Starting /dee2/code/volunteer_pipeline.sh SRR11462740 current disk space = 3051214610432 free memory = 1581765396 SRR11462740 SRAfilesize fd800017c856f35102451b4a7cd685cd SRR11462740.sra SRR11462740.sra file validated SRR11462740 is single end SRR11462740 is conventional basespace SRR11462740 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462740_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 21.1625 32.0 2.0 32.0 2.0 32.0 2 31.73 32.0 32.0 32.0 32.0 32.0 3 34.17125 37.0 32.0 37.0 32.0 37.0 4 36.0875 37.0 37.0 37.0 32.0 37.0 5 36.45125 37.0 37.0 37.0 37.0 37.0 6 39.92975 41.0 41.0 41.0 37.0 41.0 7 40.13025 41.0 41.0 41.0 37.0 41.0 8 40.06725 41.0 41.0 41.0 37.0 41.0 9 40.26775 41.0 41.0 41.0 37.0 41.0 10-14 40.1878 41.0 41.0 41.0 37.0 41.0 15-19 40.1573 41.0 41.0 41.0 37.0 41.0 20-24 40.149699999999996 41.0 41.0 41.0 37.0 41.0 25-29 40.0979 41.0 41.0 41.0 37.0 41.0 30-34 39.9698 41.0 41.0 41.0 37.0 41.0 35-39 39.88925 41.0 41.0 41.0 37.0 41.0 40-44 39.9807 41.0 41.0 41.0 37.0 41.0 45-49 39.957350000000005 41.0 41.0 41.0 37.0 41.0 50-54 39.8823 41.0 41.0 41.0 37.0 41.0 55-59 39.79755 41.0 41.0 41.0 37.0 41.0 60-64 39.84775 41.0 41.0 41.0 37.0 41.0 65-69 39.73805 41.0 41.0 41.0 37.0 41.0 70-74 39.60325 41.0 41.0 41.0 37.0 41.0 75-79 39.49115 41.0 40.2 41.0 37.0 41.0 80-84 39.943 41.0 41.0 41.0 37.0 41.0 85-89 39.80705 41.0 41.0 41.0 37.0 41.0 90-94 39.8558 41.0 41.0 41.0 37.0 41.0 95-99 39.75095 41.0 41.0 41.0 37.0 41.0 100-104 39.66345 41.0 41.0 41.0 37.0 41.0 105-109 39.6743 41.0 41.0 41.0 37.0 41.0 110-114 39.58565 41.0 41.0 41.0 37.0 41.0 115-119 39.59085 41.0 41.0 41.0 37.0 41.0 120-124 39.34685 41.0 41.0 41.0 37.0 41.0 125-129 39.2274 41.0 41.0 41.0 36.0 41.0 130-134 38.9185 41.0 41.0 41.0 33.0 41.0 135-139 38.682750000000006 41.0 41.0 41.0 32.0 41.0 140-144 38.6057 41.0 41.0 41.0 32.0 41.0 145-149 38.29735 41.0 41.0 41.0 32.0 41.0 150-151 37.372 41.0 37.0 41.0 27.0 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 1.0 22 0.0 23 1.0 24 7.0 25 2.0 26 7.0 27 8.0 28 21.0 29 15.0 30 25.0 31 38.0 32 47.0 33 81.0 34 90.0 35 84.0 36 98.0 37 121.0 38 156.0 39 360.0 40 2836.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 7.010069713400465 35.243996901626645 42.29279628195198 15.453137103020914 2 26.025 42.225 20.474999999999998 11.275 3 23.025000000000002 30.8 36.325 9.85 4 34.125 24.25 26.450000000000003 15.174999999999999 5 27.1 26.150000000000002 28.475 18.275 6 26.1 27.0 27.800000000000004 19.1 7 22.025 25.75 31.75 20.474999999999998 8 26.174999999999997 24.575 29.775000000000002 19.475 9 22.05 23.05 32.550000000000004 22.35 10-14 24.455 25.3 30.035 20.21 15-19 24.276213810690532 26.57632881644082 29.091454572728637 20.056002800140007 20-24 24.18 27.245 28.395 20.18 25-29 24.51 26.545 28.610000000000003 20.335 30-34 24.26621331066553 25.65128256412821 28.88144407220361 21.20106005300265 35-39 24.36 25.724999999999998 29.205 20.71 40-44 23.674999999999997 27.165 29.154999999999998 20.005 45-49 23.69618480924046 26.366318315915795 29.021451072553628 20.916045802290114 50-54 