Starting /dee2/code/volunteer_pipeline.sh SRR11462739 current disk space = 3051290152960 free memory = 1577542944 SRR11462739 SRAfilesize 66714315b35de8fc06409ae1bcdcd02d SRR11462739.sra SRR11462739.sra file validated SRR11462739 is single end SRR11462739 is conventional basespace SRR11462739 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462739_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 44 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 22.1 32.0 2.0 32.0 2.0 32.0 2 31.77375 32.0 32.0 32.0 32.0 32.0 3 34.425 37.0 32.0 37.0 32.0 37.0 4 36.0925 37.0 37.0 37.0 32.0 37.0 5 36.42125 37.0 37.0 37.0 37.0 37.0 6 39.9705 41.0 41.0 41.0 37.0 41.0 7 40.17175 41.0 41.0 41.0 37.0 41.0 8 40.17075 41.0 41.0 41.0 37.0 41.0 9 40.252 41.0 41.0 41.0 37.0 41.0 10-14 40.2922 41.0 41.0 41.0 37.8 41.0 15-19 40.1773 41.0 41.0 41.0 37.0 41.0 20-24 40.1454 41.0 41.0 41.0 37.0 41.0 25-29 40.0779 41.0 41.0 41.0 37.0 41.0 30-34 40.0081 41.0 41.0 41.0 37.0 41.0 35-39 39.854600000000005 41.0 41.0 41.0 37.0 41.0 40-44 39.90875 41.0 41.0 41.0 37.0 41.0 45-49 39.95985 41.0 41.0 41.0 37.0 41.0 50-54 39.907000000000004 41.0 41.0 41.0 37.0 41.0 55-59 39.751850000000005 41.0 41.0 41.0 37.0 41.0 60-64 39.771100000000004 41.0 41.0 41.0 37.0 41.0 65-69 39.77085 41.0 41.0 41.0 37.0 41.0 70-74 39.662850000000006 41.0 41.0 41.0 37.0 41.0 75-79 39.52155 41.0 40.2 41.0 37.0 41.0 80-84 39.952099999999994 41.0 41.0 41.0 37.0 41.0 85-89 39.8501 41.0 41.0 41.0 37.0 41.0 90-94 39.83275 41.0 41.0 41.0 37.0 41.0 95-99 39.7752 41.0 41.0 41.0 37.0 41.0 100-104 39.6517 41.0 41.0 41.0 37.0 41.0 105-109 39.69925 41.0 41.0 41.0 37.0 41.0 110-114 39.567550000000004 41.0 41.0 41.0 37.0 41.0 115-119 39.58545 41.0 41.0 41.0 37.0 41.0 120-124 39.37025 41.0 41.0 41.0 37.0 41.0 125-129 39.168899999999994 41.0 41.0 41.0 35.0 41.0 130-134 38.86194999999999 41.0 41.0 41.0 33.0 41.0 135-139 38.74085 41.0 41.0 41.0 32.0 41.0 140-144 38.65095 41.0 41.0 41.0 32.0 41.0 145-149 38.47324999999999 41.0 41.0 41.0 32.0 41.0 150-151 37.69075 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 2.0 24 2.0 25 3.0 26 9.0 27 8.0 28 13.0 29 24.0 30 32.0 31 41.0 32 40.0 33 61.0 34 95.0 35 86.0 36 106.0 37 157.0 38 135.0 39 303.0 40 2882.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 5.463270579549649 37.2093023255814 41.74972314507198 15.577703949796973 2 24.825 43.125 20.075000000000003 11.975 3 21.2 29.299999999999997 38.6 10.9 4 31.424999999999997 25.05 27.825 15.7 5 26.900000000000002 26.8 28.199999999999996 18.099999999999998 6 27.800000000000004 26.375 26.1 19.725 7 23.599999999999998 27.675 27.3 21.425 8 23.875 25.45 31.974999999999998 18.7 9 21.3 25.75 31.35 21.6 10-14 24.605 25.415 28.970000000000002 21.01 15-19 24.252425242524254 27.77777777777778 27.82278227822782 20.147014701470148 20-24 25.31 27.01 27.800000000000004 19.88 25-29 24.265 26.61 29.54 19.585 30-34 24.49244924492449 26.837683768376834 28.002800280028 20.667066706670667 35-39 24.15 26.02 28.395 21.435000000000002 40-44 23.805 26.38 29.275000000000002 20.54 45-49 23.552355235523553 27.13271327132713 27.722772277227726 21.59215921592159 50-54 23.7973797379738 27.262726272627262 27.53775377537754 21.402140214021404 55-59 24.597459745974597 26.51765176517652 28.197819781978197 20.687068706870686 60-64 24.46744674467447 25.54755475547555 29.992999299929995 19.99199919991999 65-69 25.64 27.01 26.955000000000002 20.395 