Starting /dee2/code/volunteer_pipeline.sh SRR11462715 current disk space = 3049649537024 free memory = 1581940948 SRR11462715 SRAfilesize e3b67954723105d161e66bbf13580320 SRR11462715.sra SRR11462715.sra file validated SRR11462715 is single end SRR11462715 is conventional basespace SRR11462715 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462715_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 24.42375 32.0 12.0 32.0 2.0 32.0 2 31.71375 32.0 32.0 32.0 32.0 32.0 3 34.68 37.0 32.0 37.0 32.0 37.0 4 36.16875 37.0 37.0 37.0 32.0 37.0 5 36.52625 37.0 37.0 37.0 37.0 37.0 6 40.04575 41.0 41.0 41.0 37.0 41.0 7 40.0855 41.0 41.0 41.0 37.0 41.0 8 40.00775 41.0 41.0 41.0 37.0 41.0 9 40.23825 41.0 41.0 41.0 37.0 41.0 10-14 40.298249999999996 41.0 41.0 41.0 38.6 41.0 15-19 40.249500000000005 41.0 41.0 41.0 38.6 41.0 20-24 40.21485 41.0 41.0 41.0 37.8 41.0 25-29 40.0963 41.0 41.0 41.0 37.8 41.0 30-34 39.98610000000001 41.0 41.0 41.0 37.0 41.0 35-39 39.9967 41.0 41.0 41.0 37.0 41.0 40-44 40.0595 41.0 41.0 41.0 37.0 41.0 45-49 39.981899999999996 41.0 41.0 41.0 37.0 41.0 50-54 39.9846 41.0 41.0 41.0 37.0 41.0 55-59 39.93755 41.0 41.0 41.0 37.0 41.0 60-64 40.025549999999996 41.0 41.0 41.0 37.0 41.0 65-69 39.9381 41.0 41.0 41.0 37.0 41.0 70-74 39.767599999999995 41.0 41.0 41.0 37.0 41.0 75-79 39.61385 41.0 40.2 41.0 37.0 41.0 80-84 40.108549999999994 41.0 41.0 41.0 37.8 41.0 85-89 40.15445 41.0 41.0 41.0 39.4 41.0 90-94 39.98465 41.0 41.0 41.0 37.0 41.0 95-99 39.888850000000005 41.0 41.0 41.0 37.0 41.0 100-104 39.80485 41.0 41.0 41.0 37.0 41.0 105-109 39.6793 41.0 41.0 41.0 37.0 41.0 110-114 39.654250000000005 41.0 41.0 41.0 37.0 41.0 115-119 39.62975 41.0 41.0 41.0 37.0 41.0 120-124 39.4432 41.0 41.0 41.0 37.0 41.0 125-129 39.421949999999995 41.0 41.0 41.0 37.0 41.0 130-134 39.17665 41.0 41.0 41.0 37.0 41.0 135-139 38.8278 41.0 41.0 41.0 33.0 41.0 140-144 38.866049999999994 41.0 41.0 41.0 35.0 41.0 145-149 38.499700000000004 41.0 41.0 41.0 32.0 41.0 150-151 37.590625 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 1.0 24 1.0 25 3.0 26 5.0 27 12.0 28 7.0 29 15.0 30 33.0 31 37.0 32 47.0 33 58.0 34 67.0 35 77.0 36 106.0 37 126.0 38 160.0 39 314.0 40 2930.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 6.82571239231279 38.66799204771372 38.601722995361165 15.904572564612327 2 26.0 42.85 19.1 12.049999999999999 3 22.15 31.225 36.5 10.125 4 35.6 24.625 25.324999999999996 14.45 5 27.975 27.6 25.924999999999997 18.5 6 28.000000000000004 25.8 26.8 19.400000000000002 7 25.174999999999997 26.55 27.700000000000003 20.575 8 25.5 25.95 28.849999999999998 19.7 9 22.95 25.474999999999998 29.775000000000002 21.8 10-14 25.915 25.52 28.17 20.395 15-19 26.115 26.845000000000002 27.310000000000002 19.73 20-24 26.35 26.400000000000002 27.355 19.895 25-29 25.825 25.915 27.439999999999998 20.82 30-34 25.755 26.945000000000004 26.365 20.935000000000002 35-39 25.105 26.11 27.045 21.740000000000002 40-44 24.825 26.08 27.765 21.33 45-49 25.235000000000003 25.515 28.09 21.16 50-54 25.4 26.33 27.450000000000003 20.82 55-59 26.125 