24.181209060453025 26.516325816290813 28.311415570778536 20.991049552477623 55-59 24.361218060903045 26.936346817340866 28.171408570428518 20.531026551327567 60-64 24.506225311265563 25.906295314765735 29.51147557377869 20.07600380019001 65-69 24.515 26.174999999999997 27.87 21.44 70-74 24.792479247924792 26.697669766976695 28.597859785978596 19.911991199119914 75-79 23.65 26.91 28.835 20.605 80-84 24.11 27.42 28.275 20.195 85-89 24.211210560528027 27.10635531776589 28.276413820691033 20.40602030101505 90-94 24.841242062103106 26.511325566278316 28.86644332216611 19.780989049452472 95-99 24.435000000000002 26.174999999999997 28.055000000000003 21.335 100-104 24.21 26.305 28.410000000000004 21.075 105-109 23.885 26.950000000000003 27.935 21.23 110-114 23.955000000000002 26.795 28.59 20.66 115-119 23.34 27.185 28.794999999999998 20.68 120-124 23.5 27.884999999999998 27.305 21.310000000000002 125-129 23.415 27.565 27.439999999999998 21.58 130-134 23.18 28.325 27.22 21.275 135-139 23.51 27.229999999999997 27.139999999999997 22.12 140-144 23.765 28.349999999999998 26.88 21.005 145-149 23.155 28.235 26.395000000000003 22.215 150-151 21.587500000000002 29.2875 26.1625 22.9625 >>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 0.5 19 0.5 20 0.0 21 0.5 22 1.0 23 0.5 24 0.0 25 2.0 26 6.5 27 10.5 28 14.0 29 15.0 30 16.5 31 22.0 32 28.5 33 38.0 34 58.5 35 78.5 36 94.0 37 111.0 38 136.0 39 163.0 40 188.5 41 204.0 42 232.0 43 255.5 44 264.5 45 277.5 46 266.0 47 254.0 48 220.5 49 193.0 50 163.5 51 117.0 52 96.5 53 86.5 54 71.0 55 67.5 56 55.0 57 36.0 58 43.5 59 33.5 60 20.5 61 13.5 62 5.5 63 9.5 64 9.0 65 3.0 66 3.5 67 3.0 68 1.0 69 2.0 70 1.0 71 2.5 72 3.0 73 0.5 74 0.0 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 35.449999999999996 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 0.005 20-24 0.0 25-29 0.0 30-34 0.005 35-39 0.0 40-44 0.0 45-49 0.005 50-54 0.005 55-59 0.005 60-64 0.005 65-69 0.0 70-74 0.01 75-79 0.0 80-84 0.0 85-89 0.005 90-94 0.005 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 88.1 #Duplication Level Percentage of deduplicated Percentage of total 1 93.04767309875142 81.975 2 4.937570942111237 8.7 3 1.0783200908059023 2.85 4 0.25539160045402953 0.8999999999999999 5 0.22701475595913734 1.0 6 0.028376844494892167 0.15 7 0.028376844494892167 0.17500000000000002 8 0.056753688989784334 0.4 9 0.0851305334846765 0.675 >10 0.25539160045402953 3.175 >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 TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 24 0.6 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 19 0.475 No Hit TAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACAC 14 0.35000000000000003 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 13 0.325 No Hit CAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTC 13 0.325 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 12 0.3 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 11 0.27499999999999997 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 11 0.27499999999999997 No Hit TGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 10 0.25 No Hit AACAAAAGGGTAAAAGCTCGTTTGATTCTGATTTCCAGTACGAATACGAA 9 0.22499999999999998 No Hit NTGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 9 0.22499999999999998 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 9 0.22499999999999998 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 8 0.2 No Hit NAGCCAAGCGTTCATAGCGACGTTGCTTTTTGATCCTTCGATGTCGGCTC 8 0.2 No Hit CTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 7 0.17500000000000002 No Hit TTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTA 6 0.15 No Hit CGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGA 5 0.125 No Hit TTTGATGATCTGGAGGGCTTGCAGGAGTATCTTGATTCTTCGGTTGTTGC 5 0.125 No Hit ACAACACTCGTCAAGTGCAGTGCATCAGTTTTATCGCCTCCAAGCCGAAG 5 0.125 No Hit TGTTTGTGTCGTCGGTGGTGTTCCGGCAGGGGGGGTGGATTTTATGATTG 5 0.125 No Hit AGGATTTCGATCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAAC 5 0.125 No Hit TATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCAT 5 0.125 No Hit NTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTA 5 0.125 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 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 0.0125 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.05 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.0625 0.0 0.0 0.0 0.0 26-27 0.075 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 0.125 0.0 0.0 0.0 0.0 36-37 0.15 0.0 0.0 0.0 0.0 38-39 0.16249999999999998 0.0 0.0 0.0 0.0 40-41 0.225 0.0 0.0 0.0 0.0 42-43 0.2875 0.0 0.0 0.0 0.0 44-45 0.32499999999999996 0.0 0.0 0.0 0.0 46-47 0.3625 0.0 0.0 0.0 0.0 48-49 0.4125 0.0 0.0 0.0 0.0 50-51 0.4875 0.0 0.0 0.0 0.0 52-53 0.5625 0.0 0.0 0.0 0.0 54-55 0.6375 0.0 0.0 0.0 0.0 56-57 0.7375 0.0 0.0 0.0 0.0 58-59 0.8 0.0 0.0 0.0 0.0 60-61 0.875 0.0 0.0 0.0 0.0 62-63 1.025 0.0 0.0 0.0 0.0 64-65 1.1749999999999998 0.0 0.0 0.0 0.0 66-67 1.35 0.0 0.0 0.0 0.0 68-69 1.525 0.0 0.0 0.0 0.0 70-71 1.725 0.0 0.0 0.0 0.0 72-73 1.9125 0.0 0.0 0.0 0.0 74-75 2.2 0.0 0.0 0.0 0.0 76-77 2.475 0.0 0.0 0.0 0.0 78-79 2.7125 0.0 0.0 0.0 0.0 80-81 3.25 0.0 0.0 0.0 0.0 82-83 3.5999999999999996 0.0 0.0 0.0 0.0 84-85 3.9875 0.0 0.0 0.0 0.0 86-87 4.35 0.0 0.0 0.0 0.0 88-89 4.6875 0.0 0.0 0.0 0.0 90-91 5.262499999999999 0.0 0.0 0.0 0.0 92-93 5.65 0.0 0.0 0.0 0.0 94-95 6.2375 0.0 0.0 0.0 0.0 96-97 6.65 0.0 0.0 0.0 0.0 98-99 7.175 0.0 0.0 0.0 0.0 100-101 7.5375 0.0 0.0 0.0 0.0 102-103 8.0125 0.0 0.0 0.0 0.0 104-105 8.55 0.0 0.0 0.0 0.0 106-107 8.9875 0.0 0.0 0.0 0.0 108-109 9.75 0.0 0.0 0.0 0.0 110-111 10.5 0.0 0.0 0.0 0.0 112-113 11.175 0.0 0.0 0.0 0.0 114-115 11.875 0.0 0.0 0.0 0.0 116-117 12.600000000000001 0.0 0.0 0.0 0.0 118-119 13.4375 0.0 0.0 0.0 0.0 120-121 14.4625 0.0 0.0 0.0 0.0 122-123 15.3125 0.0 0.0 0.0 0.0 124-125 16.5125 0.0 0.0 0.0 0.0 126-127 17.549999999999997 0.0 0.0 0.0 0.0 128-129 18.5375 0.0 0.0 0.0 0.0 130-131 19.4625 0.0 0.0 0.0 0.0 132-133 20.625 0.0 0.0 0.0 0.0 134-135 22.1 0.0 0.0 0.0 0.0 136-137 23.4625 0.0 0.0 0.0 0.0 138-139 24.7375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra Rejected 2015765 READS because READLEN < 1 Read 2015765 spots for SRR11462740.sra Written 2015765 spots for SRR11462740.sra Rejected 2015757 READS because READLEN < 1 Read 2015757 spots for SRR11462740.sra Written 2015757 spots for SRR11462740.sra SRR ids: ['SRR11462740.