Starting /dee2/code/volunteer_pipeline.sh ERR3450065 current disk space = 1543025172480 free memory = 1599630360 ERR3450065 SRAfilesize d67eb9b7ce96010d04d4d1a67bafcfde ERR3450065.sra ERR3450065.sra file validated ERR3450065 is paired end ERR3450065 is conventional basespace ERR3450065 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450065_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 36.2395 37.0 37.0 37.0 37.0 37.0 2 36.524 37.0 37.0 37.0 37.0 37.0 3 36.4985 37.0 37.0 37.0 37.0 37.0 4 36.5395 37.0 37.0 37.0 37.0 37.0 5 36.5805 37.0 37.0 37.0 37.0 37.0 6 36.563 37.0 37.0 37.0 37.0 37.0 7 36.5745 37.0 37.0 37.0 37.0 37.0 8 36.6135 37.0 37.0 37.0 37.0 37.0 9 36.632 37.0 37.0 37.0 37.0 37.0 10-11 36.559 37.0 37.0 37.0 37.0 37.0 12-13 36.576750000000004 37.0 37.0 37.0 37.0 37.0 14-15 36.597750000000005 37.0 37.0 37.0 37.0 37.0 16-17 36.556250000000006 37.0 37.0 37.0 37.0 37.0 18-19 36.5835 37.0 37.0 37.0 37.0 37.0 20-21 36.60125 37.0 37.0 37.0 37.0 37.0 22-23 36.52775 37.0 37.0 37.0 37.0 37.0 24-25 36.50575 37.0 37.0 37.0 37.0 37.0 26-27 36.467 37.0 37.0 37.0 37.0 37.0 28-29 36.548 37.0 37.0 37.0 37.0 37.0 30-31 36.485 37.0 37.0 37.0 37.0 37.0 32-33 36.41 37.0 37.0 37.0 37.0 37.0 34-35 36.361999999999995 37.0 37.0 37.0 37.0 37.0 36-37 36.423500000000004 37.0 37.0 37.0 37.0 37.0 38-39 36.455 37.0 37.0 37.0 37.0 37.0 40-41 36.469750000000005 37.0 37.0 37.0 37.0 37.0 42-43 36.408500000000004 37.0 37.0 37.0 37.0 37.0 44-45 36.32025 37.0 37.0 37.0 37.0 37.0 46-47 36.226749999999996 37.0 37.0 37.0 37.0 37.0 48-49 36.36625 37.0 37.0 37.0 37.0 37.0 50-51 36.266000000000005 37.0 37.0 37.0 37.0 37.0 52-53 36.235749999999996 37.0 37.0 37.0 37.0 37.0 54-55 36.265 37.0 37.0 37.0 37.0 37.0 56-57 36.262 37.0 37.0 37.0 37.0 37.0 58-59 36.27525 37.0 37.0 37.0 37.0 37.0 60-61 36.12025 37.0 37.0 37.0 37.0 37.0 62-63 36.081 37.0 37.0 37.0 37.0 37.0 64-65 36.116749999999996 37.0 37.0 37.0 37.0 37.0 66-67 36.15025 37.0 37.0 37.0 37.0 37.0 68-69 36.107 37.0 37.0 37.0 37.0 37.0 70-71 35.872249999999994 37.0 37.0 37.0 37.0 37.0 72-73 35.8665 37.0 37.0 37.0 37.0 37.0 74-75 36.190749999999994 37.0 37.0 37.0 37.0 37.0 76-77 36.12675 37.0 37.0 37.0 37.0 37.0 78-79 36.24125 37.0 37.0 37.0 37.0 37.0 80-81 36.075 37.0 37.0 37.0 37.0 37.0 82-83 36.206 37.0 37.0 37.0 37.0 37.0 84-85 36.21225 37.0 37.0 37.0 37.0 37.0 86-87 36.1425 37.0 37.0 37.0 37.0 37.0 88-89 36.09075 37.0 37.0 37.0 37.0 37.0 90-91 36.05475 37.0 37.0 37.0 37.0 37.0 92-93 36.15625 37.0 37.0 37.0 37.0 37.0 94-95 36.1 37.0 37.0 37.0 37.0 37.0 96-97 36.0025 37.0 37.0 37.0 37.0 37.0 98-99 35.96575 37.0 37.0 37.0 37.0 37.0 100-101 35.9775 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 3.0 23 1.0 24 6.0 25 6.0 26 10.0 27 15.0 28 21.0 29 28.0 30 32.0 31 34.0 32 40.0 33 88.0 34 106.0 35 210.0 36 1766.0 37 1633.