 30-31 0.1 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.125 0.0 0.0 0.0 0.0 36-37 0.1875 0.0 0.0 0.0 0.0 38-39 0.225 0.0 0.0 0.0 0.0 40-41 0.225 0.0 0.0 0.0 0.0 42-43 0.2375 0.0 0.0 0.0 0.0 44-45 0.2875 0.0 0.0 0.0 0.0 46-47 0.42500000000000004 0.0 0.0 0.0 0.0 48-49 0.5125 0.0 0.0 0.0 0.0 50-51 0.6 0.0 0.0 0.0 0.0 52-53 0.675 0.0 0.0 0.0 0.0 54-55 0.8125 0.0 0.0 0.0 0.0 56-57 0.9375 0.0 0.0 0.0 0.0 58-59 1.125 0.0 0.0 0.0 0.0 60-61 1.35 0.0 0.0 0.0 0.0 62-63 1.675 0.0 0.0 0.0 0.0 64-65 2.025 0.0 0.0 0.0 0.0 66-67 2.35 0.0 0.0 0.0 0.0 68-69 2.5375 0.0 0.0 0.0 0.0 70-71 2.8875 0.0 0.0 0.0 0.0 72-73 3.1875 0.0 0.0 0.0 0.0 74-75 3.5250000000000004 0.0 0.0 0.0 0.0 76-77 3.9499999999999997 0.0 0.0 0.0 0.0 78-79 4.475 0.0 0.0 0.0 0.0 80-81 5.225 0.0 0.0 0.0 0.0 82-83 5.925 0.0 0.0 0.0 0.0 84-85 6.675 0.0 0.0 0.0 0.0 86-87 7.1125 0.0 0.0 0.0 0.0 88-89 7.6625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827261 spots for ERR3450062.sra Written 827261 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra Read 827248 spots for ERR3450062.sra Written 827248 spots for ERR3450062.sra SRR ids: ['ERR3450062.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_3yhd3qf9 ERR3450062.sra spots: 16544973 blocks: [[1, 827248], [827249, 1654496], [1654497, 2481744], [2481745, 3308992], [3308993, 4136240], [4136241, 4963488], [4963489, 5790736], [5790737, 6617984], [6617985, 7445232], [7445233, 8272480], [8272481, 9099728], [9099729, 9926976], [9926977, 10754224], [10754225, 11581472], [11581473, 12408720], [12408721, 13235968], [13235969, 14063216], [14063217, 14890464], [14890465, 15717712], [15717713, 16544973]] ERR3450062 file size 3969128 ERR3450062 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 ERR3450062 ERR3450062_1.fastq ERR3450062_2.fastq Input file: ERR3450062_1.fastq Paired file: ERR3450062_2.fastq trimmed: ERR3450062-trimmed-pair1.fastq, ERR3450062-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 14:19:18 2024 >> started Sat Dec 7 14:19:34 2024 >> done (16.227s) 16544973 read pairs processed; of these: 100 ( 0.00%) short read pairs filtered out after trimming by size control 47467 ( 0.29%) empty read pairs filtered out after trimming by size control 16497406 (99.71%) read pairs available; of these: 2062875 (12.50%) trimmed read pairs available after processing 14434531 (87.50%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 44 0.00% 19 62 0.00% 20 231 0.00% 21 483 0.00% 22 631 0.00% 23 317 0.00% 24 302 0.00% 25 440 0.00% 26 611 0.00% 27 838 0.01% 28 1202 0.01% 29 1598 0.01% 30 1915 0.01% 31 2232 0.01% 32 2340 0.01% 33 2239 0.01% 34 2160 0.01% 35 2202 0.01% 36 2555 0.02% 37 2840 0.02% 38 3318 0.02% 39 3945 0.02% 40 4539 0.03% 41 5024 0.03% 42 5629 0.03% 43 6021 0.04% 44 5584 0.03% 45 5834 0.04% 46 6098 0.04% 47 6749 0.04% 48 7376 0.04% 49 7915 0.05% 50 8977 0.05% 51 10040 0.06% 52 11121 0.07% 53 11393 0.07% 54 11969 0.07% 55 12469 0.08% 56 13078 0.08% 57 13481 0.08% 58 14486 0.09% 59 16091 0.10% 60 17256 0.10% 61 18721 0.11% 62 20326 0.12% 63 21821 0.13% 64 22748 0.14% 65 23338 0.14% 66 24016 0.15% 67 25005 0.15% 68 25860 0.16% 69 26885 0.16% 70 28454 0.17% 71 30830 0.19% 72 32994 0.20% 73 34296 0.21% 74 35507 0.22% 75 37385 0.23% 76 37492 0.23% 77 38608 0.23% 78 39878 0.24% 79 42131 0.26% 80 42926 0.26% 81 44489 0.27% 82 47065 0.29% 83 48184 0.29% 84 49468 0.30% 85 52000 0.32% 86 53114 0.32% 87 55199 0.33% 