Starting /dee2/code/volunteer_pipeline.sh SRR11462741 current disk space = 3051354284032 free memory = 1487823496 SRR11462741 SRAfilesize 147e1c52f06d0b3a518f594bdf131ff5 SRR11462741.sra SRR11462741.sra file validated SRR11462741 is single end SRR11462741 is conventional basespace SRR11462741 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462741_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 45 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 21.31 32.0 2.0 32.0 2.0 32.0 2 31.77875 32.0 32.0 32.0 32.0 32.0 3 34.37 37.0 32.0 37.0 32.0 37.0 4 36.18625 37.0 37.0 37.0 32.0 37.0 5 36.50125 37.0 37.0 37.0 37.0 37.0 6 40.0355 41.0 41.0 41.0 37.0 41.0 7 40.2115 41.0 41.0 41.0 37.0 41.0 8 40.15825 41.0 41.0 41.0 37.0 41.0 9 40.251 41.0 41.0 41.0 37.0 41.0 10-14 40.303250000000006 41.0 41.0 41.0 37.8 41.0 15-19 40.189800000000005 41.0 41.0 41.0 37.0 41.0 20-24 40.192949999999996 41.0 41.0 41.0 37.0 41.0 25-29 40.1652 41.0 41.0 41.0 37.0 41.0 30-34 40.02335 41.0 41.0 41.0 37.0 41.0 35-39 39.93075 41.0 41.0 41.0 37.0 41.0 40-44 40.01655 41.0 41.0 41.0 37.0 41.0 45-49 40.05159999999999 41.0 41.0 41.0 37.0 41.0 50-54 39.9861 41.0 41.0 41.0 37.0 41.0 55-59 39.92295 41.0 41.0 41.0 37.0 41.0 60-64 39.8673 41.0 41.0 41.0 37.0 41.0 65-69 39.85395 41.0 41.0 41.0 37.0 41.0 70-74 39.75345 41.0 41.0 41.0 37.0 41.0 75-79 39.657 41.0 40.2 41.0 37.0 41.0 80-84 40.0797 41.0 41.0 41.0 37.0 41.0 85-89 40.01129999999999 41.0 41.0 41.0 37.0 41.0 90-94 39.97885 41.0 41.0 41.0 37.0 41.0 95-99 39.87355 41.0 41.0 41.0 37.0 41.0 100-104 39.804899999999996 41.0 41.0 41.0 37.0 41.0 105-109 39.77485 41.0 41.0 41.0 37.0 41.0 110-114 39.67445 41.0 41.0 41.0 37.0 41.0 115-119 39.6833 41.0 41.0 41.0 37.0 41.0 120-124 39.4562 41.0 41.0 41.0 37.0 41.0 125-129 39.3219 41.0 41.0 41.0 37.0 41.0 130-134 39.0432 41.0 41.0 41.0 34.0 41.0 135-139 38.837599999999995 41.0 41.0 41.0 34.0 41.0 140-144 38.70205 41.0 41.0 41.0 32.0 41.0 145-149 38.51105 41.0 41.0 41.0 32.0 41.0 150-151 37.694874999999996 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 1.0 22 0.0 23 1.0 24 1.0 25 0.0 26 6.0 27 5.0 28 13.0 29 17.0 30 24.0 31 36.0 32 43.0 33 59.0 34 89.0 35 89.0 36 108.0 37 138.0 38 146.0 39 323.0 40 2900.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 6.076923076923077 36.38461538461538 42.46153846153846 15.076923076923077 2 25.55 42.4 20.625 11.425 3 22.825 29.425 37.475 10.274999999999999 4 33.050000000000004 23.150000000000002 27.400000000000002 16.400000000000002 5 28.599999999999998 26.325 27.775 17.299999999999997 6 25.4 26.025 27.1 21.475 7 22.975 26.450000000000003 30.325000000000003 20.25 8 25.1 25.424999999999997 29.2 20.275000000000002 9 20.474999999999998 25.650000000000002 31.900000000000002 21.975 10-14 25.135 24.4 29.49 20.974999999999998 15-19 24.025 27.715 28.139999999999997 20.119999999999997 20-24 26.169999999999998 26.33 27.455000000000002 20.044999999999998 25-29 25.82 25.580000000000002 29.17 19.43 30-34 24.905 26.195 27.73 21.17 35-39 25.180000000000003 25.259999999999998 28.38 21.18 40-44 24.099999999999998 26.205000000000002 29.685 20.01 45-49 23.765 26.619999999999997 28.215 21.4 50-54 24.7 27.439999999999998 27.195000000000004 20.665 55-59 24.58 26.665 28.060000000000002 20.695 60-64 25.72 