Starting /dee2/code/volunteer_pipeline.sh SRR11462737 current disk space = 3051301056512 free memory = 1581977812 SRR11462737 SRAfilesize 420912b20380c665844bcfb8e3fcd0fd SRR11462737.sra SRR11462737.sra file validated SRR11462737 is single end SRR11462737 is conventional basespace SRR11462737 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462737_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 20.45375 32.0 2.0 32.0 2.0 32.0 2 31.80625 32.0 32.0 32.0 32.0 32.0 3 34.29625 37.0 32.0 37.0 32.0 37.0 4 36.17125 37.0 37.0 37.0 32.0 37.0 5 36.5675 37.0 37.0 37.0 37.0 37.0 6 40.04325 41.0 41.0 41.0 37.0 41.0 7 40.20525 41.0 41.0 41.0 37.0 41.0 8 40.1345 41.0 41.0 41.0 37.0 41.0 9 40.30075 41.0 41.0 41.0 41.0 41.0 10-14 40.30655 41.0 41.0 41.0 38.6 41.0 15-19 40.27485 41.0 41.0 41.0 39.4 41.0 20-24 40.246300000000005 41.0 41.0 41.0 38.6 41.0 25-29 40.1983 41.0 41.0 41.0 37.0 41.0 30-34 40.0563 41.0 41.0 41.0 37.0 41.0 35-39 40.030950000000004 41.0 41.0 41.0 37.0 41.0 40-44 40.08045 41.0 41.0 41.0 37.0 41.0 45-49 40.11555 41.0 41.0 41.0 37.8 41.0 50-54 40.055049999999994 41.0 41.0 41.0 37.0 41.0 55-59 39.96169999999999 41.0 41.0 41.0 37.0 41.0 60-64 39.98615 41.0 41.0 41.0 37.0 41.0 65-69 39.8763 41.0 41.0 41.0 37.0 41.0 70-74 39.78895 41.0 41.0 41.0 37.0 41.0 75-79 39.7378 41.0 41.0 41.0 37.0 41.0 80-84 40.05225 41.0 41.0 41.0 37.0 41.0 85-89 39.979699999999994 41.0 41.0 41.0 37.0 41.0 90-94 39.9654 41.0 41.0 41.0 37.0 41.0 95-99 39.904650000000004 41.0 41.0 41.0 37.0 41.0 100-104 39.8508 41.0 41.0 41.0 37.0 41.0 105-109 39.7324 41.0 41.0 41.0 37.0 41.0 110-114 39.680699999999995 41.0 41.0 41.0 37.0 41.0 115-119 39.71365 41.0 41.0 41.0 37.0 41.0 120-124 39.4402 41.0 41.0 41.0 37.0 41.0 125-129 39.16955 41.0 41.0 41.0 35.0 41.0 130-134 38.78425 41.0 41.0 41.0 32.0 41.0 135-139 38.4527 41.0 41.0 41.0 32.0 41.0 140-144 38.16029999999999 41.0 41.0 41.0 31.0 41.0 145-149 37.7962 41.0 39.4 41.0 28.0 41.0 150-151 36.744125 41.0 37.0 41.0 22.0 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 3.0 24 0.0 25 1.0 26 6.0 27 5.0 28 11.0 29 18.0 30 22.0 31 30.0 32 52.0 33 51.0 34 94.0 35 100.0 36 120.0 37 162.0 38 184.0 39 326.0 40 2815.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 5.92741935483871 36.45161290322581 42.45967741935484 15.161290322580644 2 26.1 41.225 21.325 11.35 3 23.775 28.799999999999997 37.525 9.9 4 33.85 24.125 26.224999999999998 15.8 5 28.050000000000004 26.474999999999998 26.525 18.95 6 25.2 26.1 30.45 18.25 7 22.2 26.575 30.45 20.775 8 24.625 25.25 29.75 20.375 9 20.95 22.35 34.025 22.675 10-14 24.95 25.055 30.225 19.77 15-19 23.995 26.919999999999998 29.645 19.439999999999998 20-24 24.23 26.884999999999998 29.065 19.82 25-29 25.115 25.480000000000004 29.665000000000003 19.74 30-34 23.98 26.400000000000002 28.71 20.91 35-39 25.06 25.66 28.59 20.69 40-44 24.4 26.784999999999997 29.065 19.75 45-49 24.115000000000002 26.735 29.615000000000002 19.535 50-54 23.865 27.169999999999998 29.01 19.955000000000002 55-59 24.525 28.13 28.16 19.185 60-64 24.5 26.735 29.39 19.375 65-69 24.34 27.284999999999997 28.24 20.135 70-74 24.73623681184059 26.77133856692835 28.741437071853593 19.75098754937747 75-79 23.655 27.439999999999998 28.610000000000003 20.294999999999998 80-84 24.474999999999998 26.805 28.134999999999998 20.585 85-89 24.235 27.865000000000002 27.865000000000002 20.035 90-94 24.115000000000002 27.834999999999997 27.355 20.695 95-99 23.565 27.315 27.785 21.335 100-104 24.495 27.685 26.82 21.0 105-109 23.09 28.349999999999998 26.295 22.264999999999997 110-114 23.669999999999998 