26.009999999999998 26.784999999999997 21.08 60-64 25.974999999999998 25.215 28.42 20.39 65-69 25.75 25.474999999999998 27.779999999999998 20.995 70-74 25.71 26.105 27.045 21.14 75-79 25.335 25.985000000000003 27.76 20.919999999999998 80-84 25.965 26.145000000000003 27.29 20.599999999999998 85-89 25.46 26.455000000000002 27.134999999999998 20.95 90-94 25.555 25.905 27.33 21.21 95-99 24.87 26.32 27.339999999999996 21.47 100-104 25.505 26.340000000000003 26.584999999999997 21.57 105-109 24.62 26.685 26.740000000000002 21.955 110-114 25.06 26.265 27.33 21.345 115-119 25.2 27.3 26.8 20.7 120-124 25.019999999999996 27.125 26.71 21.145 125-129 24.51 28.294999999999998 26.125 21.07 130-134 23.575 28.599999999999998 26.235000000000003 21.59 135-139 24.785 28.610000000000003 25.285000000000004 21.32 140-144 24.485 28.605000000000004 25.195 21.715 145-149 25.235000000000003 28.02 24.37 22.375 150-151 23.400000000000002 29.0875 23.75 23.7625 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 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 0.0 21 1.0 22 1.5 23 0.5 24 0.5 25 1.5 26 1.5 27 1.5 28 2.0 29 4.0 30 10.0 31 16.5 32 23.0 33 31.0 34 41.5 35 67.5 36 77.5 37 94.5 38 126.0 39 144.5 40 158.5 41 176.0 42 202.5 43 231.5 44 247.0 45 252.0 46 242.0 47 227.0 48 227.5 49 196.5 50 154.5 51 121.0 52 114.5 53 130.5 54 116.0 55 96.0 56 87.5 57 77.5 58 64.5 59 40.5 60 27.0 61 21.0 62 23.5 63 35.5 64 26.5 65 9.5 66 4.5 67 5.0 68 6.5 69 6.5 70 8.5 71 9.0 72 3.5 73 0.5 74 0.5 75 0.5 76 0.5 77 1.0 78 0.5 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 24.55 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 87.425 #Duplication Level Percentage of deduplicated Percentage of total 1 92.13611667143266 80.55 2 5.862167572204747 10.25 3 0.9150700600514727 2.4 4 0.4003431512725193 1.4000000000000001 5 0.22876751501286818 1.0 6 0.08578781812982557 0.44999999999999996 7 0.057191878753217046 0.35000000000000003 8 0.057191878753217046 0.4 9 0.028595939376608523 0.22499999999999998 >10 0.22876751501286818 2.9749999999999996 >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 TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 21 0.525 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 19 0.475 No Hit TTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTA 17 0.42500000000000004 No Hit TAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGG 17 0.42500000000000004 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 14 0.35000000000000003 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 11 0.27499999999999997 No Hit CGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGA 10 0.25 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 10 0.25 No Hit AGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGAT 9 0.22499999999999998 No Hit CGGGCCGCCTTGAAGTACAATTCCCACCGAGCGGCGGGTAGAATCCTTTG 8 0.2 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 8 0.2 No Hit AGTGGCGGACGGGTGAGTAACGCGTAAGAACCTGCCCTTGGGAGGGGAAC 7 0.17500000000000002 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 7 0.17500000000000002 