Starting /dee2/code/volunteer_pipeline.sh ERR3450070 current disk space = 1543004643328 free memory = 1600622848 ERR3450070 SRAfilesize d905b64fcccbf034c5e3ae97c065e01c ERR3450070.sra ERR3450070.sra file validated ERR3450070 is paired end ERR3450070 is conventional basespace ERR3450070 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450070_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 36.07 37.0 37.0 37.0 37.0 37.0 2 36.37 37.0 37.0 37.0 37.0 37.0 3 36.3505 37.0 37.0 37.0 37.0 37.0 4 36.4625 37.0 37.0 37.0 37.0 37.0 5 36.535 37.0 37.0 37.0 37.0 37.0 6 36.514 37.0 37.0 37.0 37.0 37.0 7 36.468 37.0 37.0 37.0 37.0 37.0 8 36.4425 37.0 37.0 37.0 37.0 37.0 9 36.5485 37.0 37.0 37.0 37.0 37.0 10-11 36.413 37.0 37.0 37.0 37.0 37.0 12-13 36.52475 37.0 37.0 37.0 37.0 37.0 14-15 36.48375 37.0 37.0 37.0 37.0 37.0 16-17 36.50075 37.0 37.0 37.0 37.0 37.0 18-19 36.487 37.0 37.0 37.0 37.0 37.0 20-21 36.521 37.0 37.0 37.0 37.0 37.0 22-23 36.489999999999995 37.0 37.0 37.0 37.0 37.0 24-25 36.4585 37.0 37.0 37.0 37.0 37.0 26-27 36.41875 37.0 37.0 37.0 37.0 37.0 28-29 36.42875 37.0 37.0 37.0 37.0 37.0 30-31 36.36425 37.0 37.0 37.0 37.0 37.0 32-33 36.337 37.0 37.0 37.0 37.0 37.0 34-35 36.21325 37.0 37.0 37.0 37.0 37.0 36-37 36.3655 37.0 37.0 37.0 37.0 37.0 38-39 36.369249999999994 37.0 37.0 37.0 37.0 37.0 40-41 36.34625 37.0 37.0 37.0 37.0 37.0 42-43 36.289500000000004 37.0 37.0 37.0 37.0 37.0 44-45 36.2245 37.0 37.0 37.0 37.0 37.0 46-47 36.122749999999996 37.0 37.0 37.0 37.0 37.0 48-49 36.182 37.0 37.0 37.0 37.0 37.0 50-51 36.167 37.0 37.0 37.0 37.0 37.0 52-53 36.028999999999996 37.0 37.0 37.0 37.0 37.0 54-55 36.12075 37.0 37.0 37.0 37.0 37.0 56-57 36.07125 37.0 37.0 37.0 37.0 37.0 58-59 36.051500000000004 37.0 37.0 37.0 37.0 37.0 60-61 35.994 37.0 37.0 37.0 37.0 37.0 62-63 36.058499999999995 37.0 37.0 37.0 37.0 37.0 64-65 35.92375 37.0 37.0 37.0 37.0 37.0 66-67 35.98725 37.0 37.0 37.0 37.0 37.0 68-69 35.97125 37.0 37.0 37.0 37.0 37.0 70-71 35.8375 37.0 37.0 37.0 37.0 37.0 72-73 35.70675 37.0 37.0 37.0 37.0 37.0 74-75 36.048 37.0 37.0 37.0 37.0 37.0 76-77 36.147000000000006 37.0 37.0 37.0 37.0 37.0 78-79 36.170249999999996 37.0 37.0 37.0 37.0 37.0 80-81 36.1005 37.0 37.0 37.0 37.0 37.0 82-83 36.12875 37.0 37.0 37.0 37.0 37.0 84-85 36.129000000000005 37.0 37.0 37.0 37.0 37.0 86-87 36.039249999999996 37.0 37.0 37.0 37.0 37.0 88-89 36.074 37.0 37.0 37.0 37.0 37.0 90-91 36.02675000000001 37.0 37.0 37.0 37.0 37.0 92-93 35.973749999999995 37.0 37.0 37.0 37.0 37.0 94-95 36.070750000000004 37.0 37.0 37.0 37.0 37.0 96-97 35.945 37.0 37.0 37.0 37.0 37.0 98-99 35.948 37.0 37.0 37.0 37.0 37.0 100-101 35.92275 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 2.0 22 1.0 23 3.0 24 6.0 25 5.0 26 9.0 27 18.0 28 31.0 29 29.0 30 39.0 31 56.0 32 36.0 33 96.0 34 138.0 35 201.0 36 1816.0 37 1514.