28.49 25.55 22.29 115-119 23.494999999999997 28.244999999999997 25.66 22.6 120-124 23.165 28.535 25.540000000000003 22.759999999999998 125-129 21.77 29.060000000000002 24.94 24.23 130-134 22.34 29.244999999999997 24.995 23.419999999999998 135-139 21.46 29.270000000000003 24.85 24.42 140-144 22.09 29.720000000000002 24.095 24.095 145-149 21.265 30.225 24.015 24.495 150-151 20.474999999999998 31.1 24.4875 23.9375 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 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 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 1.0 21 2.0 22 1.5 23 1.0 24 1.5 25 5.0 26 8.0 27 8.5 28 11.5 29 17.0 30 19.5 31 30.0 32 40.5 33 52.0 34 76.5 35 92.0 36 108.0 37 123.5 38 143.0 39 169.5 40 188.0 41 204.0 42 244.5 43 258.5 44 248.0 45 266.5 46 257.0 47 211.0 48 185.0 49 166.0 50 129.5 51 99.5 52 119.5 53 124.0 54 89.5 55 90.0 56 62.5 57 28.0 58 24.0 59 20.0 60 15.5 61 11.0 62 9.5 63 10.0 64 7.0 65 1.5 66 0.0 67 1.5 68 3.0 69 2.5 70 3.5 71 4.5 72 2.5 73 1.0 74 0.5 75 0.0 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 38.0 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 0.005 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 89.375 #Duplication Level Percentage of deduplicated Percentage of total 1 94.34965034965035 84.325 2 4.083916083916083 7.3 3 0.7552447552447552 2.025 4 0.3076923076923077 1.0999999999999999 5 0.027972027972027972 0.125 6 0.1958041958041958 1.05 7 0.027972027972027972 0.17500000000000002 8 0.08391608391608392 0.6 9 0.0 0.0 >10 0.16783216783216784 3.3000000000000003 >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 ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 37 0.9249999999999999 No Hit NTGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 30 0.75 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 27 0.675 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 14 0.35000000000000003 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 13 0.325 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 11 0.27499999999999997 No Hit TGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 8 0.2 No Hit NGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 8 0.2 No Hit TATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCAT 8 0.2 No Hit CATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCAT 7 0.17500000000000002 No Hit NACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 6 0.15 No Hit ATTGGGTTTTTGGAGATGAATATCATTCTACTTTGTTTTTGTTTTTAGCT 6 0.15 No Hit NAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTC 6 0.15 No Hit AACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGC 6 0.15 No Hit CGGGCCGCCTTGAAGTACAATTCCCACCGAGCGGCGGGTAGAATCCTTTG 6 0.15 No Hit TTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGA 6 0.15 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 6 0.15 No Hit AATGTACGTCAAGAACTACTCCTACTAAGCTGTTGTGATTGAAATCTATA 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 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.037500000000000006 0.0 0.0 0.0 0.0 26-27 0.0625 0.0 0.0 0.0 0.0 28-29 0.1 0.0 0.0 0.0 0.0 30-31 0.1 0.0 0.0 0.0 0.0 32-33 0.125 0.0 0.0 0.0 0.0 34-35 0.1875 0.0 0.0 0.0 0.0 36-37 0.2 0.0 0.0 0.0 0.0 38-39 0.225 0.0 0.0 0.0 0.0 40-41 0.275 0.0 0.0 0.0 0.0 42-43 0.35 0.0 0.0 0.0 0.0 44-45 0.38749999999999996 0.0 0.0 0.0 0.0 46-47 0.5 0.0 0.0 0.0 0.0 48-49 0.7250000000000001 0.0 0.0 0.0 0.0 50-51 0.875 0.0 0.0 0.0 0.0 52-53 1.05 0.0 0.0 0.0 0.0 54-55 1.275 0.0 0.0 0.0 0.0 56-57 1.55 0.0 0.0 0.0 0.0 58-59 1.75 0.0 0.0 0.0 0.0 60-61 2.0125 0.0 0.0 0.0 0.0 62-63 