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 6 0.15 No Hit NAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 6 0.15 No Hit ACCTGGGGCTGTAGTATGTTCCAAGGGTTGGGCTGTTCGCCCATTAAAGC 6 0.15 No Hit ATGGTGGTGACGGGTGACGGAGAATTAGGGTTCGATTCCGGAGAGGGAGC 5 0.125 No Hit CTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 5 0.125 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 5 0.125 No Hit AATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGACTTT 5 0.125 No Hit NGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGAT 5 0.125 No Hit AAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCC 5 0.125 No Hit TAAGGATATTGTAGCTCTCTCTGGGGGCCACACCCTGGGAAGGTGCCACA 5 0.125 No Hit AGTTGGAGAAAGGTTGGGTCTACCGTGAGCACCACAGCTCACCAGGGTAC 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 0.025 0.0 0.0 0.0 0.0 20-21 0.1125 0.0 0.0 0.0 0.0 22-23 0.15 0.0 0.0 0.0 0.0 24-25 0.15 0.0 0.0 0.0 0.0 26-27 0.1875 0.0 0.0 0.0 0.0 28-29 0.2375 0.0 0.0 0.0 0.0 30-31 0.2625 0.0 0.0 0.0 0.0 32-33 0.275 0.0 0.0 0.0 0.0 34-35 0.32499999999999996 0.0 0.0 0.0 0.0 36-37 0.3625 0.0 0.0 0.0 0.0 38-39 0.425 0.0 0.0 0.0 0.0 40-41 0.475 0.0 0.0 0.0 0.0 42-43 0.5 0.0 0.0 0.0 0.0 44-45 0.575 0.0 0.0 0.0 0.0 46-47 0.6125 0.0 0.0 0.0 0.0 48-49 0.65 0.0 0.0 0.0 0.0 50-51 0.725 0.0 0.0 0.0 0.0 52-53 0.8374999999999999 0.0 0.0 0.0 0.0 54-55 0.9750000000000001 0.0 0.0 0.0 0.0 56-57 1.0875 0.0 0.0 0.0 0.0 58-59 1.375 0.0 0.0 0.0 0.0 60-61 1.4249999999999998 0.0 0.0 0.0 0.0 62-63 1.525 0.0 0.0 0.0 0.0 64-65 1.625 0.0 0.0 0.0 0.0 66-67 1.6625 0.0 0.0 0.0 0.0 68-69 1.725 0.0 0.0 0.0 0.0 70-71 1.8375 0.0 0.0 0.0 0.0 72-73 2.0625 0.0 0.0 0.0 0.0 74-75 2.25 0.0 0.0 0.0 0.0 76-77 2.4375 0.0 0.0 0.0 0.0 78-79 2.7625 0.0 0.0 0.0 0.0 80-81 2.9875 0.0 0.0 0.0 0.0 82-83 3.2249999999999996 0.0 0.0 0.0 0.0 84-85 3.4749999999999996 0.0 0.0 0.0 0.0 86-87 3.675 0.0 0.0 0.0 0.0 88-89 4.0875 0.0 0.0 0.0 0.0 90-91 4.425 0.0 0.0 0.0 0.0 92-93 4.7 0.0 0.0 0.0 0.0 94-95 5.1375 0.0 0.0 0.0 0.0 96-97 5.5625 0.0 0.0 0.0 0.0 98-99 6.1125 0.0 0.0 0.0 0.0 100-101 6.5375 0.0 0.0 0.0 0.0 102-103 7.0125 0.0 0.0 0.0 0.0 104-105 7.55 0.0 0.0 0.0 0.0 106-107 8.1 0.0 0.0 0.0 0.0 108-109 8.65 0.0 0.0 0.0 0.0 110-111 9.45 0.0 0.0 0.0 0.0 112-113 10.2875 0.0 0.0 0.0 0.0 114-115 11.075 0.0 0.0 0.0 0.0 116-117 11.8 0.0 0.0 0.0 0.0 118-119 12.8125 0.0 0.0 0.0 0.0 120-121 13.6875 0.0 0.0 0.0 0.0 122-123 14.5875 0.0 0.0 0.0 0.0 124-125 15.8125 0.0 0.0 0.0 0.0 126-127 16.700000000000003 0.0 0.0 0.0 0.0 128-129 18.0125 0.0 0.0 0.0 0.0 130-131 19.1875 0.0 0.0 0.0 0.0 132-133 20.25 0.0 0.0 0.0 0.0 134-135 21.8 0.0 0.0 0.0 0.0 136-137 23.5625 0.0 0.0 0.0 0.0 138-139 25.0375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAGGACT 10 0.0068661636 144.75 2 AGTTCTG 10 0.0068661636 144.75 8 GATCGGA 130 0.0071310783 11.134616 145 AGATCGG 125 0.0051637976 9.264 140-144 >>END_MODULE Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951416 READS because READLEN < 1 Read 1951416 spots for SRR11462715.sra Written 1951416 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra Rejected 1951404 READS because READLEN < 1 Read 1951404 spots for SRR11462715.sra Written 1951404 spots for SRR11462715.sra SRR ids: ['SRR11462715.