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 41.14400401404917 9.157049673858504 10.110386352232815 39.58855995985951 2 22.45 13.425 29.049999999999997 35.075 3 21.925 17.775 25.275 35.025 4 28.65 22.425 17.8 31.125000000000004 5 27.875 26.35 20.724999999999998 25.05 6 23.799999999999997 31.900000000000002 23.35 20.95 7 20.175 23.5 36.6 19.725 8 21.45 20.825 30.349999999999998 27.375 9 23.225 21.099999999999998 29.825000000000003 25.85 10-11 24.5125 28.325 22.15 25.0125 12-13 23.974999999999998 22.6375 24.725 28.6625 14-15 23.6625 24.825 25.174999999999997 26.337500000000002 16-17 25.1 23.375 25.137500000000003 26.387500000000003 18-19 24.712500000000002 24.337500000000002 25.674999999999997 25.275 20-21 24.4875 24.762500000000003 24.4875 26.2625 22-23 25.05 24.7875 24.2625 25.900000000000002 24-25 25.2 24.1125 24.3125 26.375 26-27 23.5 24.349999999999998 24.474999999999998 27.675 28-29 25.637500000000003 23.8625 24.125 26.375 30-31 24.212500000000002 23.5125 24.224999999999998 28.050000000000004 32-33 24.6625 23.7125 24.9125 26.7125 34-35 24.525 23.400000000000002 25.337500000000002 26.737499999999997 36-37 24.474999999999998 23.3125 24.212500000000002 28.000000000000004 38-39 24.6125 24.275 24.125 26.987499999999997 40-41 24.0375 24.3 24.325 27.3375 42-43 24.775 23.7125 24.7375 26.775 44-45 24.1625 23.8375 25.0 27.0 46-47 25.5 23.3125 23.3875 27.800000000000004 48-49 24.275 23.7375 25.25 26.737499999999997 50-51 24.7 23.3375 25.025 26.937499999999996 52-53 25.575 23.8625 24.2875 26.275 54-55 24.887500000000003 23.6875 24.05 27.375 56-57 24.175 23.125 24.9125 27.787499999999998 58-59 25.2 23.9375 24.3 26.5625 60-61 26.075 22.6 24.2375 27.0875 62-63 24.7 23.5375 24.712500000000002 27.05 64-65 25.474999999999998 23.7875 24.3 26.437500000000004 66-67 24.7375 23.400000000000002 24.2875 27.575 68-69 24.25 24.25 24.3875 27.1125 70-71 24.5 23.175 24.1875 28.1375 72-73 25.775 23.0625 24.375 26.787499999999998 74-75 26.450000000000003 22.8375 24.05 26.6625 76-77 26.337500000000002 25.087500000000002 22.55 26.025 78-79 26.0125 23.849999999999998 22.875 27.2625 80-81 24.85 23.6375 23.962500000000002 27.55 82-83 26.700000000000003 24.6875 23.200000000000003 25.412499999999998 84-85 25.0 23.05 23.8375 28.1125 86-87 25.687500000000004 24.4375 23.3875 26.487500000000004 88-89 26.174999999999997 23.8625 23.1375 26.825 90-91 25.9875 23.5125 23.8875 26.6125 92-93 25.4875 23.6125 24.224999999999998 26.674999999999997 94-95 26.6625 23.2125 22.8875 27.237499999999997 96-97 25.7 25.5375 22.7 26.0625 98-99 24.8 24.9125 23.05 27.237499999999997 100-101 25.7625 25.474999999999998 21.8 26.9625 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 7.0 1 4.5 2 1.0 3 0.5 4 1.5 5 1.5 6 1.0 7 1.5 8 1.0 9 1.5 10 