70-74 24.61369205380807 26.969045356803523 27.269090363554533 21.148172225833875 75-79 23.47 26.840000000000003 29.315 20.375 80-84 24.715 26.76 28.384999999999998 20.14 85-89 24.062406240624064 28.36283628362836 27.27272727272727 20.3020302030203 90-94 25.72757275727573 25.312531253125314 28.147814781478147 20.812081208120812 95-99 24.275 26.31 28.08 21.335 100-104 24.55 25.679999999999996 27.875 21.895 105-109 23.56 26.900000000000002 27.339999999999996 22.2 110-114 24.355 26.25 28.305000000000003 21.09 115-119 24.560000000000002 26.650000000000002 28.17 20.62 120-124 23.835 27.505000000000003 28.335 20.325 125-129 23.82 28.515 26.495 21.17 130-134 23.355 28.615000000000002 27.595 20.435 135-139 24.015 27.834999999999997 26.3 21.85 140-144 24.795 28.605000000000004 25.430000000000003 21.17 145-149 24.060000000000002 28.449999999999996 24.035 23.455000000000002 150-151 21.7875 28.549999999999997 25.5625 24.099999999999998 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 2.0 1 1.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 1.0 21 0.5 22 0.5 23 1.5 24 2.0 25 5.0 26 6.5 27 5.0 28 6.5 29 12.5 30 16.5 31 21.5 32 30.5 33 46.5 34 70.5 35 88.5 36 97.0 37 102.0 38 130.5 39 151.0 40 175.0 41 209.0 42 245.0 43 248.5 44 283.0 45 298.0 46 233.0 47 207.0 48 201.5 49 174.0 50 132.0 51 103.5 52 107.5 53 112.0 54 84.0 55 78.0 56 62.0 57 41.0 58 43.5 59 33.5 60 24.5 61 21.5 62 18.0 63 16.5 64 9.5 65 3.0 66 2.0 67 3.5 68 6.5 69 7.5 70 4.5 71 7.0 72 5.0 73 0.0 74 0.5 75 0.5 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 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 fail #Base N-Count 1 32.275 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.01 20-24 0.0 25-29 0.0 30-34 0.01 35-39 0.0 40-44 0.0 45-49 0.01 50-54 0.01 55-59 0.01 60-64 0.01 65-69 0.0 70-74 0.015 75-79 0.0 80-84 0.0 85-89 0.01 90-94 0.01 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 86.075 #Duplication Level Percentage of deduplicated Percentage of total 1 93.43595701423178 80.425 2 4.676154516410107 8.05 3 0.5808887598024978 1.5 4 0.4066221318617485 1.4000000000000001 5 0.4066221318617485 1.7500000000000002 6 0.05808887598024978 0.3 7 0.05808887598024978 0.35000000000000003 8 0.08713331397037467 0.6 9 0.02904443799012489 0.22499999999999998 >10 0.23235550392099913 3.875 >50 0.02904443799012489 1.525 >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 fail #Sequence Count Percentage Possible Source TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 61 1.525 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 43 1.075 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 29 0.7250000000000001 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 21 0.525 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 15 0.375 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 13 0.325 No Hit TGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 12 0.3 No Hit NTGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 12 0.3 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 10 0.25 No Hit NACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 9 0.22499999999999998 No Hit AGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTA 8 0.2 No Hit CTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 8 0.2 No Hit AATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGACTTT 8 0.2 No Hit NAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 7 