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_smy5nkhr SRR11462715.sra spots: 39028092 blocks: [[1, 1951404], [1951405, 3902808], [3902809, 5854212], [5854213, 7805616], [7805617, 9757020], [9757021, 11708424], [11708425, 13659828], [13659829, 15611232], [15611233, 17562636], [17562637, 19514040], [19514041, 21465444], [21465445, 23416848], [23416849, 25368252], [25368253, 27319656], [27319657, 29271060], [29271061, 31222464], [31222465, 33173868], [33173869, 35125272], [35125273, 37076676], [37076677, 39028092]] SRR11462715 file size 13241752 SRR11462715 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 SRR11462715 SRR11462715_1.fastq Input file: SRR11462715_1.fastq trimmed: SRR11462715-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 08:44:26 2025 >> started Wed Feb 12 08:44:48 2025 >> done (21.631s) 39028092 reads processed; of these: 14235 ( 0.04%) short reads filtered out after trimming by size control 2908 ( 0.01%) empty reads filtered out after trimming by size control 39010949 (99.96%) reads available; of these: 5260977 (13.49%) trimmed reads available after processing 33749972 (86.51%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3269 0.01% 19 3638 0.01% 20 4597 0.01% 21 4435 0.01% 22 5233 0.01% 23 5201 0.01% 24 6052 0.02% 25 5676 0.01% 26 5618 0.01% 27 7861 0.02% 28 6705 0.02% 29 6779 0.02% 30 7047 0.02% 31 7398 0.02% 32 7171 0.02% 33 7411 0.02% 34 8009 0.02% 35 8043 0.02% 36 8292 0.02% 37 11991 0.03% 38 8760 0.02% 39 8955 0.02% 40 9083 0.02% 41 9161 0.02% 42 10756 0.03% 43 10273 0.03% 44 10203 0.03% 45 10893 0.03% 46 11878 0.03% 47 14078 0.04% 48 13281 0.03% 49 14665 0.04% 50 12982 0.03% 51 14098 0.04% 52 14903 0.04% 53 15518 0.04% 54 17185 0.04% 55 16146 0.04% 56 17084 0.04% 57 19749 0.05% 58 18505 0.05% 59 20083 0.05% 60 21064 0.05% 61 21598 0.06% 62 56889 0.15% 63 22094 0.06% 64 23966 0.06% 65 22739 0.06% 66 24468 0.06% 67 27857 0.07% 68 24267 0.06% 69 30009 0.08% 70 27336 0.07% 71 31868 0.08% 72 34370 0.09% 73 34820 0.09% 74 37540 0.10% 75 37400 0.10% 76 33074 0.08% 77 38910 0.10% 78 38065 0.10% 79 48443 0.12% 80 40461 0.10% 81 41543 0.11% 82 54838 0.14% 83 61930 0.16% 84 53505 0.14% 85 55227 0.14% 86 57426 0.15% 87 74370 0.19% 88 72083 0.18% 89 85127 0.22% 90 66379 0.17% 91 68721 0.18% 92 63468 0.16% 93 67406 0.17% 94 77771 0.20% 95 78537 0.20% 96 92840 0.24% 97 87383 0.22% 98 83532 0.21% 99 89011 0.23% 100 89603 0.23% 101 99241 0.25% 102 118068 0.30% 103 118750 0.30% 104 113834 0.29% 105 109794 0.28% 106 115898 0.30% 107 122981 0.32% 108 124474 0.32% 109 141168 0.36% 110 137210 0.35% 111 138257 0.35% 112 211090 0.54% 113 151777 0.39% 114 152328 0.39% 115 153689 0.39% 116 161588 0.41% 117 179061 0.46% 118 191385 0.49% 119 193781 0.50% 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 0 0.00% 151 33749972 86.51% 39010949 reads passed initial QC criterion=sequence-density sequence-density=11.26 sequence-density-rank=1 fanout-score=42.09 