2.0 11 0.5 12 0.0 13 0.0 14 0.0 15 0.5 16 1.0 17 2.0 18 2.0 19 1.0 20 1.5 21 1.5 22 1.0 23 0.5 24 0.0 25 1.5 26 2.5 27 1.0 28 1.5 29 2.5 30 3.5 31 5.5 32 8.0 33 11.0 34 14.0 35 19.0 36 28.5 37 32.5 38 33.5 39 48.5 40 65.5 41 76.5 42 98.0 43 117.0 44 137.0 45 161.0 46 185.5 47 194.5 48 187.5 49 172.5 50 163.5 51 179.5 52 188.0 53 177.5 54 151.5 55 134.0 56 132.5 57 112.5 58 98.5 59 90.0 60 77.0 61 77.0 62 72.0 63 71.0 64 65.0 65 66.5 66 66.0 67 53.0 68 53.5 69 54.5 70 43.0 71 38.5 72 44.5 73 39.0 74 24.0 75 21.5 76 18.0 77 11.5 78 11.5 79 10.5 80 8.0 81 3.5 82 1.5 83 1.5 84 1.5 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 pass #Base N-Count 1 0.35000000000000003 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 86.775 #Duplication Level Percentage of deduplicated Percentage of total 1 89.13857677902621 77.35 2 8.354940939210602 14.499999999999998 3 1.5557476231633534 4.05 4 0.6050129645635264 2.1 5 0.14405070584845864 0.625 6 0.02881014116969173 0.15 7 0.11524056467876692 0.7000000000000001 8 0.0 0.0 9 0.0 0.0 >10 0.05762028233938346 0.525 >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 11 0.27499999999999997 No Hit CTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGCACGT 10 0.25 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACTCCGCGAAATCTCGTAT 7 0.17500000000000002 TruSeq Adapter, Index 6 (97% over 36bp) CTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACT 7 0.17500000000000002 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 7 0.17500000000000002 No Hit GCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGC 7 0.17500000000000002 No Hit GGCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTC 6 0.15 No Hit CCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAAT 5 0.125 No Hit CCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAG 5 0.125 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 5 0.125 No Hit GGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCG 5 0.125 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 32-33 0.0625 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.1 0.0 0.0 0.0 0.0 38-39 0.1125 0.0 0.0 0.0 0.0 40-41 0.16249999999999998 0.0 0.0 0.0 0.0 42-43 0.2 0.0 0.0 0.0 0.0 44-45 0.25 0.0 0.0 0.0 0.0 46-47 0.3 0.0 0.0 0.0 0.0 48-49 0.3625 0.0 0.0 0.0 0.0 50-51 0.5 0.0 0.0 0.0 0.0 52-53 0.5625 0.0 0.0 0.0 0.0 54-55 0.6375 0.0 0.0 0.0 0.0 56-57 0.675 0.0 0.0 0.0 0.0 58-59 0.8500000000000001 0.0 0.0 0.0 0.0 60-61 0.9874999999999999 0.0 0.0 0.0 0.0 62-63 1.1749999999999998 0.0 0.0 0.0 0.0 64-65 1.5 0.0 0.0 0.0 0.0 66-67 1.8125 0.0 0.0 0.0 0.0 68-69 2.2249999999999996 0.0 0.0 0.0 0.0 70-71 2.425 0.0 0.0 0.0 0.0 72-73 2.6624999999999996 0.0 0.0 0.0 0.0 74-75 3.1625 0.0 0.0 0.0 0.0 76-77 3.7 0.0 0.0 0.0 0.0 78-79 4.15 0.0 0.0 0.0 0.0 80-81 4.6 0.0 0.0 0.0 