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9kstuy43 SRR11462740.sra spots: 40315148 blocks: [[1, 2015757], [2015758, 4031514], [4031515, 6047271], [6047272, 8063028], [8063029, 10078785], [10078786, 12094542], [12094543, 14110299], [14110300, 16126056], [16126057, 18141813], [18141814, 20157570], [20157571, 22173327], [22173328, 24189084], [24189085, 26204841], [26204842, 28220598], [28220599, 30236355], [30236356, 32252112], [32252113, 34267869], [34267870, 36283626], [36283627, 38299383], [38299384, 40315148]] SRR11462740 file size 13679150 SRR11462740 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 SRR11462740 SRR11462740_1.fastq Input file: SRR11462740_1.fastq trimmed: SRR11462740-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 12:25:38 2025 >> started Wed Feb 12 12:26:00 2025 >> done (21.938s) 40315148 reads processed; of these: 9967 ( 0.02%) short reads filtered out after trimming by size control 1002 ( 0.00%) empty reads filtered out after trimming by size control 40304179 (99.97%) reads available; of these: 5562735 (13.80%) trimmed reads available after processing 34741444 (86.20%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2288 0.01% 19 2458 0.01% 20 3123 0.01% 21 2925 0.01% 22 3692 0.01% 23 4029 0.01% 24 4177 0.01% 25 4189 0.01% 26 4421 0.01% 27 6201 0.02% 28 5102 0.01% 29 5852 0.01% 30 5557 0.01% 31 5930 0.01% 32 5891 0.01% 33 6032 0.01% 34 6338 0.02% 35 6964 0.02% 36 6896 0.02% 37 10137 0.03% 38 7570 0.02% 39 8718 0.02% 40 7983 0.02% 41 8310 0.02% 42 10310 0.03% 43 9690 0.02% 44 9890 0.02% 45 13837 0.03% 46 11316 0.03% 47 17223 0.04% 48 13890 0.03% 49 17043 0.04% 50 13658 0.03% 51 14815 0.04% 52 15372 0.04% 53 15922 0.04% 54 18716 0.05% 55 17540 0.04% 56 19610 0.05% 57 20757 0.05% 58 18946 0.05% 59 21104 0.05% 60 23624 0.06% 61 23406 0.06% 62 81137 0.20% 63 24057 0.06% 64 29059 0.07% 65 25924 0.06% 66 26154 0.06% 67 30773 0.08% 68 28981 0.07% 69 39040 0.10% 70 30961 0.08% 71 35519 0.09% 72 38090 0.09% 73 43600 0.11% 74 54516 0.14% 75 41259 0.10% 76 37235 0.09% 77 44286 0.11% 78 44850 0.11% 79 55002 0.14% 80 45226 0.11% 81 49209 0.12% 82 49547 0.12% 83 52939 0.13% 84 58877 0.15% 85 59334 0.15% 86 67506 0.17% 87 64735 0.16% 88 62952 0.16% 89 185492 0.46% 90 69218 0.17% 91 77049 0.19% 92 71332 0.18% 93 76186 0.19% 94 86444 0.21% 95 81394 0.20% 96 97208 0.24% 97 91925 0.23% 98 87511 0.22% 99 90303 0.22% 100 89609 0.22% 101 99685 0.25% 102 160851 0.40% 103 107944 0.27% 104 109620 0.27% 105 110074 0.27% 106 117696 0.29% 107 125670 0.31% 108 126132 0.31% 109 160495 0.40% 110 134737 0.33% 111 137737 0.34% 112 233048 0.58% 113 146789 0.36% 114 149270 0.37% 115 155212 0.39% 116 158319 0.39% 117 172271 0.43% 118 185237 0.46% 119 186043 0.46% 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 14 0.00% 151 34741444 86.20% 40304179 reads passed initial QC criterion=sequence-density sequence-density=10.52 sequence-density-rank=1 fanout-score=37.95 fanout-score-rank=1 prefix-density=12.73 prefix-fanout=31.