2.3875 0.0 0.0 0.0 0.0 64-65 2.875 0.0 0.0 0.0 0.0 66-67 3.2 0.0 0.0 0.0 0.0 68-69 3.5625 0.0 0.0 0.0 0.0 70-71 4.0625 0.0 0.0 0.0 0.0 72-73 4.5625 0.0 0.0 0.0 0.0 74-75 5.175 0.0 0.0 0.0 0.0 76-77 5.975 0.0 0.0 0.0 0.0 78-79 6.7125 0.0 0.0 0.0 0.0 80-81 7.475 0.0 0.0 0.0 0.0 82-83 8.3 0.0 0.0 0.0 0.0 84-85 9.3125 0.0 0.0 0.0 0.0 86-87 10.274999999999999 0.0 0.0 0.0 0.0 88-89 11.3125 0.0 0.0 0.0 0.0 90-91 12.9 0.0 0.0 0.0 0.0 92-93 14.2 0.0 0.0 0.0 0.0 94-95 15.5125 0.0 0.0 0.0 0.0 96-97 16.975 0.0 0.0 0.0 0.0 98-99 18.5125 0.0 0.0 0.0 0.0 100-101 20.0625 0.0 0.0 0.0 0.0 102-103 21.675 0.0 0.0 0.0 0.0 104-105 23.075 0.0 0.0 0.0 0.0 106-107 24.6375 0.0 0.0 0.0 0.0 108-109 26.262500000000003 0.0 0.0 0.0 0.0 110-111 27.6375 0.0 0.0 0.0 0.0 112-113 30.025 0.0 0.0 0.0 0.0 114-115 32.3125 0.0 0.0 0.0 0.0 116-117 33.525 0.0 0.0 0.0 0.0 118-119 35.2375 0.0 0.0 0.0 0.0 120-121 36.9875 0.0 0.0 0.0 0.0 122-123 38.7625 0.0 0.0 0.0 0.0 124-125 40.4875 0.0 0.0 0.0 0.0 126-127 42.175 0.0 0.0 0.0 0.0 128-129 43.95 0.0 0.0 0.0 0.0 130-131 45.2375 0.0 0.0 0.0 0.0 132-133 47.0125 0.0 0.0 0.0 0.0 134-135 49.1875 0.0 0.0 0.0 0.0 136-137 50.75 0.0 0.0 0.0 0.0 138-139 52.55 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146284 READS because READLEN < 1 Read 2146284 spots for SRR11462737.sra Written 2146284 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra Rejected 2146273 READS because READLEN < 1 Read 2146273 spots for SRR11462737.sra Written 2146273 spots for SRR11462737.sra SRR ids: ['SRR11462737.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_lq9entnm SRR11462737.sra spots: 42925471 blocks: [[1, 2146273], [2146274, 4292546], [4292547, 6438819], [6438820, 8585092], [8585093, 10731365], [10731366, 12877638], [12877639, 15023911], [15023912, 17170184], [17170185, 19316457], [19316458, 21462730], [21462731, 23609003], [23609004, 25755276], [25755277, 27901549], [27901550, 30047822], [30047823, 32194095], [32194096, 34340368], [34340369, 36486641], [36486642, 38632914], [38632915, 40779187], [40779188, 42925471]] SRR11462737 file size 14566252 SRR11462737 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 SRR11462737 SRR11462737_1.fastq Input file: SRR11462737_1.fastq trimmed: SRR11462737-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 12:00:35 2025 >> started Wed Feb 12 12:00:58 2025 >> done (22.968s) 42925471 reads processed; of these: 13218 ( 0.03%) short reads filtered out after trimming by size control 1225 ( 0.00%) empty reads filtered out after trimming by size control 42911028 (99.97%) reads available; of these: 16379677 (38.17%) trimmed reads available after processing 26531351 (61.83%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3442 0.01% 19 3694 0.01% 20 4096 0.01% 21 4823 0.01% 22 5403 0.01% 23 6143 0.01% 24 6610 0.02% 25 6974 0.02% 26 7131 0.02% 27 9004 0.02% 28 8537 0.02% 29 9259 0.02% 30 9887 0.02% 31 10609 0.02% 32 10708 0.02% 33 10990 0.03% 34 12817 0.03% 35 12553 0.03% 36 13119 0.03% 37 16366 0.04% 38 14700 0.03% 39 16252 0.04% 40 17254 0.04% 41 17776 0.04% 42 21017 0.05% 43 21526 0.05% 44 21254 0.05% 45 24582 0.06% 46 25560 0.06% 47 35923 0.08% 48 30435 0.07% 49 38011 0.09% 50 31042 0.07% 51 35432 0.08% 52 35916 0.08% 53 39460 0.09% 54 45007 0.10% 55 45106 0.11% 56 48107 0.11% 57 55109 0.13% 58 54318 0.13% 59 58602 0.14% 60 65958 0.15% 61 66650 0.16% 62 145334 0.34% 63 75541 0.18% 64 83709 0.20% 65 80635 0.19% 66 86352 0.20% 67 94525 0.22% 68 95232 0.22% 69 124814 0.29% 70 112046 0.26% 71 126307 0.29% 72 139324 0.32% 73 178471 0.42% 74 159134 0.37% 75 148900 0.35% 