0.0 82-83 5.137499999999999 0.0 0.0 0.0 0.0 84-85 5.574999999999999 0.0 0.0 0.0 0.0 86-87 6.125 0.0 0.0 0.0 0.0 88-89 6.7875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450070 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450070_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 36.193 37.0 37.0 37.0 37.0 37.0 2 36.008 37.0 37.0 37.0 37.0 37.0 3 35.9995 37.0 37.0 37.0 37.0 37.0 4 35.9675 37.0 37.0 37.0 37.0 37.0 5 36.1105 37.0 37.0 37.0 37.0 37.0 6 36.2305 37.0 37.0 37.0 37.0 37.0 7 36.0085 37.0 37.0 37.0 37.0 37.0 8 36.0675 37.0 37.0 37.0 37.0 37.0 9 36.1355 37.0 37.0 37.0 37.0 37.0 10-11 35.99425 37.0 37.0 37.0 37.0 37.0 12-13 36.01575 37.0 37.0 37.0 37.0 37.0 14-15 35.995000000000005 37.0 37.0 37.0 37.0 37.0 16-17 36.006 37.0 37.0 37.0 37.0 37.0 18-19 35.9925 37.0 37.0 37.0 37.0 37.0 20-21 35.83725 37.0 37.0 37.0 37.0 37.0 22-23 36.007999999999996 37.0 37.0 37.0 37.0 37.0 24-25 35.803 37.0 37.0 37.0 37.0 37.0 26-27 35.701750000000004 37.0 37.0 37.0 37.0 37.0 28-29 35.70375 37.0 37.0 37.0 37.0 37.0 30-31 35.707499999999996 37.0 37.0 37.0 37.0 37.0 32-33 35.723749999999995 37.0 37.0 37.0 37.0 37.0 34-35 35.56075 37.0 37.0 37.0 37.0 37.0 36-37 35.5155 37.0 37.0 37.0 37.0 37.0 38-39 35.466499999999996 37.0 37.0 37.0 37.0 37.0 40-41 35.6 37.0 37.0 37.0 37.0 37.0 42-43 35.655249999999995 37.0 37.0 37.0 37.0 37.0 44-45 35.5625 37.0 37.0 37.0 37.0 37.0 46-47 35.497 37.0 37.0 37.0 37.0 37.0 48-49 35.4195 37.0 37.0 37.0 37.0 37.0 50-51 35.5285 37.0 37.0 37.0 37.0 37.0 52-53 35.6555 37.0 37.0 37.0 37.0 37.0 54-55 35.54125 37.0 37.0 37.0 37.0 37.0 56-57 35.535250000000005 37.0 37.0 37.0 37.0 37.0 58-59 35.535250000000005 37.0 37.0 37.0 37.0 37.0 60-61 35.65925 37.0 37.0 37.0 37.0 37.0 62-63 35.5945 37.0 37.0 37.0 37.0 37.0 64-65 35.665 37.0 37.0 37.0 37.0 37.0 66-67 35.6 37.0 37.0 37.0 37.0 37.0 68-69 35.5135 37.0 37.0 37.0 37.0 37.0 70-71 35.43375 37.0 37.0 37.0 37.0 37.0 72-73 35.42 37.0 37.0 37.0 37.0 37.0 74-75 35.38125 37.0 37.0 37.0 37.0 37.0 76-77 35.427 37.0 37.0 37.0 37.0 37.0 78-79 35.3095 37.0 37.0 37.0 37.0 37.0 80-81 35.21425 37.0 37.0 37.0 31.0 37.0 82-83 35.31075 37.0 37.0 37.0 31.0 37.0 84-85 35.372 37.0 37.0 37.0 37.0 37.0 86-87 35.3685 37.0 37.0 37.0 37.0 37.0 88-89 35.431 37.0 37.0 37.0 37.0 37.0 90-91 35.38225 37.0 37.0 37.0 37.0 37.0 92-93 35.357749999999996 37.0 37.0 37.0 37.0 37.0 94-95 35.427 37.0 37.0 37.0 37.0 37.0 96-97 35.355500000000006 37.0 37.0 37.0 37.0 37.0 98-99 35.4025 37.0 37.0 37.0 37.0 37.0 100-101 35.29575 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 3.0 16 3.0 17 3.0 18 7.0 19 15.0 20 8.0 21 8.0 22 15.0 23 17.0 24 13.0 25 15.0 26 20.0 27 15.0 28 32.0 29 32.0 30 33.0 31 55.0 32 59.0 33 109.0 34 163.0 35 421.0 36 2278.0 37 676.