25.94 28.965000000000003 19.375 65-69 25.36 26.35 27.42 20.87 70-74 25.61 26.674999999999997 27.02 20.695 75-79 23.51 27.084999999999997 28.84 20.565 80-84 25.779999999999998 26.21 28.205000000000002 19.805 85-89 24.97 26.740000000000002 27.665 20.625 90-94 25.825 26.25 27.49 20.435 95-99 24.86 26.965 27.189999999999998 20.985 100-104 25.585 26.064999999999998 27.43 20.919999999999998 105-109 24.18 27.415 26.32 22.085 110-114 24.065 27.77 26.974999999999998 21.19 115-119 24.48 26.88 27.74 20.9 120-124 24.44 27.855 26.46 21.245 125-129 23.96 28.470000000000002 25.855 21.715 130-134 23.87 28.610000000000003 25.965 21.555 135-139 24.285 27.73 25.314999999999998 22.67 140-144 24.490000000000002 28.37 24.240000000000002 22.900000000000002 145-149 23.27 28.555000000000003 24.22 23.955000000000002 150-151 22.175 28.4125 24.4125 25.0 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 2.0 1 1.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.5 8 0.5 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 0.0 20 0.0 21 0.0 22 0.0 23 0.5 24 1.0 25 2.0 26 3.5 27 2.5 28 2.5 29 7.0 30 18.0 31 28.0 32 35.5 33 42.0 34 59.0 35 87.0 36 101.5 37 119.0 38 132.5 39 143.5 40 174.5 41 199.5 42 211.0 43 227.5 44 265.5 45 262.5 46 221.0 47 206.5 48 206.5 49 183.5 50 146.0 51 116.5 52 128.0 53 141.5 54 110.0 55 95.0 56 70.0 57 44.5 58 41.0 59 29.5 60 18.5 61 16.0 62 19.5 63 21.5 64 13.0 65 3.5 66 3.0 67 3.0 68 6.0 69 8.0 70 6.0 71 7.5 72 4.5 73 0.0 74 1.0 75 1.0 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 35.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 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 85.425 #Duplication Level Percentage of deduplicated Percentage of total 1 92.80070237050045 79.27499999999999 2 5.033655253146034 8.6 3 0.7316359379572724 1.875 4 0.4389815627743635 1.5 5 0.2633889376646181 1.125 6 0.17559262510974538 0.8999999999999999 7 0.1463271875914545 0.8750000000000001 8 0.08779631255487269 0.6 9 0.08779631255487269 0.675 >10 0.2048580626280363 3.2 >50 0.029265437518290898 1.375 >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 ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 55 1.375 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 46 1.15 No Hit NTGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 21 0.525 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 18 0.44999999999999996 No Hit TGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 11 0.27499999999999997 No Hit AGGGCAAGTCTGGTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTA 11 0.27499999999999997 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 11 0.27499999999999997 No Hit TAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGG 10 0.25 No Hit NATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCAT 9 0.22499999999999998 No Hit CTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 9 0.22499999999999998 No Hit TTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGA 9 0.22499999999999998 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 8 0.2 No Hit GAAGGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGC 8 0.2 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 8 0.2 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 7 0.17500000000000002 No Hit TATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCAT 7 0.17500000000000002 No Hit TATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTATGAACTAATTC 7 0.17500000000000002 No Hit NAGGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCT 7 0.17500000000000002 No Hit TACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCCG 7 0.17500000000000002 No Hit NACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 6 0.15 No Hit TGCAACAAACCCCGACTTCTGGAAGGGACGCATTTATTAGATAAAAGGTC 6 0.15 No Hit TGTGTAAGTATGAACTAATTCAGACTGTGAAACTGCGAATGGCTCATTAA 6 0.15 No Hit GATGTCGGCTCTTCGCCACCTGGGGCTGTAGTATGTTCCAAGGGTTGGGC 6 0.15 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 6 0.15 No Hit AAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAAT 6 0.15 No Hit AATCCGGGCTAGATGCGACGCGTGCGCCCGCCGTCCGATTGCCGACCTGC 5 0.125 No Hit NAAGGGACGCATTTATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGC 5 0.125 No Hit NGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 5 0.125 No Hit AGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGAT 5 0.125 No Hit TAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACAC 5 0.125 No Hit NTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGA 5 0.125 No Hit NTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTA 5 0.125 No Hit NTATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTG 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 0.05 0.0 0.0 0.0 0.0 22-23 0.0875 0.0 0.0 0.0 0.0 24-25 0.1 0.0 0.0 0.0 0.0 26-27 0.15 0.0 0.0 0.0 0.0 28-29 0.21250000000000002 0.0 0.0 0.0 0.0 30-31 0.225 0.0 0.0 0.0 0.0 32-33 0.35 0.0 0.0 0.0 0.0 34-35 0.3625 0.0 0.0 0.0 0.0 36-37 0.4 0.0 0.0 0.0 0.0 38-39 0.5125 0.0 0.0 0.0 0.0 40-41 0.525 0.0 0.0 0.0 0.0 42-43 0.55 0.0 0.0 0.0 0.0 44-45 0.5874999999999999 0.0 0.0 0.0 0.0 46-47 0.6 0.0 0.0 0.0 0.0 48-49 0.625 0.0 0.0 0.0 0.0 50-51 0.65 0.0 0.0 0.0 0.0 52-53 0.6875 0.0 0.0 0.0 0.0 54-55 0.75 0.0 0.0 0.0 0.0 56-57 0.8125 0.0 0.0 0.0 0.0 58-59 0.9 0.0 0.0 0.0 0.0 60-61 0.9750000000000001 0.0 0.0 0.0 0.0 62-63 1.275 0.0 0.0 0.0 0.0 64-65 1.5 0.0 0.0 0.0 0.0 66-67 1.5625 0.0 0.0 0.0 0.0 68-69 1.675 0.0 0.0 0.0 0.0 70-71 1.7625 0.0 0.0 0.0 0.0 72-73 1.925 0.0 0.0 0.0 0.0 74-75 2.1625 0.0 0.0 0.0 0.0 76-77 2.375 0.0 0.0 0.0 0.0 78-79 2.7125 0.0 0.0 0.0 0.0 80-81 3.0875 0.0 0.0 0.0 0.0 82-83 3.525 0.0 0.0 0.0 0.0 84-85 3.925 0.0 0.0 0.0 0.0 86-87 4.325 0.0 0.0 0.0 0.0 88-89 4.85 0.0 0.0 0.0 0.0 90-91 5.8375 0.0 0.0 0.0 0.0 92-93 6.512499999999999 0.0 0.0 0.0 0.0 94-95 7.05 0.0 0.0 0.0 0.0 96-97 7.725 0.0 0.0 0.0 0.0 98-99 8.7 0.0 0.0 0.0 0.0 100-101 9.475 0.0 0.0 0.0 0.0 102-103 10.25 0.0 0.0 0.0 0.0 104-105 11.1375 0.0 0.0 0.0 0.0 106-107 12.075 0.0 0.0 0.0 0.0 108-109 13.0375 0.0 0.0 0.0 0.0 110-111 14.225000000000001 0.0 0.0 0.0 0.0 112-113 15.5625 0.0 0.0 0.0 0.0 114-115 17.15 0.0 0.0 0.0 0.0 116-117 18.5625 0.0 0.0 0.0 0.0 118-119 19.9375 0.0 0.0 0.0 0.0 120-121 21.6875 0.0 0.0 0.0 0.0 122-123 23.362499999999997 0.0 0.0 0.0 0.0 124-125 25.4375 0.0 0.0 0.0 0.0 126-127 27.0875 0.0 0.0 0.0 0.0 128-129 28.75 0.0 0.0 0.0 0.0 130-131 30.325 0.0 0.0 0.0 0.0 132-133 32.1375 0.0 0.0 0.0 0.0 134-135 34.425 0.0 0.0 0.0 0.0 136-137 35.8125 0.0 0.0 0.0 0.0 138-139 37.7375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATGCGCT 10 0.0019681407 218.35849 1 AAGTATG 10 0.0068785893 144.66249 6 TGCGCTC 10 0.0068785893 144.66249 2 CTCCTGG 10 0.0068785893 144.66249 6 TAAGTAT 10 0.0068785893 144.66249 5 GTGTAAG 10 0.0068785893 144.66249 2 CGCTCCT 10 0.0068785893 144.66249 4 GTCGAGA 10 0.0068785893 144.66249 8 AGTATGA 10 0.0068785893 144.66249 7 GCGCTCC 10 0.0068785893 144.66249 3 GTAAGTA 10 0.0068785893 144.66249 4 CGTCGAG 10 0.0068785893 144.66249 7 TGGGAGA 10 0.0068785893 144.66249 145 TCCTGGC 10 0.0068785893 144.66249 7 TATTTGC 30 3.3964476E-4 109.179245 1 GTATGAA 20 3.6211254E-4 108.49687 8 ATTTGCT 30 1.4282761E-5 96.44166 2 TTTGCTA 30 1.4282761E-5 96.44166 3 CACGGCC 30 1.4282761E-5 96.44166 145 GCTACTC 25 8.794345E-4 86.79749 6 >>END_MODULE Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra Rejected 1954890 READS because READLEN < 1 Read 1954890 spots for SRR11462741.sra Written 1954890 spots for SRR11462741.sra SRR ids: ['SRR11462741.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_og16rq62 SRR11462741.sra spots: 39097800 blocks: [[1, 1954890], [1954891, 3909780], [3909781, 5864670], [5864671, 7819560], [7819561, 9774450], [9774451, 11729340], [11729341, 13684230], [13684231, 15639120], [15639121, 17594010], [17594011, 19548900], [19548901, 21503790], [21503791, 23458680], [23458681, 25413570], [25413571, 27368460], [27368461, 29323350], [29323351, 31278240], [31278241, 33233130], [33233131, 35188020], [35188021, 37142910], [37142911, 39097800]] SRR11462741 file size 13265442 SRR11462741 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 SRR11462741 SRR11462741_1.fastq Input file: SRR11462741_1.fastq trimmed: SRR11462741-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 11:26:50 2025 >> started Wed Feb 12 11:27:13 2025 >> done (23.332s) 39097800 reads processed; of these: 11553 ( 0.03%) short reads filtered out after trimming by size control 676 ( 0.00%) empty reads filtered out after trimming by size control 39085571 (99.97%) reads available; of these: 8599756 (22.00%) trimmed reads available after processing 30485815 (78.00%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2464 0.01% 19 2689 0.01% 20 3112 0.01% 21 3333 0.01% 22 3729 0.01% 23 4133 0.01% 24 4390 0.01% 25 4262 0.01% 26 4281 0.01% 27 6001 0.02% 28 4750 0.01% 29 5072 0.01% 30 5462 0.01% 31 5626 0.01% 32 5485 0.01% 33 5612 0.01% 34 6158 0.02% 35 6070 0.02% 36 6567 0.02% 37 8522 0.02% 38 7007 0.02% 39 7454 0.02% 40 7701 0.02% 41 7621 0.02% 42 9348 0.02% 43 10559 0.03% 44 8703 0.02% 45 9720 0.02% 46 10010 0.03% 47 13591 0.03% 48 11957 0.03% 49 14190 0.04% 50 12353 0.03% 51 13840 0.04% 52 14159 0.04% 53 15460 0.04% 54 17317 0.04% 55 16812 0.04% 56 17759 0.05% 57 20665 0.05% 58 20204 0.05% 59 22330 0.06% 60 24017 0.06% 61 23013 0.06% 62 65973 0.17% 63 25626 0.07% 64 29656 0.08% 65 27979 0.07% 66 29335 0.08% 67 32992 0.08% 68 32534 0.08% 69 45255 0.12% 70 36541 0.09% 71 42098 0.11% 72 45377 0.12% 73 57672 0.15% 74 60721 0.16% 75 51617 0.13% 76 48924 0.13% 77 72600 0.19% 78 56729 0.15% 79 73976 0.19% 80 61184 0.16% 81 65857 0.17% 82 73272 0.19% 83 77563 0.20% 84 86190 0.22% 85 83237 0.21% 86 88077 0.23% 87 102801 0.26% 88 94920 0.24% 89 208219 0.53% 90 106021 0.27% 91 124207 0.32% 92 112458 0.29% 93 118789 0.30% 94 131069 0.34% 