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=10.52 sequence-density-rank=1 fanout-score=37.95 fanout-score-rank=1 prefix-density=12.73 prefix-fanout=31.4 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR11462740 - Input file: STDIN trimmed: SRR11462740-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATTCCTATCTCGTATGCCGTCTTCTGCTTG -- 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 12:27:25 2025 >> started Wed Feb 12 12:28:02 2025 >> done (37.317s) 32976147 reads processed; of these: 261 ( 0.00%) short reads filtered out after trimming by size control 11 ( 0.00%) empty reads filtered out after trimming by size control 32975875 (100.00%) reads available; of these: 6951945 (21.08%) trimmed reads available after processing 26023930 (78.92%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1920 0.01% 19 2040 0.01% 20 2573 0.01% 21 2444 0.01% 22 3100 0.01% 23 3348 0.01% 24 3422 0.01% 25 3428 0.01% 26 3709 0.01% 27 5104 0.02% 28 4281 0.01% 29 4977 0.02% 30 4546 0.01% 31 4929 0.01% 32 4852 0.01% 33 5029 0.02% 34 5206 0.02% 35 5729 0.02% 36 5788 0.02% 37 8376 0.03% 38 6214 0.02% 39 7214 0.02% 40 6562 0.02% 41 6843 0.02% 42 8422 0.03% 43 8021 0.02% 44 8176 0.02% 45 11507 0.03% 46 9312 0.03% 47 14134 0.04% 48 11439 0.03% 49 14195 0.04% 50 11438 0.03% 51 12265 0.04% 52 12641 0.04% 53 13188 0.04% 54 15411 0.05% 55 14458 0.04% 56 15995 0.05% 57 17236 0.05% 58 15598 0.05% 59 17386 0.05% 60 19503 0.06% 61 19463 0.06% 62 66739 0.20% 63 19876 0.06% 64 23798 0.07% 65 21500 0.07% 66 21615 0.07% 67 25487 0.08% 68 24085 0.07% 69 32078 0.10% 70 25951 0.08% 71 29074 0.09% 72 31581 0.10% 73 36045 0.11% 74 44842 0.14% 75 33643 0.10% 76 30845 0.09% 77 36713 0.11% 78 37113 0.11% 79 45213 0.14% 80 37447 0.11% 81 43053 0.13% 82 40566 0.12% 83 43633 0.13% 84 46501 0.14% 85 48742 0.15% 86 55527 0.17% 87 53519 0.16% 88 52416 0.16% 89 152936 0.46% 90 58389 0.18% 91 63547 0.19% 92 59239 0.18% 93 62541 0.19% 94 71166 0.22% 95 66749 0.20% 96 80215 0.24% 97 75168 0.23% 98 72263 0.22% 99 75111 0.23% 100 73692 0.22% 101 82204 0.25% 102 131768 0.40% 103 89776 0.27% 104 90650 0.27% 105 90876 0.28% 106 96749 0.29% 107 103161 0.31% 108 104157 0.32% 109 131878 0.40% 110 111020 0.34% 111 113655 0.34% 112 193322 0.59% 113 120568 0.37% 114 123154 0.37% 115 126869 0.38% 116 130891 0.40% 117 137698 0.42% 118 147983 0.45% 119 150463 0.46% 120 168556 0.51% 121 156226 0.47% 122 158899 0.48% 123 244088 0.74% 124 197408 0.60% 125 168159 0.51% 126 186745 0.57% 127 198398 0.60% 128 187033 0.57% 129 181189 0.55% 130 184812 0.56% 131 206149 0.63% 132 213848 0.65% 133 234272 0.71% 134 207074 0.63% 135 232867 0.71% 136 214590 0.65% 137 230966 0.70% 138 244285 0.74% 139 235843 0.72% 140 255340 0.77% 141 229440 0.70% 142 231686 0.70% 143 248040 0.75% 144 243406 0.74% 145 253343 0.77% 146 256985 0.78% 147 353704 