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.45 17.45 11.325000000000001 30.775000000000002 2 27.175 23.025000000000002 26.724999999999998 23.075000000000003 3 25.674999999999997 22.85 27.275 24.2 4 30.675 27.224999999999998 17.1 25.0 5 29.975 29.349999999999998 18.275 22.400000000000002 6 23.974999999999998 32.375 20.724999999999998 22.925 7 25.05 19.650000000000002 30.625000000000004 24.675 8 25.924999999999997 20.275000000000002 23.35 30.45 9 27.525 22.3 24.925 25.25 10-11 27.85 26.35 21.087500000000002 24.712500000000002 12-13 28.349999999999998 20.925 22.775000000000002 27.950000000000003 14-15 26.6 25.362499999999997 23.5 24.5375 16-17 27.8375 23.375 22.8 25.9875 18-19 28.125 24.1375 22.900000000000002 24.837500000000002 20-21 26.900000000000002 25.2625 22.412499999999998 25.424999999999997 22-23 27.962500000000002 24.55 21.837500000000002 25.650000000000002 24-25 28.1 23.45 23.35 25.1 26-27 27.5875 24.925 21.825 25.662499999999998 28-29 28.462500000000002 23.9875 22.3625 25.1875 30-31 27.6625 24.474999999999998 21.7375 26.125 32-33 27.187499999999996 25.2125 22.4625 25.137500000000003 34-35 28.1375 24.2 22.0625 25.6 36-37 27.825 24.05 22.275 25.85 38-39 27.425 25.05 21.9 25.624999999999996 40-41 28.5875 24.0625 21.725 25.624999999999996 42-43 27.287499999999998 23.8875 22.900000000000002 25.924999999999997 44-45 28.8375 24.2875 21.8 25.074999999999996 46-47 27.0125 24.525 21.9375 26.525 48-49 27.462500000000002 24.075 22.6375 25.825 50-51 27.987499999999997 23.6625 23.05 25.3 52-53 27.987499999999997 23.9875 21.3 26.724999999999998 54-55 27.725 24.55 22.112499999999997 25.6125 56-57 27.9375 24.125 22.725 25.2125 58-59 28.3125 23.9875 22.85 24.85 60-61 28.287499999999998 24.1125 21.9625 25.637500000000003 62-63 27.6 24.3875 22.575 25.4375 64-65 28.1125 23.375 22.2125 26.3 66-67 27.0125 24.462500000000002 23.25 25.275 68-69 27.474999999999998 25.15 22.287499999999998 25.087500000000002 70-71 28.175 24.3625 22.6375 24.825 72-73 28.175 23.7 22.975 25.15 74-75 28.1125 24.6875 22.0 25.2 76-77 28.849999999999998 24.3875 22.2625 24.5 78-79 28.325 24.3 22.0125 25.362499999999997 80-81 28.3625 25.087500000000002 23.1125 23.4375 82-83 28.3625 25.387500000000003 21.224999999999998 25.025 84-85 28.825 24.0375 22.9625 24.175 86-87 27.825 24.2625 22.8875 25.025 88-89 29.099999999999998 25.174999999999997 21.1875 24.5375 90-91 28.95 25.5125 22.0 23.5375 92-93 29.1375 24.6125 22.5625 23.6875 94-95 29.95 25.137500000000003 21.0 23.9125 96-97 29.9375 25.525 21.4375 23.1 98-99 30.025000000000002 25.575 21.9625 22.4375 100-101 30.625000000000004 25.087500000000002 20.9875 23.3 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.5 8 1.5 9 1.5 10 1.0 11 1.5 12 1.5 13 2.0 14 3.0 15 2.0 16 0.5 17 1.5 18 2.0 19 1.5 20 2.0 21 1.0 22 0.0 23 0.5 24 0.5 25 0.0 26 0.0 27 1.5 28 4.0 29 4.0 30 