0.17500000000000002 No Hit TGCAACAAACCCCGACTTCTGGAAGGGACGCATTTATTAGATAAAAGGTC 7 0.17500000000000002 No Hit NGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGAT 6 0.15 No Hit TGGAACAAAAGGGTAAAAGCTCGTTTGATTCTGATTTCCAGTACGAATAC 6 0.15 No Hit AATCCGGGCTAGATGCGACGCGTGCGCCCGCCGTCCGATTGCCGACCTGC 5 0.125 No Hit NAAACAATCTCAAAACACAGAGAAGTTTCTTTGGTTTTTTTATCATGTCG 5 0.125 No Hit TAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACAC 5 0.125 No Hit NATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 5 0.125 No Hit GCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCC 5 0.125 No Hit TTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTA 5 0.125 No Hit TATAGCCTGTCCCAGTGATTGTCCAGAAACATAAACACTTCCTCCTCCTT 5 0.125 No Hit NAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTC 5 0.125 No Hit TATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCAT 5 0.125 No Hit TGTGTAAGTATGAACTAATTCAGACTGTGAAACTGCGAATGGCTCATTAA 5 0.125 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 5 0.125 No Hit AATTCAGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGT 5 0.125 No Hit TAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGG 5 0.125 No Hit CAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTC 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.0125 0.0 0.0 0.0 0.0 20-21 0.025 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 0.075 0.0 0.0 0.0 0.0 28-29 0.075 0.0 0.0 0.0 0.0 30-31 0.0875 0.0 0.0 0.0 0.0 32-33 0.1 0.0 0.0 0.0 0.0 34-35 0.1125 0.0 0.0 0.0 0.0 36-37 0.1375 0.0 0.0 0.0 0.0 38-39 0.175 0.0 0.0 0.0 0.0 40-41 0.2 0.0 0.0 0.0 0.0 42-43 0.25 0.0 0.0 0.0 0.0 44-45 0.3 0.0 0.0 0.0 0.0 46-47 0.375 0.0 0.0 0.0 0.0 48-49 0.5 0.0 0.0 0.0 0.0 50-51 0.5375000000000001 0.0 0.0 0.0 0.0 52-53 0.575 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 0.7625 0.0 0.0 0.0 0.0 60-61 0.8875 0.0 0.0 0.0 0.0 62-63 0.9874999999999999 0.0 0.0 0.0 0.0 64-65 1.05 0.0 0.0 0.0 0.0 66-67 1.1375000000000002 0.0 0.0 0.0 0.0 68-69 1.2374999999999998 0.0 0.0 0.0 0.0 70-71 1.325 0.0 0.0 0.0 0.0 72-73 1.4375 0.0 0.0 0.0 0.0 74-75 1.6124999999999998 0.0 0.0 0.0 0.0 76-77 1.75 0.0 0.0 0.0 0.0 78-79 2.0 0.0 0.0 0.0 0.0 80-81 2.1875 0.0 0.0 0.0 0.0 82-83 2.3875 0.0 0.0 0.0 0.0 84-85 2.525 0.0 0.0 0.0 0.0 86-87 2.7 0.0 0.0 0.0 0.0 88-89 3.0625 0.0 0.0 0.0 0.0 90-91 3.7249999999999996 0.0 0.0 0.0 0.0 92-93 4.1375 0.0 0.0 0.0 0.0 94-95 4.449999999999999 0.0 0.0 0.0 0.0 96-97 4.85 0.0 0.0 0.0 0.0 98-99 5.324999999999999 0.0 0.0 0.0 0.0 100-101 5.725 0.0 0.0 0.0 0.0 102-103 6.0875 0.0 0.0 0.0 0.0 104-105 6.5125 0.0 0.0 0.0 0.0 106-107 6.8875 0.0 0.0 0.0 0.0 108-109 7.4625 0.0 0.0 0.0 0.0 110-111 8.1 0.0 0.0 0.0 0.0 112-113 8.9375 0.0 0.0 0.0 0.0 114-115 9.875 0.0 0.0 0.0 0.0 116-117 10.5 0.0 0.0 0.0 0.0 118-119 11.2375 0.0 0.0 0.0 0.0 120-121 12.0875 0.0 0.0 0.0 0.0 122-123 12.837499999999999 0.0 0.0 0.0 0.0 124-125 13.9375 0.0 0.0 0.0 0.0 126-127 14.8875 0.0 0.0 0.0 0.0 128-129 15.837499999999999 0.0 0.0 0.0 0.0 130-131 17.0625 0.0 0.0 0.0 0.0 132-133 18.35 0.0 0.0 0.0 0.0 134-135 19.825000000000003 0.0 0.0 0.0 0.0 136-137 21.262500000000003 0.0 0.0 0.0 0.0 138-139 22.35 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGAGGCT 15 0.007408205 140.30302 1 CACGGCC 20 3.6186364E-4 108.515625 145 GCTACTC 30 0.0018128043 72.34375 6 TTGCTAC 30 0.0018128043 72.34375 4 ACTCGGA 35 0.0033408657 62.00893 9 ATTTGCT 35 0.0033408657 62.00893 2 TACTCGG 35 0.0033408657 62.00893 8 TTTGCTA 35 0.0033408657 62.00893 3 CTACTCG 35 0.0033408657 62.00893 7 TGCTACT 40 0.005669544 54.257812 5 >>END_MODULE Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950432 READS because READLEN < 1 Read 1950432 spots for SRR11462739.sra Written 1950432 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra Rejected 1950416 READS because READLEN < 1 Read 1950416 spots for SRR11462739.sra Written 1950416 spots for SRR11462739.sra SRR ids: ['SRR11462739.