1.07% 148 695388 2.11% 149 0 0.00% 150 5 0.00% 151 21580249 65.44% criterion=sequence-density sequence-density=0.78 sequence-density-rank=1 fanout-score=1.95 fanout-score-rank=35 prefix-density=0.78 prefix-fanout=1.9 sequence=CGTCGTGAGACAG criterion=fanout-score sequence-density=0.04 sequence-density-rank=29 fanout-score=130.60 fanout-score-rank=1 prefix-density=0.32 prefix-fanout=16.4 sequence=TTGATGCTGAGAATTCTCCAAGCGTGGTTGCCATCAACGTGAGCCCTATTGAATATGGGCATGTGCTGTTAATCCCACGTGTCCTGGATTGCTTGCCTCAGAGGATTGATCGTGATAGCTTCTTGCTTGCACTTCACATGGCAGCTGAAGCTGGGGATCCATACTTCCGACTGGGTTACAATAGCTTGGGTGCTTTTGCAACCATTAACCATCTTCACTTCCAGGCTTACTACTTGACTGTGCCTTTTCCGATTGAGAAGG Started job on | Feb 12 12:28:38 Started mapping on | Feb 12 12:28:38 Finished on | Feb 12 12:30:01 Mapping speed, Million of reads per hour | 1748.12 Number of input reads | 40303907 Average input read length | 140 UNIQUE READS: Uniquely mapped reads number | 34247572 Uniquely mapped reads % | 84.97% Average mapped length | 138.59 Number of splices: Total | 14674999 Number of splices: Annotated (sjdb) | 14370491 Number of splices: GT/AG | 14403334 Number of splices: GC/AG | 211688 Number of splices: AT/AC | 9113 Number of splices: Non-canonical | 50864 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.02% Deletion average length | 2.22 Insertion rate per base | 0.01% Insertion average length | 1.83 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1126719 % of reads mapped to multiple loci | 2.80% Number of reads mapped to too many loci | 3117722 % of reads mapped to too many loci | 7.74% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.37% % of reads unmapped: other | 0.13% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4929616 4929616 4929616 N_multimapping 1126719 1126719 1126719 N_noFeature 1915334 2546875 33169471 N_ambiguous 577221 130536 802 UnstrandedReadsAssigned:31755017 PositiveStrandReadsAssigned:31570161 NegativeStrandReadsAssigned:1077299 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=130 echo kmer=125 SRR11462740 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: SRR11462740-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 40,303,907 reads, 33,096,185 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,272 rounds 52401 SRR11462740.ke.tsv 34699 SRR11462740.se.tsv 87100 total ==> SRR11462740.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 1586 27.3683 Potri.005G024800.1.v4.1 1035 936 541 19.14 Potri.004G059700.1.v4.1 961 862 38 1.45981 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 3515.68 40.9354 Potri.016G087400.1.v4.1 270 171 2407 466.122 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 364 7.20055 Potri.012G127500.1.v4.1 977 878 137 5.16709 ==> SRR11462740.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 181 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 164 Potri.001G212900.v4.1 134 Potri.001G182400.v4.1 3 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 4 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 67 SRR11462740 completed mapping pipeline successfully