4.0 31 3.0 32 1.5 33 2.0 34 7.0 35 18.5 36 24.0 37 27.5 38 36.0 39 55.0 40 71.0 41 83.0 42 119.5 43 131.0 44 135.0 45 150.0 46 155.5 47 169.0 48 167.5 49 155.0 50 158.5 51 171.0 52 165.0 53 150.0 54 132.0 55 140.0 56 145.0 57 116.0 58 93.0 59 80.0 60 88.0 61 91.5 62 81.0 63 73.5 64 71.5 65 78.5 66 80.0 67 62.5 68 52.0 69 63.5 70 58.0 71 43.0 72 35.0 73 30.0 74 30.0 75 26.5 76 22.0 77 19.0 78 17.0 79 11.5 80 6.5 81 6.0 82 4.5 83 2.0 84 0.5 85 2.5 86 3.0 87 2.0 88 2.5 89 2.5 90 2.0 91 2.0 92 1.0 93 0.0 94 1.0 95 1.5 96 0.5 97 1.0 98 1.5 99 2.5 100 11.5 >>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 88.325 #Duplication Level Percentage of deduplicated Percentage of total 1 89.92357769600906 79.425 2 8.123407868666856 14.35 3 1.5284460798188508 4.05 4 0.2830455703368242 1.0 5 0.05660911406736484 0.25 6 0.0 0.0 7 0.05660911406736484 0.35000000000000003 8 0.0 0.0 9 0.0 0.0 >10 0.02830455703368242 0.575 >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 23 0.575 No Hit CTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTT 7 0.17500000000000002 No Hit GGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGC 7 0.17500000000000002 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 5 0.125 No Hit GTTTGTTTGATGGTACGTGCTACTCGGATAACCGTAGTAATTCTAGAGCT 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 32-33 0.0625 0.0 0.0 0.0 0.0 34-35 0.075 0.0 0.0 0.0 0.0 36-37 0.1 0.0 0.0 0.0 0.0 38-39 0.1125 0.0 0.0 0.0 0.0 40-41 0.16249999999999998 0.0 0.0 0.0 0.0 42-43 0.225 0.0 0.0 0.0 0.0 44-45 0.275 0.0 0.0 0.0 0.0 46-47 0.325 0.0 0.0 0.0 0.0 48-49 0.3875 0.0 0.0 0.0 0.0 50-51 0.525 0.0 0.0 0.0 0.0 52-53 0.5874999999999999 0.0 0.0 0.0 0.0 54-55 0.6625000000000001 0.0 0.0 0.0 0.0 56-57 0.7 0.0 0.0 0.0 0.0 58-59 0.875 0.0 0.0 0.0 0.0 60-61 1.0125 0.0 0.0 0.0 0.0 62-63 1.2000000000000002 0.0 0.0 0.0 0.0 64-65 1.525 0.0 0.0 0.0 0.0 66-67 1.8375 0.0 0.0 0.0 0.0 68-69 2.25 0.0 0.0 0.0 0.0 70-71 2.45 0.0 0.0 0.0 0.0 72-73 2.6875 0.0 0.0 0.0 0.0 74-75 3.2125 0.0 0.0 0.0 0.0 76-77 3.75 0.0 0.0 0.0 0.0 78-79 4.199999999999999 0.0 0.0 0.0 0.0 80-81 4.65 0.0 0.0 0.0 0.0 82-83 5.1875 0.0 0.0 0.0 0.0 84-85 5.65 0.0 0.0 0.0 0.0 86-87 6.1625 0.0 0.0 0.0 0.0 88-89 6.8875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042166 spots for ERR3450070.sra Written 1042166 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra Read 1042158 spots for ERR3450070.sra Written 1042158 spots for ERR3450070.sra SRR ids: ['ERR3450070.