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.77448518332496 9.919638372677046 10.346559517830237 40.95931692616775 2 21.4 13.925 29.775000000000002 34.9 3 20.9 17.525 26.275 35.3 4 28.675 22.55 18.224999999999998 30.55 5 28.199999999999996 26.625 21.85 23.325000000000003 6 22.825 31.574999999999996 24.175 21.425 7 19.925 22.6 37.3 20.175 8 21.8 20.95 29.2 28.050000000000004 9 23.175 19.650000000000002 31.324999999999996 25.85 10-11 23.1125 29.462500000000002 22.9625 24.462500000000002 12-13 23.5625 22.9875 25.587500000000002 27.8625 14-15 23.075000000000003 24.8 26.487500000000004 25.637500000000003 16-17 23.8875 23.8875 25.5625 26.6625 18-19 24.0625 24.837500000000002 25.324999999999996 25.775 20-21 25.25 24.462500000000002 25.2375 25.05 22-23 25.124999999999996 24.025 25.074999999999996 25.775 24-25 24.25 24.2 24.875 26.674999999999997 26-27 23.3375 24.7375 24.887500000000003 27.037499999999998 28-29 25.2375 24.075 24.8 25.887500000000003 30-31 24.3625 23.6375 24.9 27.1 32-33 24.25 24.375 25.025 26.35 34-35 24.7 24.762500000000003 24.4 26.137500000000003 36-37 24.7375 24.474999999999998 24.25 26.5375 38-39 24.65 23.9 25.15 26.3 40-41 24.712500000000002 23.6125 24.6125 27.0625 42-43 24.9375 23.425 24.125 27.5125 44-45 24.575 23.599999999999998 25.624999999999996 26.200000000000003 46-47 25.724999999999998 23.825 24.625 25.825 48-49 23.8125 24.3 25.0375 26.85 50-51 25.662499999999998 23.849999999999998 23.849999999999998 26.637499999999996 52-53 24.825 24.3875 23.5 27.287499999999998 54-55 25.6 23.2625 24.1125 27.025 56-57 23.7875 23.6875 25.8625 26.6625 58-59 23.400000000000002 24.5125 24.6625 27.425 60-61 25.674999999999997 23.1375 25.0625 26.125 62-63 24.637500000000003 24.625 24.462500000000002 26.275 64-65 24.337500000000002 23.575 25.124999999999996 26.9625 66-67 25.25 24.474999999999998 23.5375 26.737499999999997 68-69 24.8 24.4875 24.075 26.637499999999996 70-71 25.05 23.7875 24.45 26.7125 72-73 26.2125 24.5125 22.787499999999998 26.487500000000004 74-75 25.15 24.1375 23.75 26.9625 76-77 25.0625 24.825 24.1875 25.924999999999997 78-79 24.7375 23.9125 23.225 28.125 80-81 24.962500000000002 24.8 24.0125 26.224999999999998 82-83 25.9625 24.725 23.0375 26.275 84-85 25.174999999999997 24.0625 23.6375 27.125 86-87 25.45 24.85 22.2 27.500000000000004 88-89 24.637500000000003 24.7875 23.0625 27.5125 90-91 26.4625 24.4125 22.537499999999998 26.5875 92-93 24.9 24.474999999999998 23.375 27.250000000000004 94-95 25.0625 24.6125 23.474999999999998 26.85 96-97 24.962500000000002 23.825 23.8125 27.400000000000002 98-99 26.5125 24.525 22.375 26.5875 100-101 24.05 25.387500000000003 23.0375 27.525 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 14.0 1 7.5 2 2.0 3 2.5 4 1.0 5 1.5 6 2.5 7 1.5 8 1.0 9 1.0 10 1.5 11 1.5 12 0.5 13 0.0 14 0.0 15 1.0 16 1.0 17 1.0 18 1.