76 143104 0.33% 77 184836 0.43% 78 163734 0.38% 79 208506 0.49% 80 176936 0.41% 81 184545 0.43% 82 196841 0.46% 83 209751 0.49% 84 232768 0.54% 85 223604 0.52% 86 237249 0.55% 87 258508 0.60% 88 240738 0.56% 89 359523 0.84% 90 262811 0.61% 91 284316 0.66% 92 264166 0.62% 93 269669 0.63% 94 286850 0.67% 95 288759 0.67% 96 369180 0.86% 97 340867 0.79% 98 305843 0.71% 99 316233 0.74% 100 308433 0.72% 101 330921 0.77% 102 386683 0.90% 103 338258 0.79% 104 341948 0.80% 105 338066 0.79% 106 344703 0.80% 107 349140 0.81% 108 369238 0.86% 109 398851 0.93% 110 362541 0.84% 111 367239 0.86% 112 839900 1.96% 113 374592 0.87% 114 361734 0.84% 115 355395 0.83% 116 364657 0.85% 117 384418 0.90% 118 378702 0.88% 119 387411 0.90% 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 24 0.00% 151 26531351 61.83% 42911028 reads passed initial QC criterion=sequence-density sequence-density=16.70 sequence-density-rank=1 fanout-score=37.65 fanout-score-rank=1 prefix-density=19.26 prefix-fanout=32.6 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACGATATCTCGTATGCCGTCTTCTGCTTGAAAAAA criterion=fanout-score sequence-density=16.70 sequence-density-rank=1 fanout-score=37.65 fanout-score-rank=1 prefix-density=19.26 prefix-fanout=32.6 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACGATATCTCGTATGCCGTCTTCTGCTTGAAAAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACGATATCTCGTATGCCGTCTTCTGCTTGAAAAAA -o SRR11462737 - Input file: STDIN trimmed: SRR11462737-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACGATATCTCGTATGCCGTCTTCTGCTTG -- 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 12:02:20 2025 >> started Wed Feb 12 12:03:01 2025 >> done (41.119s) 37862672 reads processed; of these: 531 ( 0.00%) short reads filtered out after trimming by size control 14 ( 0.00%) empty reads filtered out after trimming by size control 37862127 (100.00%) reads available; of these: 10403581 (27.48%) trimmed reads available after processing 27458546 (72.52%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3129 0.01% 19 3300 0.01% 20 3746 0.01% 21 4296 0.01% 22 4829 0.01% 23 5479 0.01% 24 5953 0.02% 25 6270 0.02% 26 6415 0.02% 27 8033 0.02% 28 7602 0.02% 29 8302 0.02% 30 8769 0.02% 31 9457 0.02% 32 9544 0.03% 33 9904 0.03% 34 11526 0.03% 35 11180 0.03% 36 11788 0.03% 37 14645 0.04% 38 13165 0.03% 39 14544 0.04% 40 15345 0.04% 41 15741 0.04% 42 18631 0.05% 43 19227 0.05% 44 18971 0.05% 45 21937 0.06% 46 22846 0.06% 47 32039 0.08% 48 27191 0.07% 49 33852 0.09% 50 27792 0.07% 51 31545 0.08% 52 32073 0.08% 53 35678 0.09% 54 39946 0.11% 55 40302 0.11% 56 42433 0.11% 57 49299 0.13% 58 48401 0.13% 59 52351 0.14% 60 58969 0.16% 61 59414 0.16% 62 129515 0.34% 63 67496 0.18% 64 74641 0.20% 65 72025 0.19% 66 76936 0.20% 67 84036 0.22% 68 85783 0.23% 69 111320 0.29% 70 101194 0.27% 71 111723 0.30% 72 124204 0.33% 73 158306 0.42% 74 141800 0.37% 75 131514 0.35% 76 127839 0.34% 77 164848 0.44% 78 145533 0.38% 79 185163 0.49% 80 156808 0.41% 81 169008 0.45% 82 175045 0.46% 83 186659 0.49% 84 202588 0.54% 85 198799 0.53% 86 210844 0.56% 87 230583 0.61% 88 214669 0.57% 89 319215 0.84% 90 234613 0.62% 91 253058 0.67% 92 234905 0.62% 93 238520 0.63% 94 254762 0.67% 95 256906 0.68% 96 328198 0.87% 97 302959 0.80% 98 271148 0.72% 99 282222 0.75% 100 273625 0.72% 101 294832 0.78% 102 343311 0.91% 103 300816 0.79% 104 303150 0.80% 105 299197 0.79% 106 305616 0.81% 107 309026 0.82% 108 328879 0.87% 109 353892 0.93% 110 321887 0.85% 111 325397 0.86% 112 747990 1.98% 113 331310 0.88% 114 320216 0.85% 115 312169 0.82% 116 322278 0.85% 117 