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd__a58lz3z ERR3450070.sra spots: 20843168 blocks: [[1, 1042158], [1042159, 2084316], [2084317, 3126474], [3126475, 4168632], [4168633, 5210790], [5210791, 6252948], [6252949, 7295106], [7295107, 8337264], [8337265, 9379422], [9379423, 10421580], [10421581, 11463738], [11463739, 12505896], [12505897, 13548054], [13548055, 14590212], [14590213, 15632370], [15632371, 16674528], [16674529, 17716686], [17716687, 18758844], [18758845, 19801002], [19801003, 20843168]] ERR3450070 file size 5005899 ERR3450070 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 ERR3450070 ERR3450070_1.fastq ERR3450070_2.fastq Input file: ERR3450070_1.fastq Paired file: ERR3450070_2.fastq trimmed: ERR3450070-trimmed-pair1.fastq, ERR3450070-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 14:33:33 2024 >> started Sat Dec 7 14:33:55 2024 >> done (21.476s) 20843168 read pairs processed; of these: 185 ( 0.00%) short read pairs filtered out after trimming by size control 112346 ( 0.54%) empty read pairs filtered out after trimming by size control 20730637 (99.46%) read pairs available; of these: 2490263 (12.01%) trimmed read pairs available after processing 18240374 (87.99%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 46 0.00% 19 94 0.00% 20 288 0.00% 21 639 0.00% 22 774 0.00% 23 392 0.00% 24 344 0.00% 25 476 0.00% 26 653 0.00% 27 844 0.00% 28 1332 0.01% 29 1610 0.01% 30 1998 0.01% 31 2439 0.01% 32 2557 0.01% 33 2516 0.01% 34 2511 0.01% 35 2540 0.01% 36 2689 0.01% 37 2981 0.01% 38 3468 0.02% 39 4100 0.02% 40 4656 0.02% 41 5751 0.03% 42 6270 0.03% 43 6754 0.03% 44 5988 0.03% 45 6141 0.03% 46 6528 0.03% 47 7223 0.03% 48 7772 0.04% 49 8831 0.04% 50 9958 0.05% 51 10822 0.05% 52 11900 0.06% 53 12342 0.06% 54 12905 0.06% 55 13373 0.06% 56 13910 0.07% 57 14693 0.07% 58 16024 0.08% 59 17631 0.09% 60 18938 0.09% 61 20959 0.10% 62 22800 0.11% 63 24515 0.12% 64 25419 0.12% 65 25935 0.13% 66 27359 0.13% 67 29088 0.14% 68 30189 0.15% 69 30977 0.15% 70 33349 0.16% 71 36058 0.17% 72 38305 0.18% 73 40286 0.19% 74 42422 0.20% 75 43619 0.21% 76 45093 0.22% 77 46046 0.22% 78 47744 0.23% 79 49769 0.24% 80 51778 0.25% 81 54322 0.26% 82 57747 0.28% 83 58863 0.28% 84 61519 0.30% 85 63626 0.31% 86 65081 0.31% 87 67474 0.33% 88 69384 0.33% 89 72090 0.35% 90 73305 0.35% 91 77441 0.37% 92 80318 0.39% 93 82760 0.40% 94 85140 0.41% 95 87425 0.42% 96 88544 0.43% 97 91939 0.44% 98 93041 0.45% 99 92416 0.45% 100 102417 0.49% 101 18240374 87.99% 20730637 reads passed initial QC criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=2.53 fanout-score-rank=32 prefix-density=0.19 prefix-fanout=2.5 sequence=GTCAAATTAAGCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATAAGCAACATCCGCCGATCCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTCACCTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGACCGGAATCCTATGATGTTATCCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGATGCCGGAGGCACGACCCGGCCAATTAAGGCTAGGAGCGCATCGCCGGCTGAAGGGTCGAGTA criterion=fanout-score sequence-density=0.06 sequence-density-rank=19 fanout-score=236.12 fanout-score-rank=1 