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_aam2yxal SRR11462739.sra spots: 39008336 blocks: [[1, 1950416], [1950417, 3900832], [3900833, 5851248], [5851249, 7801664], [7801665, 9752080], [9752081, 11702496], [11702497, 13652912], [13652913, 15603328], [15603329, 17553744], [17553745, 19504160], [19504161, 21454576], [21454577, 23404992], [23404993, 25355408], [25355409, 27305824], [27305825, 29256240], [29256241, 31206656], [31206657, 33157072], [33157073, 35107488], [35107489, 37057904], [37057905, 39008336]] SRR11462739 file size 13235038 SRR11462739 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 SRR11462739 SRR11462739_1.fastq Input file: SRR11462739_1.fastq trimmed: SRR11462739-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- 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 -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Wed Feb 12 12:13:14 2025 >> started Wed Feb 12 12:13:36 2025 >> done (21.846s) 39008336 reads processed; of these: 10885 ( 0.03%) short reads filtered out after trimming by size control 652 ( 0.00%) empty reads filtered out after trimming by size control 38996799 (99.97%) reads available; of these: 4862818 (12.47%) trimmed reads available after processing 34133981 (87.53%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2244 0.01% 19 2426 0.01% 20 2767 0.01% 21 2818 0.01% 22 3271 0.01% 23 3378 0.01% 24 3827 0.01% 25 3719 0.01% 26 4028 0.01% 27 5066 0.01% 28 4166 0.01% 29 4540 0.01% 30 4714 0.01% 31 4792 0.01% 32 4812 0.01% 33 5210 0.01% 34 5434 0.01% 35 5644 0.01% 36 5698 0.01% 37 7962 0.02% 38 6287 0.02% 39 7036 0.02% 40 6533 0.02% 41 6885 0.02% 42 8109 0.02% 43 8760 0.02% 44 7839 0.02% 45 8766 0.02% 46 9159 0.02% 47 11924 0.03% 48 10416 0.03% 49 13244 0.03% 50 10383 0.03% 51 11391 0.03% 52 12159 0.03% 53 12420 0.03% 54 14002 0.04% 55 13338 0.03% 56 14107 0.04% 57 15966 0.04% 58 15965 0.04% 59 16363 0.04% 60 18463 0.05% 61 17630 0.05% 62 54552 0.14% 63 18077 0.05% 64 21737 0.06% 65 19275 0.05% 66 20467 0.05% 67 21938 0.06% 68 21864 0.06% 69 31180 0.08% 70 23508 0.06% 71 27085 0.07% 72 29756 0.08% 73 35526 0.09% 74 38061 0.10% 75 31998 0.08% 76 29228 0.07% 77 42774 0.11% 78 33602 0.09% 79 44775 0.11% 80 35081 0.09% 81 36858 0.09% 82 40450 0.10% 83 42573 0.11% 84 46978 0.12% 85 45648 0.12% 86 48622 0.12% 87 53674 0.14% 88 50975 0.13% 89 144474 0.37% 90 56731 0.15% 91 65985 0.17% 92 58364 0.15% 93 61174 0.16% 94 69304 0.18% 95 68194 0.17% 96 81857 0.21% 97 86406 0.22% 98 74561 0.19% 99 77813 0.20% 100 78253 0.20% 101 87933 0.23% 102 104002 0.27% 103 92020 0.24% 104 95921 0.25% 105 98911 0.25% 106 102018 0.26% 107 108739 0.28% 108 114273 0.29% 109 141646 0.36% 110 121198 0.31% 111 127129 0.33% 112 385829 0.99% 113 137603 0.35% 114 138921 0.36% 115 138705 0.36% 116 145516 0.37% 117 159783 0.41% 118 164131 0.42% 119 165482 0.42% 120 0 0.00% 121 0 0.00% 122 0 0.00% 123 0 0.00% 124 0 0.00% 125 0 0.00% 126 0 0.00% 127 0 0.00% 