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.5 24 1.5 25 1.5 26 3.0 27 3.5 28 2.0 29 1.5 30 1.5 31 6.0 32 9.5 33 10.5 34 14.0 35 17.0 36 29.5 37 42.0 38 44.5 39 63.5 40 87.0 41 99.5 42 118.0 43 144.5 44 154.5 45 168.5 46 193.0 47 172.0 48 156.0 49 171.5 50 159.5 51 162.0 52 171.5 53 152.5 54 132.0 55 134.5 56 128.0 57 101.5 58 99.0 59 88.0 60 71.5 61 73.5 62 72.0 63 72.5 64 64.5 65 62.0 66 70.5 67 65.0 68 58.0 69 46.5 70 41.0 71 34.5 72 31.0 73 32.5 74 29.5 75 22.5 76 14.0 77 13.5 78 15.5 79 11.5 80 6.0 81 5.5 82 2.5 83 0.5 84 1.5 85 2.0 86 1.0 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 0.44999999999999996 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 87.125 #Duplication Level Percentage of deduplicated Percentage of total 1 89.21090387374461 77.725 2 8.55093256814921 14.899999999999999 3 1.4634146341463417 3.8249999999999997 4 0.430416068866571 1.5 5 0.1721664275466284 0.75 6 0.0860832137733142 0.44999999999999996 7 0.028694404591104734 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.05738880918220947 0.675 >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 17 0.42500000000000004 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGCTCATTATCTCGTAT 10 0.25 TruSeq Adapter, Index 2 (97% over 37bp) CAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTG 7 0.17500000000000002 No Hit CCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCAT 6 0.15 No Hit GCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGAT 6 0.15 No Hit TCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGC 6 0.15 No Hit CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 5 0.125 No Hit GCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGC 5 0.125 No Hit CTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTG 5 0.125 No Hit GTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCAT 5 0.125 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 5 0.125 No Hit CCCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAAT 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 0.025 26-27 0.0125 0.0 0.0 0.0 0.025 28-29 0.025 0.0 0.0 0.0 0.025 30-31 0.025 0.0 0.0 0.0 0.025 32-33 0.037500000000000006 0.0 0.0 0.0 0.025 34-35 0.0625 0.0 0.0 0.0 0.025 36-37 0.1 0.0 0.0 0.0 0.025 38-39 0.1375 0.0 0.0 0.0 0.025 40-41 0.175 0.0 0.0 0.0 0.025 42-43 0.2 0.0 0.0 0.0 0.025 44-45 0.275 0.0 0.0 0.0 0.025 46-47 0.35 0.0 0.0 0.0 0.025 48-49 0.3625 0.0 0.0 0.0 0.025 50-51 0.4375 0.0 0.0 0.0 0.025 52-53 0.55 0.0 0.0 0.0 0.025 54-55 0.7 0.0 0.0 0.0 0.025 56-57 0.8125 0.0 0.0 0.0 0.025 58-59 0.8999999999999999 0.0 0.0 0.0 0.025 60-61 1.1 0.0 0.0 0.0 0.025 62-63 1.2625 0.0 0.0 0.0 0.025 64-65 1.5625 0.0 0.0 0.0 0.025 66-67 1.9 0.0 0.0 0.0 0.025 68-69 2.1875 0.0 0.0 0.0 0.025 70-71 2.55 0.0 0.0 0.0 0.025 72-73 2.8625 0.0 0.0 0.0 0.025 74-75 3.45 0.0 0.0 0.0 0.025 76-77 3.75 0.0 0.0 0.0 0.025 78-79 4.225 0.0 0.0 0.0 0.025 80-81 4.65 0.0 0.0 0.0 0.025 82-83 5.125 0.0 0.0 0.0 0.025 84-85 5.4875 0.0 0.0 0.0 0.025 86-87 6.15 0.0 0.0 0.0 0.025 88-89 6.85 0.0 0.0 0.0 0.025 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3450065 