95 135099 0.35% 96 157183 0.40% 97 171600 0.44% 98 147452 0.38% 99 155125 0.40% 100 153394 0.39% 101 170259 0.44% 102 197982 0.51% 103 180444 0.46% 104 189109 0.48% 105 190558 0.49% 106 198011 0.51% 107 207486 0.53% 108 220517 0.56% 109 256904 0.66% 110 226959 0.58% 111 238440 0.61% 112 708764 1.81% 113 254809 0.65% 114 251389 0.64% 115 249028 0.64% 116 262765 0.67% 117 292196 0.75% 118 289299 0.74% 119 291986 0.75% 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 21 0.00% 151 30485815 78.00% 39085571 reads passed initial QC criterion=sequence-density sequence-density=16.51 sequence-density-rank=1 fanout-score=39.07 fanout-score-rank=1 prefix-density=19.28 prefix-fanout=33.5 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTGAAA criterion=fanout-score sequence-density=16.51 sequence-density-rank=1 fanout-score=39.07 fanout-score-rank=1 prefix-density=19.28 prefix-fanout=33.5 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTGAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTGAAA -o SRR11462741 - Input file: STDIN trimmed: SRR11462741-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATGAGCATCTCGTATGCCGTCTTCTGCTTG -- 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 11:28:39 2025 >> started Wed Feb 12 11:29:24 2025 >> done (45.710s) 34487269 reads processed; of these: 366 ( 0.00%) short reads filtered out after trimming by size control 4 ( 0.00%) empty reads filtered out after trimming by size control 34486899 (100.00%) reads available; of these: 9766140 (28.32%) trimmed reads available after processing 24720759 (71.68%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2200 0.01% 19 2374 0.01% 20 2800 0.01% 21 2942 0.01% 22 3270 0.01% 23 3674 0.01% 24 3914 0.01% 25 3756 0.01% 26 3810 0.01% 27 5307 0.02% 28 4188 0.01% 29 4491 0.01% 30 4837 0.01% 31 5005 0.01% 32 4850 0.01% 33 5030 0.01% 34 5466 0.02% 35 5424 0.02% 36 5847 0.02% 37 7516 0.02% 38 6228 0.02% 39 6611 0.02% 40 6896 0.02% 41 6776 0.02% 42 8294 0.02% 43 9358 0.03% 44 7726 0.02% 45 8702 0.03% 46 9001 0.03% 47 12167 0.04% 48 10609 0.03% 49 12565 0.04% 50 10961 0.03% 51 12377 0.04% 52 12674 0.04% 53 14070 0.04% 54 15311 0.04% 55 14943 0.04% 56 15544 0.05% 57 18441 0.05% 58 17861 0.05% 59 19831 0.06% 60 21570 0.06% 61 20581 0.06% 62 58540 0.17% 63 22823 0.07% 64 26240 0.08% 65 25053 0.07% 66 25995 0.08% 67 29303 0.08% 68 29012 0.08% 69 40222 0.12% 70 33541 0.10% 71 37483 0.11% 72 40494 0.12% 73 51176 0.15% 74 53823 0.16% 75 45355 0.13% 76 43804 0.13% 77 64612 0.19% 78 50382 0.15% 79 65714 0.19% 80 54500 0.16% 81 60698 0.18% 82 65019 0.19% 83 68929 0.20% 84 74603 0.22% 85 73970 0.21% 86 78315 0.23% 87 91587 0.27% 88 84903 0.25% 89 184651 0.54% 90 94889 0.28% 91 110287 0.32% 92 100244 0.29% 93 105233 0.31% 94 116740 0.34% 95 120379 0.35% 96 139744 0.41% 97 151955 0.44% 98 131010 0.38% 99 138155 0.40% 100 136169 0.39% 101 151738 0.44% 102 175782 0.51% 103 160684 0.47% 104 168449 0.49% 105 168779 0.49% 106 175775 0.51% 107 183829 0.53% 108 197094 0.57% 109 228259 0.66% 110 201285 0.58% 111 211049 0.61% 112 629196 1.82% 113 224621 0.65% 114 223042 0.65% 115 218817 0.63% 116 231809 0.67% 117 250246 0.73% 118 248300 0.72% 119 254325 0.74% 120 280438 0.81% 121 281982 0.82% 122 283814 0.82% 123 317366 0.92% 124 