128 0 0.00% 129 0 0.00% 130 0 0.00% 131 0 0.00% 132 0 0.00% 133 0 0.00% 134 0 0.00% 135 0 0.00% 136 0 0.00% 137 0 0.00% 138 0 0.00% 139 0 0.00% 140 0 0.00% 141 0 0.00% 142 0 0.00% 143 0 0.00% 144 0 0.00% 145 0 0.00% 146 0 0.00% 147 0 0.00% 148 0 0.00% 149 0 0.00% 150 19 0.00% 151 34133981 87.53% 38996799 reads passed initial QC criterion=sequence-density sequence-density=10.75 sequence-density-rank=1 fanout-score=40.93 fanout-score-rank=1 prefix-density=12.92 prefix-fanout=34.1 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATCTCGTATGCCGTCTTCTGCTTGAAAA criterion=fanout-score sequence-density=10.75 sequence-density-rank=1 fanout-score=40.93 fanout-score-rank=1 prefix-density=12.92 prefix-fanout=34.1 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATCTCGTATGCCGTCTTCTGCTTGAAAA Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 1 (100.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 0 (0.00%) aligned >1 times 0.00% overall alignment rate Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATCTCGTATGCCGTCTTCTGCTTGAAAA -o SRR11462739 - Input file: STDIN trimmed: SRR11462739-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCAAAAGATCTCGTATGCCGTCTTCTGCTTG -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): 3 -- number of concurrent threads (-t): 20 Wed Feb 12 12:15:01 2025 >> started Wed Feb 12 12:15:37 2025 >> done (35.997s) 31906472 reads processed; of these: 350 ( 0.00%) short reads filtered out after trimming by size control 4 ( 0.00%) empty reads filtered out after trimming by size control 31906118 (100.00%) reads available; of these: 6732620 (21.10%) trimmed reads available after processing 25173498 (78.90%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1863 0.01% 19 2023 0.01% 20 2291 0.01% 21 2310 0.01% 22 2732 0.01% 23 2790 0.01% 24 3193 0.01% 25 3013 0.01% 26 3364 0.01% 27 4207 0.01% 28 3433 0.01% 29 3732 0.01% 30 3860 0.01% 31 3982 0.01% 32 4017 0.01% 33 4295 0.01% 34 4439 0.01% 35 4633 0.01% 36 4695 0.01% 37 6592 0.02% 38 5211 0.02% 39 5820 0.02% 40 5464 0.02% 41 5678 0.02% 42 6701 0.02% 43 7271 0.02% 44 6450 0.02% 45 7286 0.02% 46 7583 0.02% 47 9824 0.03% 48 8536 0.03% 49 10932 0.03% 50 8611 0.03% 51 9466 0.03% 52 10045 0.03% 53 10468 0.03% 54 11517 0.04% 55 10993 0.03% 56 11435 0.04% 57 13249 0.04% 58 13166 0.04% 59 13435 0.04% 60 15261 0.05% 61 14599 0.05% 62 45098 0.14% 63 14936 0.05% 64 17802 0.06% 65 16014 0.05% 66 16850 0.05% 67 18137 0.06% 68 18105 0.06% 69 25763 0.08% 70 19912 0.06% 71 22187 0.07% 72 24615 0.08% 73 29235 0.09% 74 31223 0.10% 75 25915 0.08% 76 24298 0.08% 77 35272 0.11% 78 27818 0.09% 79 36817 0.12% 80 28872 0.09% 81 31647 0.10% 82 33478 0.10% 83 35143 0.11% 84 37365 0.12% 85 37685 0.12% 86 39840 0.12% 87 44228 0.14% 88 42176 0.13% 89 118815 0.37% 90 47286 0.15% 91 54698 0.17% 92 48294 0.15% 93 50010 0.16% 94 57158 0.18% 95 56237 0.18% 96 67556 0.21% 97 71048 0.22% 98 61094 0.19% 99 64302 0.20% 100 64436 0.20% 101 72535 0.23% 102 85695 0.27% 103 76126 0.24% 104 79127 0.25% 105 81277 0.25% 106 83777 0.26% 107 89662 0.28% 108 94700 0.30% 109 116808 0.37% 110 100269 0.31% 111 104813 0.33% 112 317742 1.00% 113 112826 0.35% 114 114168 0.36% 115 113600 0.36% 116 119422 0.37% 117 126679 0.40% 118 129902 0.41% 119 133193 0.42% 120 149059 0.47% 121 154002 0.48% 122 154445 0.48% 123 184398 0.58% 124 190937 0.60% 125 156215 0.49% 126 172508 0.54% 127 180560 0.57% 128 179263 0.56% 129 