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3450065_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 36.2125 37.0 37.0 37.0 37.0 37.0 2 35.9405 37.0 37.0 37.0 37.0 37.0 3 36.045 37.0 37.0 37.0 37.0 37.0 4 36.181 37.0 37.0 37.0 37.0 37.0 5 36.2005 37.0 37.0 37.0 37.0 37.0 6 36.32 37.0 37.0 37.0 37.0 37.0 7 36.119 37.0 37.0 37.0 37.0 37.0 8 36.13 37.0 37.0 37.0 37.0 37.0 9 36.2375 37.0 37.0 37.0 37.0 37.0 10-11 36.12525 37.0 37.0 37.0 37.0 37.0 12-13 36.191 37.0 37.0 37.0 37.0 37.0 14-15 36.07925 37.0 37.0 37.0 37.0 37.0 16-17 36.0845 37.0 37.0 37.0 37.0 37.0 18-19 36.02825 37.0 37.0 37.0 37.0 37.0 20-21 36.042500000000004 37.0 37.0 37.0 37.0 37.0 22-23 36.1755 37.0 37.0 37.0 37.0 37.0 24-25 35.982749999999996 37.0 37.0 37.0 37.0 37.0 26-27 35.8985 37.0 37.0 37.0 37.0 37.0 28-29 35.771249999999995 37.0 37.0 37.0 37.0 37.0 30-31 35.7995 37.0 37.0 37.0 37.0 37.0 32-33 35.8565 37.0 37.0 37.0 37.0 37.0 34-35 35.741749999999996 37.0 37.0 37.0 37.0 37.0 36-37 35.673500000000004 37.0 37.0 37.0 37.0 37.0 38-39 35.684 37.0 37.0 37.0 37.0 37.0 40-41 35.73425 37.0 37.0 37.0 37.0 37.0 42-43 35.786249999999995 37.0 37.0 37.0 37.0 37.0 44-45 35.74575 37.0 37.0 37.0 37.0 37.0 46-47 35.792500000000004 37.0 37.0 37.0 37.0 37.0 48-49 35.72325 37.0 37.0 37.0 37.0 37.0 50-51 35.73325 37.0 37.0 37.0 37.0 37.0 52-53 35.83225 37.0 37.0 37.0 37.0 37.0 54-55 35.870000000000005 37.0 37.0 37.0 37.0 37.0 56-57 35.82175 37.0 37.0 37.0 37.0 37.0 58-59 35.87975 37.0 37.0 37.0 37.0 37.0 60-61 35.917249999999996 37.0 37.0 37.0 37.0 37.0 62-63 35.89925 37.0 37.0 37.0 37.0 37.0 64-65 35.975750000000005 37.0 37.0 37.0 37.0 37.0 66-67 35.80525 37.0 37.0 37.0 37.0 37.0 68-69 35.82825 37.0 37.0 37.0 37.0 37.0 70-71 35.740750000000006 37.0 37.0 37.0 37.0 37.0 72-73 35.71825 37.0 37.0 37.0 37.0 37.0 74-75 35.59575 37.0 37.0 37.0 37.0 37.0 76-77 35.5715 37.0 37.0 37.0 37.0 37.0 78-79 35.58025 37.0 37.0 37.0 37.0 37.0 80-81 35.55575 37.0 37.0 37.0 37.0 37.0 82-83 35.573499999999996 37.0 37.0 37.0 37.0 37.0 84-85 35.64125 37.0 37.0 37.0 37.0 37.0 86-87 35.728750000000005 37.0 37.0 37.0 37.0 37.0 88-89 35.747 37.0 37.0 37.0 37.0 37.0 90-91 35.616 37.0 37.0 37.0 37.0 37.0 92-93 35.66775 37.0 37.0 37.0 37.0 37.0 94-95 35.622 37.0 37.0 37.0 37.0 37.0 96-97 35.64725 37.0 37.0 37.0 37.0 37.0 98-99 35.61425 37.0 37.0 37.0 37.0 37.0 100-101 35.633250000000004 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 1.0 16 2.0 17 1.0 18 6.0 19 7.0 20 8.0 21 13.0 22 15.0 23 7.0 24 6.0 25 7.0 26 17.0 27 18.0 28 18.0 29 32.0 30 48.0 31 32.0 32 56.0 33 90.0 34 139.0 35 371.0 36 2368.0 37 738.