88 56064 0.34% 89 57582 0.35% 90 59584 0.36% 91 62113 0.38% 92 64622 0.39% 93 65587 0.40% 94 66954 0.41% 95 69109 0.42% 96 69769 0.42% 97 71994 0.44% 98 72925 0.44% 99 73161 0.44% 100 81036 0.49% 101 14434531 87.50% 16497406 reads passed initial QC criterion=sequence-density sequence-density=0.44 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=37 prefix-density=0.45 prefix-fanout=1.9 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.09 sequence-density-rank=22 fanout-score=43.26 fanout-score-rank=1 prefix-density=1.28 prefix-fanout=3.0 sequence=GGCGGCGGCGGCCTCGCCGTCGCTGGTGTACTTCCCCAGCTGCGCCAGGGAGTTTGCCTTGGCGCGCAGCAGCAGTGCCTCCTGGGCCGCCGCCACGTTCTCCGGCCGTCCTC criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=1.96 fanout-score-rank=29 prefix-density=0.33 prefix-fanout=2.0 sequence=CAAGTGTTGGATT criterion=fanout-score sequence-density=0.08 sequence-density-rank=27 fanout-score=169.95 fanout-score-rank=1 prefix-density=0.65 prefix-fanout=22.0 sequence=CGGCGGCGGCGA ERR3450062 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:20:21 Started mapping on | Dec 07 14:20:21 Finished on | Dec 07 14:21:56 Mapping speed, Million of reads per hour | 625.16 Number of input reads | 16497406 Average input read length | 196 UNIQUE READS: Uniquely mapped reads number | 10948448 Uniquely mapped reads % | 66.36% Average mapped length | 196.63 Number of splices: Total | 6693223 Number of splices: Annotated (sjdb) | 6343607 Number of splices: GT/AG | 6604843 Number of splices: GC/AG | 76483 Number of splices: AT/AC | 3890 Number of splices: Non-canonical | 8007 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.01% Deletion average length | 2.12 Insertion rate per base | 0.01% Insertion average length | 1.90 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1312858 % of reads mapped to multiple loci | 7.96% Number of reads mapped to too many loci | 755057 % of reads mapped to too many loci | 4.58% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.16% % of reads unmapped: other | 17.94% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4236100 4236100 4236100 N_multimapping 1312858 1312858 1312858 N_noFeature 494509 10523133 754186 N_ambiguous 210180 1694 47482 UnstrandedReadsAssigned:10243759 PositiveStrandReadsAssigned:423621 NegativeStrandReadsAssigned:10146780 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450062 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: ERR3450062-trimmed-pair1.fastq ERR3450062-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,497,406 reads, 10,969,944 reads pseudoaligned [quant] estimated average fragment length: 180.748 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,117 rounds 52973 ERR3450062.ke.tsv 35125 ERR3450062.se.tsv 88098 total ==> ERR3450062.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 756.453 1.39741 0.24543 PNS24247 1044 864.252 26.9451 4.14214 PNS24249 1928 1748.25 100.549 7.6412 PNS24246 1044 864.252 26.9451 4.14214 PNS24248 1044 864.252 26.9451 4.14214 PNS24244 1471 1291.25 38.218 3.93226 PNS24243 293 134.439 0 0 KQK14069 1603 1423.25 2288.35 213.612 KQK14071 474 297.845 127.743 56.9815 ==> ERR3450062.se.tsv <== BRADI_1g14170v3 2539 BRADI_1g53295v3 12 BRADI_1g59795v3 134 BRADI_1g07683v3 0 BRADI_1g00485v3 10 BRADI_1g20270v3 1435 BRADI_1g74790v3 144 BRADI_1g09890v3 8 BRADI_1g77505v3 135 BRADI_1g48960v3 2 ERR3450062 completed mapping pipeline successfully