prefix-density=0.62 prefix-fanout=22.9 sequence=GCCGCCGCCGCG criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=1.95 fanout-score-rank=33 prefix-density=0.20 prefix-fanout=1.9 sequence=CAAGTGTTGGATT criterion=fanout-score sequence-density=0.07 sequence-density-rank=21 fanout-score=249.35 fanout-score-rank=1 prefix-density=0.76 prefix-fanout=22.7 sequence=CGGCGGCGGCGC ERR3450070 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:34:32 Started mapping on | Dec 07 14:34:32 Finished on | Dec 07 14:37:25 Mapping speed, Million of reads per hour | 431.39 Number of input reads | 20730637 Average input read length | 197 UNIQUE READS: Uniquely mapped reads number | 14980375 Uniquely mapped reads % | 72.26% Average mapped length | 196.92 Number of splices: Total | 9069600 Number of splices: Annotated (sjdb) | 8573301 Number of splices: GT/AG | 8952798 Number of splices: GC/AG | 100558 Number of splices: AT/AC | 6020 Number of splices: Non-canonical | 10224 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.01% Deletion average length | 2.18 Insertion rate per base | 0.01% Insertion average length | 1.95 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 808807 % of reads mapped to multiple loci | 3.90% Number of reads mapped to too many loci | 858869 % of reads mapped to too many loci | 4.14% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.82% % of reads unmapped: other | 15.87% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4941455 4941455 4941455 N_multimapping 808807 808807 808807 N_noFeature 456098 14377870 846544 N_ambiguous 255344 2352 44880 UnstrandedReadsAssigned:14268933 PositiveStrandReadsAssigned:600153 NegativeStrandReadsAssigned:14088951 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450070 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: ERR3450070-trimmed-pair1.fastq ERR3450070-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,730,637 reads, 14,788,931 reads pseudoaligned [quant] estimated average fragment length: 179.114 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,188 rounds 52973 ERR3450070.ke.tsv 35125 ERR3450070.se.tsv 88098 total ==> ERR3450070.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 758.157 1.88905e-06 2.60223e-07 PNS24247 1044 865.886 34.0285 4.10435 PNS24249 1928 1749.89 185.311 11.06 PNS24246 1044 865.886 34.0285 4.10435 PNS24248 1044 865.886 34.0285 4.10435 PNS24244 1471 1292.89 40.6033 3.27992 PNS24243 293 134.084 0 0 KQK14069 1603 1424.89 4147.94 304.029 KQK14071 474 299.437 201.938 70.4328 ==> ERR3450070.se.tsv <== BRADI_1g14170v3 4422 BRADI_1g53295v3 32 BRADI_1g59795v3 147 BRADI_1g07683v3 0 BRADI_1g00485v3 19 BRADI_1g20270v3 2428 BRADI_1g74790v3 167 BRADI_1g09890v3 20 BRADI_1g77505v3 165 BRADI_1g48960v3 0 ERR3450070 completed mapping pipeline successfully