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.125 16.575 12.25 31.05 2 27.1 22.125 26.0 24.775 3 24.2 23.925 26.974999999999998 24.9 4 31.3 25.924999999999997 16.825000000000003 25.95 5 29.5 30.475 18.825 21.2 6 24.15 32.75 20.4 22.7 7 26.1 19.325 30.525000000000002 24.05 8 25.45 21.025 23.875 29.65 9 25.25 22.25 24.15 28.349999999999998 10-11 28.1625 27.2625 20.1 24.474999999999998 12-13 28.125 22.0875 22.162499999999998 27.625 14-15 27.800000000000004 24.375 23.799999999999997 24.025 16-17 28.175 24.7875 23.0 24.0375 18-19 28.237499999999997 24.337500000000002 23.275000000000002 24.15 20-21 26.900000000000002 25.525 22.0 25.575 22-23 27.775 24.6125 22.7375 24.875 24-25 28.799999999999997 24.65 22.112499999999997 24.4375 26-27 27.775 25.025 22.6125 24.587500000000002 28-29 28.0625 23.925 22.425 25.587500000000002 30-31 28.4 24.0125 22.6125 24.975 32-33 27.474999999999998 24.625 23.3375 24.5625 34-35 27.9375 24.762500000000003 23.1 24.2 36-37 26.387500000000003 25.7125 22.5125 25.387500000000003 38-39 28.325 24.25 22.662499999999998 24.762500000000003 40-41 27.762500000000003 23.724999999999998 23.3625 25.15 42-43 27.750000000000004 24.0625 23.05 25.137500000000003 44-45 27.3 24.837500000000002 22.6375 25.224999999999998 46-47 28.012500000000003 24.462500000000002 22.662499999999998 24.8625 48-49 28.299999999999997 24.575 23.075000000000003 24.05 50-51 27.1375 23.9 23.25 25.7125 52-53 28.125 24.55 21.875 25.45 54-55 27.125 25.174999999999997 23.150000000000002 24.55 56-57 26.737499999999997 24.7 23.400000000000002 25.162499999999998 58-59 28.1375 24.349999999999998 22.975 24.5375 60-61 28.9125 25.3 22.25 23.5375 62-63 27.8125 24.6875 23.724999999999998 23.775 64-65 28.962500000000002 24.474999999999998 21.6 24.962500000000002 66-67 27.250000000000004 24.3625 23.0 25.387500000000003 68-69 27.625 24.462500000000002 22.775000000000002 25.137500000000003 70-71 28.499999999999996 24.05 22.650000000000002 24.8 72-73 28.449999999999996 24.2375 23.0875 24.224999999999998 74-75 28.1125 24.762500000000003 23.3375 23.7875 76-77 28.6125 24.775 22.5625 24.05 78-79 28.3625 24.2625 22.037499999999998 25.337500000000002 80-81 28.65 24.675 22.650000000000002 24.025 82-83 28.037499999999998 24.95 23.225 23.7875 84-85 29.175 24.087500000000002 22.25 24.4875 86-87 28.262500000000003 24.675 23.05 24.0125 88-89 29.212500000000002 24.275 22.8125 23.7 90-91 28.762500000000003 25.362499999999997 21.95 23.925 92-93 29.3375 25.074999999999996 22.237499999999997 23.35 94-95 29.4 25.2 22.1875 23.2125 96-97 30.25 24.25 22.3875 23.1125 98-99 28.3875 25.55 23.0375 23.025000000000002 100-101 29.7125 24.875 22.287499999999998 23.125 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 1.0 2 1.5 3 1.0 4 0.0 5 0.0 6 2.0 7 2.0 8 0.5 9 1.0 10 0.5 11 0.5 12 2.5 13 2.5 14 3.5 15 4.5 16 2.0 17 1.5 18 1.0 19 0.0 20 1.5 21 1.5 22 0.5 23 1.0 24 0.5 25 1.0 26 2.0 27 2.5 28 1.5 29 1.0 30 2.0 31 3.0 32 3.5 33 6.5 34 12.0 35 21.5 36 31.5 37 41.0 38 53.0 39 59.5 40 67.0 41 88.5 42 126.5 43 139.5 44 136.0 45 143.5 46 152.0 47 168.0 48 163.5 49 157.0 50 160.0 51 154.5 52 153.5 53 157.0 54 151.5 55 141.5 56 124.0 57 107.0 58 98.5 59 89.0 60 89.0 61 83.5 62 72.5 63 71.5 64 65.5 65 56.0 66 62.5 67 68.5 