fanout-score-rank=1 prefix-density=13.59 prefix-fanout=34.9 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=11.26 sequence-density-rank=1 fanout-score=42.09 fanout-score-rank=1 prefix-density=13.59 prefix-fanout=34.9 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR11462715 - Input file: STDIN trimmed: SRR11462715-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACATCACGATCTCGTATGCCGTCTTCTGCTTG -- 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 08:46:11 2025 >> started Wed Feb 12 08:46:48 2025 >> done (36.795s) 32509124 reads processed; of these: 410 ( 0.00%) short reads filtered out after trimming by size control 13 ( 0.00%) empty reads filtered out after trimming by size control 32508701 (100.00%) reads available; of these: 7259022 (22.33%) trimmed reads available after processing 25249679 (77.67%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2784 0.01% 19 3081 0.01% 20 3992 0.01% 21 3756 0.01% 22 4439 0.01% 23 4390 0.01% 24 5037 0.02% 25 4820 0.01% 26 4770 0.01% 27 6648 0.02% 28 5656 0.02% 29 5699 0.02% 30 5917 0.02% 31 6252 0.02% 32 5971 0.02% 33 6170 0.02% 34 6736 0.02% 35 6730 0.02% 36 6968 0.02% 37 9987 0.03% 38 7288 0.02% 39 7523 0.02% 40 7580 0.02% 41 7707 0.02% 42 9022 0.03% 43 8626 0.03% 44 8632 0.03% 45 9117 0.03% 46 9959 0.03% 47 11805 0.04% 48 11163 0.03% 49 12367 0.04% 50 11000 0.03% 51 11774 0.04% 52 12450 0.04% 53 13137 0.04% 54 14430 0.04% 55 13672 0.04% 56 14160 0.04% 57 16657 0.05% 58 15444 0.05% 59 16821 0.05% 60 17754 0.05% 61 18308 0.06% 62 47804 0.15% 63 18435 0.06% 64 20003 0.06% 65 19139 0.06% 66 20500 0.06% 67 23331 0.07% 68 20498 0.06% 69 25241 0.08% 70 23205 0.07% 71 26607 0.08% 72 28955 0.09% 73 29209 0.09% 74 31434 0.10% 75 31274 0.10% 76 27869 0.09% 77 32872 0.10% 78 32053 0.10% 79 40705 0.13% 80 34372 0.11% 81 37060 0.11% 82 46064 0.14% 83 51168 0.16% 84 42504 0.13% 85 46155 0.14% 86 48452 0.15% 87 62590 0.19% 88 60602 0.19% 89 71379 0.22% 90 58749 0.18% 91 57850 0.18% 92 53733 0.17% 93 56368 0.17% 94 65380 0.20% 95 64835 0.20% 96 78265 0.24% 97 71608 0.22% 98 70097 0.22% 99 74849 0.23% 100 74954 0.23% 101 84195 0.26% 102 98804 0.30% 103 100167 0.31% 104 94682 0.29% 105 92085 0.28% 106 96603 0.30% 107 103196 0.32% 108 106467 0.33% 109 120250 0.37% 110 115251 0.35% 111 115643 0.36% 112 177341 0.55% 113 124736 0.38% 114 127448 0.39% 115 128198 0.39% 116 134860 0.41% 117 144327 0.44% 118 155102 0.48% 119 159650 0.49% 120 177239 0.55% 121 180908 0.56% 122 170947 0.53% 123 230876 0.71% 124 213066 0.66% 125 173916 0.53% 126 193707 0.60% 127 208184 0.64% 128 191888 0.59% 129 187402 0.58% 130 185886 0.57% 131 204789 0.63% 132 223499 0.69% 133 231799 0.71% 134 212106 0.65% 135 251403 0.77% 136 215947 0.66% 137 243726 0.75% 138 256323 0.79% 139 241400 0.74% 140 257558 0.79% 141 232406 0.71% 142 251074 0.77% 143 243044 0.75% 144 245150 0.75% 145 387909 1.19% 146 255724 0.79% 147 352237 1.08% 148 684259 2.10% 149 0 0.00% 150 0 0.00% 151 21002957 64.61% criterion=sequence-density sequence-density=0.58 sequence-density-rank=1 fanout-score=4.54 