176511 0.55% 130 177936 0.56% 131 191572 0.60% 132 287181 0.90% 133 229947 0.72% 134 203285 0.64% 135 221535 0.69% 136 209577 0.66% 137 223398 0.70% 138 233466 0.73% 139 229068 0.72% 140 238954 0.75% 141 222235 0.70% 142 247087 0.77% 143 245465 0.77% 144 226250 0.71% 145 290609 0.91% 146 241253 0.76% 147 340187 1.07% 148 641615 2.01% 149 0 0.00% 150 14 0.00% 151 21313435 66.80% criterion=sequence-density sequence-density=1.19 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=31 prefix-density=1.20 prefix-fanout=2.0 sequence=ACGTGAGCTGGGTTCAGAACGTCGTGAGAC criterion=fanout-score sequence-density=0.03 sequence-density-rank=31 fanout-score=229.12 fanout-score-rank=1 prefix-density=0.30 prefix-fanout=20.4 sequence=TTGATGCTGAGAATTCTCCAAGCGTGGTTGCCATCAACGTGAGCCCTATTGAATATGGGCATGTGCTGTTAATCCCACGTGTCCTGGATTGCTTGCCTCAGAGGATTGATCGTGATAGCTTCTTGCTTGCACTTCACATGGCAGCTGAAGCTGGGGATCCATACTTCCGACTGGGTTACAATAGCTTGGGTGCTTTTGCAACCATTAACCATCTTCACTTCCAGGCTTACTACTTGACTGTGCCTTTTCCGATTGAGAAGG Started job on | Feb 12 12:16:17 Started mapping on | Feb 12 12:16:18 Finished on | Feb 12 12:18:11 Mapping speed, Million of reads per hour | 1242.36 Number of input reads | 38996445 Average input read length | 141 UNIQUE READS: Uniquely mapped reads number | 28679556 Uniquely mapped reads % | 73.54% Average mapped length | 138.65 Number of splices: Total | 12658067 Number of splices: Annotated (sjdb) | 12377756 Number of splices: GT/AG | 12440290 Number of splices: GC/AG | 167084 Number of splices: AT/AC | 8375 Number of splices: Non-canonical | 42318 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.02% Deletion average length | 2.09 Insertion rate per base | 0.01% Insertion average length | 1.80 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 935248 % of reads mapped to multiple loci | 2.40% Number of reads mapped to too many loci | 6473192 % of reads mapped to too many loci | 16.60% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.18% % of reads unmapped: other | 0.28% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9381641 9381641 9381641 N_multimapping 935248 935248 935248 N_noFeature 1946448 2280290 27878587 N_ambiguous 571752 104690 826 UnstrandedReadsAssigned:26161356 PositiveStrandReadsAssigned:26294576 NegativeStrandReadsAssigned:800143 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=133 echo kmer=129 SRR11462739 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in single-end mode [quant] will process file 1: SRR11462739-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 38,996,445 reads, 28,424,395 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,237 rounds 52401 SRR11462739.ke.tsv 34699 SRR11462739.se.tsv 87100 total ==> SRR11462739.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 1336 27.596 Potri.005G024800.1.v4.1 1035 936 581 24.6045 Potri.004G059700.1.v4.1 961 862 31 1.42551 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 3043.11 42.4134 Potri.016G087400.1.v4.1 270 171 1646 381.547 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 384.85 9.11278 Potri.012G127500.1.v4.1 977 878 197 8.89378 ==> SRR11462739.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 111 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 196 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 3 Potri.001G040500.v4.1 26 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 45 SRR11462739 completed mapping pipeline successfully