68 60.0 69 58.5 70 59.0 71 53.5 72 47.5 73 37.0 74 29.5 75 24.0 76 23.0 77 19.0 78 10.0 79 5.0 80 3.0 81 4.5 82 4.5 83 2.0 84 1.0 85 0.5 86 0.5 87 1.0 88 0.5 89 1.5 90 1.5 91 0.0 92 1.0 93 1.5 94 1.0 95 2.0 96 2.0 97 2.0 98 3.0 99 4.0 100 9.0 >>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 0.0 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 88.8 #Duplication Level Percentage of deduplicated Percentage of total 1 90.06193693693693 79.975 2 8.333333333333332 14.799999999999999 3 1.097972972972973 2.9250000000000003 4 0.2533783783783784 0.8999999999999999 5 0.16891891891891891 0.75 6 0.05630630630630631 0.3 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.028153153153153154 0.35000000000000003 >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 14 0.35000000000000003 No Hit GATTAAGCCATGCATGTGCAAGTATGAACTAATTTGAACTGTGAAACTGC 6 0.15 No Hit CTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTTTCTT 6 0.15 No Hit GCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAAC 5 0.125 No Hit GGAAATTTCATCGTGATGGGGATAGATCATTGCAATTGTTGGTCTTCAAC 5 0.125 No Hit GCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAAC 5 0.125 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAA 5 0.125 No Hit CGGGGAGGTAGTGACAATAAATAACAATACCGGGCACATTAGTGTCTGGT 5 0.125 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGCAAG 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 0.0125 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.037500000000000006 0.0 0.0 0.0 0.0 34-35 0.0625 0.0 0.0 0.0 0.0 36-37 0.1 0.0 0.0 0.0 0.0 38-39 0.1375 0.0 0.0 0.0 0.0 40-41 0.175 0.0 0.0 0.0 0.0 42-43 0.2 0.0 0.0 0.0 0.0 44-45 0.30000000000000004 0.0 0.0 0.0 0.0 46-47 0.375 0.0 0.0 0.0 0.0 48-49 0.3875 0.0 0.0 0.0 0.0 50-51 0.4625 0.0 0.0 0.0 0.0 52-53 0.575 0.0 0.0 0.0 0.0 54-55 0.7250000000000001 0.0 0.0 0.0 0.0 56-57 0.8374999999999999 0.0 0.0 0.0 0.0 58-59 0.925 0.0 0.0 0.0 0.0 60-61 1.1 0.0 0.0 0.0 0.0 62-63 1.2625 0.0 0.0 0.0 0.0 64-65 1.5750000000000002 0.0 0.0 0.0 0.0 66-67 1.925 0.0 0.0 0.0 0.0 68-69 2.2375 0.0 0.0 0.0 0.0 70-71 2.6 0.0 0.0 0.0 0.0 72-73 2.95 0.0 0.0 0.0 0.0 74-75 3.575 0.0 0.0 0.0 0.0 76-77 3.8625 0.0 0.0 0.0 0.0 78-79 4.375 0.0 0.0 0.0 0.0 80-81 4.824999999999999 0.0 0.0 0.0 0.0 82-83 5.300000000000001 0.0 0.0 0.0 0.0 84-85 5.6625 0.0 0.0 0.0 0.0 86-87 6.3125 0.0 0.0 0.0 0.0 88-89 7.0125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797641 spots for ERR3450065.sra Written 1797641 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra Read 1797633 spots for ERR3450065.sra Written 1797633 spots for ERR3450065.sra SRR ids: ['ERR3450065.