fanout-score-rank=9 prefix-density=0.96 prefix-fanout=2.7 sequence=GTGCCAGCAGCCGCGGTAATTCCAGCTCCAATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGGTGTGCACCGGTCGCCTCGTCCCTTCTACCGGCGATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATAGGATTTCGATCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATTGGCGGATGTTGCTTTTAGGACTCCGCC criterion=fanout-score sequence-density=0.01 sequence-density-rank=35 fanout-score=41.75 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=5.1 sequence=GAGAAAATCATAAACGACTTCACTCATCTGGTCAATCAAGTTGAACCCTTGAAGAGCTTACACTGGGGCACTAATCTGGGTATTCACGACCTCAATTTCGGATATACTCATGCTTTTGAAACTACCTTTGATGATCTGGAGGGCTTGCAGGAGTATCTTGATTCTTCGGTTGTTGCTAAATTCGCAGAAGGATTCTTGCCAACCATGTCGCA Started job on | Feb 12 08:47:22 Started mapping on | Feb 12 08:47:22 Finished on | Feb 12 08:48:42 Mapping speed, Million of reads per hour | 1755.47 Number of input reads | 39010526 Average input read length | 140 UNIQUE READS: Uniquely mapped reads number | 30661884 Uniquely mapped reads % | 78.60% Average mapped length | 138.66 Number of splices: Total | 14143954 Number of splices: Annotated (sjdb) | 13887718 Number of splices: GT/AG | 13853463 Number of splices: GC/AG | 225211 Number of splices: AT/AC | 8045 Number of splices: Non-canonical | 57235 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.02% Deletion average length | 2.10 Insertion rate per base | 0.01% Insertion average length | 1.90 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1130902 % of reads mapped to multiple loci | 2.90% Number of reads mapped to too many loci | 5856676 % of reads mapped to too many loci | 15.01% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.35% % of reads unmapped: other | 0.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7217740 7217740 7217740 N_multimapping 1130902 1130902 1130902 N_noFeature 1795157 2291741 29724148 N_ambiguous 569076 128037 625 UnstrandedReadsAssigned:28297651 PositiveStrandReadsAssigned:28242106 NegativeStrandReadsAssigned:937111 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=130 echo kmer=125 SRR11462715 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: SRR11462715-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 39,010,526 reads, 30,824,973 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,290 rounds 52401 SRR11462715.ke.tsv 34699 SRR11462715.se.tsv 87100 total ==> SRR11462715.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 973 17.7574 Potri.005G024800.1.v4.1 1035 936 278 10.4019 Potri.004G059700.1.v4.1 961 862 85 3.45345 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 2151.64 26.4961 Potri.016G087400.1.v4.1 270 171 1977 404.904 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 67 1.40172 Potri.012G127500.1.v4.1 977 878 80 3.19108 ==> SRR11462715.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 400 Potri.001G233950.v4.1 3 Potri.001G122700.v4.1 181 Potri.001G212900.v4.1 9 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 12 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 54 SRR11462715 completed mapping pipeline successfully