350291 1.02% 125 271454 0.79% 126 305045 0.88% 127 306003 0.89% 128 298286 0.86% 129 289223 0.84% 130 284720 0.83% 131 304453 0.88% 132 465144 1.35% 133 349658 1.01% 134 304664 0.88% 135 327175 0.95% 136 309204 0.90% 137 329121 0.95% 138 337183 0.98% 139 316970 0.92% 140 321191 0.93% 141 301205 0.87% 142 331358 0.96% 143 321231 0.93% 144 283061 0.82% 145 370710 1.07% 146 292787 0.85% 147 369981 1.07% 148 613898 1.78% 149 0 0.00% 150 16 0.00% 151 17354838 50.32% criterion=sequence-density sequence-density=0.69 sequence-density-rank=1 fanout-score=2.06 fanout-score-rank=31 prefix-density=0.69 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTA criterion=fanout-score sequence-density=0.09 sequence-density-rank=18 fanout-score=21.05 fanout-score-rank=1 prefix-density=1.79 prefix-fanout=1.1 sequence=CGGCGATGCGCCCCGGTCGGATGTGGAACGGTTACAGCCGGTCCGCCGATCGGCTCGGGGCGTGGACC Started job on | Feb 12 11:30:00 Started mapping on | Feb 12 11:30:01 Finished on | Feb 12 11:33:21 Mapping speed, Million of reads per hour | 703.53 Number of input reads | 39085201 Average input read length | 135 UNIQUE READS: Uniquely mapped reads number | 28839570 Uniquely mapped reads % | 73.79% Average mapped length | 132.26 Number of splices: Total | 12121029 Number of splices: Annotated (sjdb) | 11877163 Number of splices: GT/AG | 11915704 Number of splices: GC/AG | 158666 Number of splices: AT/AC | 7817 Number of splices: Non-canonical | 38842 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.02% Deletion average length | 2.08 Insertion rate per base | 0.01% Insertion average length | 1.84 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1062231 % of reads mapped to multiple loci | 2.72% Number of reads mapped to too many loci | 7135614 % of reads mapped to too many loci | 18.26% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.03% % of reads unmapped: other | 0.21% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9183400 9183400 9183400 N_multimapping 1062231 1062231 1062231 N_noFeature 1798306 2188068 28068381 N_ambiguous 491842 110587 765 UnstrandedReadsAssigned:26549422 PositiveStrandReadsAssigned:26540915 NegativeStrandReadsAssigned:770424 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=117 echo kmer=113 SRR11462741 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: SRR11462741-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 39,085,201 reads, 28,421,920 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,272 rounds 52401 SRR11462741.ke.tsv 34699 SRR11462741.se.tsv 87100 total ==> SRR11462741.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 1984 39.9835 Potri.005G024800.1.v4.1 1035 936 616 25.4518 Potri.004G059700.1.v4.1 961 862 22 0.987029 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 3251.24 44.2113 Potri.016G087400.1.v4.1 270 171 1667 377.011 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 325 7.50831 Potri.012G127500.1.v4.1 977 878 279 12.2892 ==> SRR11462741.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 188 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 227 Potri.001G212900.v4.1 16 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 15 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 61 SRR11462741 completed mapping pipeline successfully