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_i7u01vee ERR3450065.sra spots: 35952668 blocks: [[1, 1797633], [1797634, 3595266], [3595267, 5392899], [5392900, 7190532], [7190533, 8988165], [8988166, 10785798], [10785799, 12583431], [12583432, 14381064], [14381065, 16178697], [16178698, 17976330], [17976331, 19773963], [19773964, 21571596], [21571597, 23369229], [23369230, 25166862], [25166863, 26964495], [26964496, 28762128], [28762129, 30559761], [30559762, 32357394], [32357395, 34155027], [34155028, 35952668]] ERR3450065 file size 8650476 ERR3450065 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 ERR3450065 ERR3450065_1.fastq ERR3450065_2.fastq Input file: ERR3450065_1.fastq Paired file: ERR3450065_2.fastq trimmed: ERR3450065-trimmed-pair1.fastq, ERR3450065-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 14:22:27 2024 >> started Sat Dec 7 14:23:03 2024 >> done (35.518s) 35952668 read pairs processed; of these: 330 ( 0.00%) short read pairs filtered out after trimming by size control 86827 ( 0.24%) empty read pairs filtered out after trimming by size control 35865511 (99.76%) read pairs available; of these: 4390748 (12.24%) trimmed read pairs available after processing 31474763 (87.76%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 78 0.00% 19 154 0.00% 20 583 0.00% 21 1583 0.00% 22 1671 0.00% 23 828 0.00% 24 626 0.00% 25 970 0.00% 26 1333 0.00% 27 1812 0.01% 28 2661 0.01% 29 3421 0.01% 30 4174 0.01% 31 5027 0.01% 32 5022 0.01% 33 4819 0.01% 34 4684 0.01% 35 4777 0.01% 36 5403 0.02% 37 6012 0.02% 38 6959 0.02% 39 8104 0.02% 40 9712 0.03% 41 11083 0.03% 42 12523 0.03% 43 13214 0.04% 44 12338 0.03% 45 12123 0.03% 46 12851 0.04% 47 14276 0.04% 48 15502 0.04% 49 17266 0.05% 50 19202 0.05% 51 21236 0.06% 52 22928 0.06% 53 24339 0.07% 54 24644 0.07% 55 26204 0.07% 56 26730 0.07% 57 28395 0.08% 58 30561 0.09% 59 33188 0.09% 60 35768 0.10% 61 39208 0.11% 62 43032 0.12% 63 45291 0.13% 64 46713 0.13% 65 47775 0.13% 66 49796 0.14% 67 52669 0.15% 68 55086 0.15% 69 56374 0.16% 70 61035 0.17% 71 64917 0.18% 72 69152 0.19% 73 72851 0.20% 74 75427 0.21% 75 77146 0.22% 76 79715 0.22% 77 81648 0.23% 78 84108 0.23% 79 88406 0.25% 80 91480 0.26% 81 94893 0.26% 82 100406 0.28% 83 102788 0.29% 84 106198 0.30% 85 110466 0.31% 86 113151 0.32% 87 116327 0.32% 88 118978 0.33% 89 123484 0.34% 90 126078 0.35% 91 133756 0.37% 92 138017 0.38% 93 139797 0.39% 94 143110 0.40% 95 147751 0.41% 96 149159 0.42% 97 152951 0.43% 98 155468 0.43% 99 156855 0.44% 100 184502 0.51% 101 31474763 87.76% 35865511 reads passed initial QC criterion=sequence-density sequence-density=0.34 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=32 prefix-density=0.34 prefix-fanout=1.9 sequence=GTATTTAGCCTTG criterion=fanout-score sequence-density=0.08 sequence-density-rank=19 fanout-score=149.75 fanout-score-rank=1 prefix-density=0.58 prefix-fanout=19.9 sequence=CGCCGCCGCCGC criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=31 prefix-density=0.24 prefix-fanout=1.9 