328908 0.87% 118 324929 0.86% 119 338046 0.89% 120 365183 0.96% 121 348482 0.92% 122 336702 0.89% 123 391534 1.03% 124 385973 1.02% 125 328591 0.87% 126 340553 0.90% 127 345401 0.91% 128 335341 0.89% 129 345317 0.91% 130 315419 0.83% 131 327413 0.86% 132 412067 1.09% 133 389289 1.03% 134 314454 0.83% 135 332029 0.88% 136 305253 0.81% 137 321125 0.85% 138 362237 0.96% 139 316285 0.84% 140 312459 0.83% 141 283526 0.75% 142 314862 0.83% 143 318772 0.84% 144 271231 0.72% 145 325125 0.86% 146 275693 0.73% 147 345277 0.91% 148 532468 1.41% 149 0 0.00% 150 5 0.00% 151 13437343 35.49% criterion=sequence-density sequence-density=0.88 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=38 prefix-density=0.88 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTACTCTGCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=37 fanout-score=43.03 fanout-score-rank=1 prefix-density=0.29 prefix-fanout=1.8 sequence=ATTTGAAGCCATGAAAGCTGTAGAAACCACTGTCAATCTGGGTCCAATTGCAACTGCTTAATCTTCTTCGAGGAGGATTTGGAGTCGTCTTATTTTTATTTTTTAAGAGTCGTCCAAGGTCTTTCTAGTAGATTCTGTTGCTTCCATAAAGATATCAGTTTCGTGTAGTACCGAGTGTCAATTTGTTCCATGTAGAAAATTACCTTGATTACTATATTATAAATAAACATTATTTCACAGAAATAATTTATA Started job on | Feb 12 12:03:36 Started mapping on | Feb 12 12:03:36 Finished on | Feb 12 12:04:58 Mapping speed, Million of reads per hour | 1883.87 Number of input reads | 42910483 Average input read length | 125 UNIQUE READS: Uniquely mapped reads number | 35061780 Uniquely mapped reads % | 81.71% Average mapped length | 122.72 Number of splices: Total | 13397205 Number of splices: Annotated (sjdb) | 13142437 Number of splices: GT/AG | 13190675 Number of splices: GC/AG | 160821 Number of splices: AT/AC | 7147 Number of splices: Non-canonical | 38562 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.02% Deletion average length | 2.01 Insertion rate per base | 0.01% Insertion average length | 1.77 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1206056 % of reads mapped to multiple loci | 2.81% Number of reads mapped to too many loci | 4491797 % of reads mapped to too many loci | 10.47% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.90% % of reads unmapped: other | 0.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6642647 6642647 6642647 N_multimapping 1206056 1206056 1206056 N_noFeature 2065336 2673304 34020530 N_ambiguous 560911 128101 874 UnstrandedReadsAssigned:32435533 PositiveStrandReadsAssigned:32260375 NegativeStrandReadsAssigned:1040376 Dataset is classified positive stranded MeadianReadLen=132 20thPercentileLength=99 echo kmer=95 SRR11462737 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: SRR11462737-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 42,910,483 reads, 33,809,369 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,276 rounds 52401 SRR11462737.ke.tsv 34699 SRR11462737.se.tsv 87100 total ==> SRR11462737.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 1717.54 26.6728 Potri.005G024800.1.v4.1 1035 936 784 24.9619 Potri.004G059700.1.v4.1 961 862 11 0.380296 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 4292.87 44.9837 Potri.016G087400.1.v4.1 270 171 1427 248.694 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 626 11.1444 Potri.012G127500.1.v4.1 977 878 121 4.10703 ==> SRR11462737.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 49 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 401 Potri.001G212900.v4.1 59 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 6 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 10 SRR11462737 completed mapping pipeline successfully