sequence=CAAGTGTTGGATTTAAAGCTGGTGTTAAAGATTATAGATTGACTTACTACACCCCGGAGTATGAAACCAAGGATACTGATATCTTGGCAGCATTCCGAGTATCTCCTCAACCTGGGGTTCCGCCCGAAGAAGCAGGGGCTGCAGTAGCTGCCGAATCTTCTACTGGTACATGGACAACTGTTTGGACTGATGGACTTACTAGTCTTGATCGTTACAAAGGACGATGCTATCACATCGAGCCTGTTCCTGGGGAAGACAGTCAATGGATCTGTTATGTAGCTTATCCATTAGATCTATTTGAAGAGGGTTCCGTTACTAACATGTTTACTTCCATTGTAGGTAACGTATTTGGTTTCAAAGCCCTACGTGCTCTACGTCTGGAGGATCTACGAATTCCCCCTACTTATTCAAAAACTTTCCAAGGCCCGCCTCACGGTATCCAAGTGGAAAGAGATAAGTTGAACAAGTATGGTCGTCCTTTATTGGGATGTACTATTAAGCCAAAATTGGG criterion=fanout-score sequence-density=0.08 sequence-density-rank=19 fanout-score=211.95 fanout-score-rank=1 prefix-density=0.73 prefix-fanout=22.8 sequence=CGGCGGCGGCGC ERR3450065 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 14:24:03 Started mapping on | Dec 07 14:24:04 Finished on | Dec 07 14:27:56 Mapping speed, Million of reads per hour | 556.53 Number of input reads | 35865511 Average input read length | 197 UNIQUE READS: Uniquely mapped reads number | 26037387 Uniquely mapped reads % | 72.60% Average mapped length | 196.68 Number of splices: Total | 16161642 Number of splices: Annotated (sjdb) | 15305870 Number of splices: GT/AG | 15949046 Number of splices: GC/AG | 182869 Number of splices: AT/AC | 10104 Number of splices: Non-canonical | 19623 Mismatch rate per base, % | 0.25% Deletion rate per base | 0.01% Deletion average length | 2.08 Insertion rate per base | 0.01% Insertion average length | 1.90 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1808288 % of reads mapped to multiple loci | 5.04% Number of reads mapped to too many loci | 1394069 % of reads mapped to too many loci | 3.89% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.34% % of reads unmapped: other | 15.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 8019836 8019836 8019836 N_multimapping 1808288 1808288 1808288 N_noFeature 894485 25072046 1474160 N_ambiguous 472405 3926 90730 UnstrandedReadsAssigned:24670497 PositiveStrandReadsAssigned:961415 NegativeStrandReadsAssigned:24472497 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR3450065 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: ERR3450065-trimmed-pair1.fastq ERR3450065-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 35,865,511 reads, 25,907,121 reads pseudoaligned [quant] estimated average fragment length: 182.786 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,220 rounds 52973 ERR3450065.ke.tsv 35125 ERR3450065.se.tsv 88098 total ==> ERR3450065.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 754.318 0 0 PNS24247 1044 862.214 52.7029 3.59789 PNS24249 1928 1746.21 284.985 9.60624 PNS24246 1044 862.214 52.7029 3.59789 PNS24248 1044 862.214 52.7029 3.59789 PNS24244 1471 1289.21 45.9059 2.09591 PNS24243 293 133.611 0 0 KQK14069 1603 1421.21 8130.96 336.752 KQK14071 474 296.691 414.441 82.2217 ==> ERR3450065.se.tsv <== BRADI_1g14170v3 8866 BRADI_1g53295v3 28 BRADI_1g59795v3 310 BRADI_1g07683v3 0 BRADI_1g00485v3 51 BRADI_1g20270v3 2613 BRADI_1g74790v3 268 BRADI_1g09890v3 15 BRADI_1g77505v3 351 BRADI_1g48960v3 0 ERR3450065 completed mapping pipeline successfully