Starting /dee2/code/volunteer_pipeline.sh SRR11462731 current disk space = 3049895677952 free memory = 1425974700 SRR11462731 SRAfilesize 2477c6fd3a7ea106a0ebb5f40898a7fa SRR11462731.sra SRR11462731.sra file validated SRR11462731 is single end SRR11462731 is conventional basespace SRR11462731 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462731_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 44 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 22.91375 32.0 2.0 32.0 2.0 32.0 2 31.785 32.0 32.0 32.0 32.0 32.0 3 34.64625 37.0 32.0 37.0 32.0 37.0 4 36.13625 37.0 37.0 37.0 32.0 37.0 5 36.49875 37.0 37.0 37.0 37.0 37.0 6 39.95325 41.0 41.0 41.0 37.0 41.0 7 40.13425 41.0 41.0 41.0 37.0 41.0 8 40.18175 41.0 41.0 41.0 37.0 41.0 9 40.254 41.0 41.0 41.0 37.0 41.0 10-14 40.28 41.0 41.0 41.0 37.8 41.0 15-19 40.2161 41.0 41.0 41.0 37.0 41.0 20-24 40.2238 41.0 41.0 41.0 37.0 41.0 25-29 40.20145 41.0 41.0 41.0 37.8 41.0 30-34 40.0543 41.0 41.0 41.0 37.0 41.0 35-39 39.95925 41.0 41.0 41.0 37.0 41.0 40-44 40.061949999999996 41.0 41.0 41.0 37.0 41.0 45-49 40.0656 41.0 41.0 41.0 37.8 41.0 50-54 40.0496 41.0 41.0 41.0 37.0 41.0 55-59 39.86875 41.0 41.0 41.0 37.0 41.0 60-64 39.899 41.0 41.0 41.0 37.0 41.0 65-69 39.8719 41.0 41.0 41.0 37.0 41.0 70-74 39.7413 41.0 41.0 41.0 37.0 41.0 75-79 39.7081 41.0 40.2 41.0 37.0 41.0 80-84 40.075649999999996 41.0 41.0 41.0 37.0 41.0 85-89 40.0135 41.0 41.0 41.0 37.0 41.0 90-94 39.9651 41.0 41.0 41.0 37.0 41.0 95-99 39.85295000000001 41.0 41.0 41.0 37.0 41.0 100-104 39.783100000000005 41.0 41.0 41.0 37.0 41.0 105-109 39.71575 41.0 41.0 41.0 37.0 41.0 110-114 39.643649999999994 41.0 41.0 41.0 37.0 41.0 115-119 39.6827 41.0 41.0 41.0 37.0 41.0 120-124 39.41435 41.0 41.0 41.0 37.0 41.0 125-129 39.1802 41.0 41.0 41.0 36.0 41.0 130-134 38.89275 41.0 41.0 41.0 33.0 41.0 135-139 38.637 41.0 41.0 41.0 32.0 41.0 140-144 38.519600000000004 41.0 41.0 41.0 32.0 41.0 145-149 38.21065 41.0 40.2 41.0 31.0 41.0 150-151 37.349000000000004 41.0 37.0 41.0 27.0 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 1.0 24 1.0 25 0.0 26 4.0 27 4.0 28 7.0 29 15.0 30 29.0 31 46.0 32 52.0 33 57.0 34 80.0 35 100.0 36 119.0 37 145.0 38 137.0 39 350.0 40 2852.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 4.912780348878605 36.91705233179067 42.61302954788181 15.557137771448915 2 24.375 42.3 22.2 11.125 3 22.2 29.4 38.35 10.05 4 34.150000000000006 23.75 25.624999999999996 16.475 5 27.05 28.175 27.175 17.599999999999998 6 25.1 25.1 29.25 20.549999999999997 7 21.75 26.6 30.875000000000004 20.775 8 24.15 24.7 31.574999999999996 19.575 9 21.725 24.15 31.874999999999996 22.25 10-14 24.47 25.505 30.005 20.02 15-19 23.37116855842792 27.26136306815341 29.856492824641233 19.51097554877744 20-24 24.52 26.63 28.799999999999997 20.05 25-29 25.09 25.825 29.404999999999998 19.68 30-34 24.016200810040502 25.156257812890644 29.53147657382869 21.29606480324016 35-39 24.27 25.83 29.035 20.865000000000002 40-44 23.799999999999997 26.32 29.5 20.380000000000003 45-49 22.796139806990347 27.301365068253414 29.566478323916197 20.336016800840042 50-54 24.18620931046552 26.86134306715336 29.286464323216162 19.665983299164957 55-59 24.33621681084054 26.856342817140856 29.016450822541128 19.790989549477477 60-64 24.746237311865592 27.01635081754088 29.27646382319116 18.960948047402372 65-69 24.085 26.715 28.735 20.465 70-74 24.457445744574457 27.197719771977198 28.222822282228222 20.122012201220123 75-79 23.51 27.16 29.455 19.875 80-84 24.315 26.85 28.625 20.21 85-89 23.68118405920296 27.801390069503473 28.41642082104105 20.101005050252514 90-94 24.72123606180309 27.141357067853395 27.78638931946597 20.351017550877543 95-99 24.375 27.215 28.299999999999997 20.11 100-104 24.54 27.29 27.834999999999997 20.335 105-109 23.375 27.815 27.084999999999997 21.725 110-114 23.285 27.79 28.249999999999996 20.674999999999997 115-119 24.610000000000003 27.525 27.315 20.549999999999997 120-124 24.92 28.075 26.615 20.39 125-129 23.66 28.470000000000002 25.915 21.955 130-134 24.305 28.735 26.040000000000003 20.919999999999998 135-139 24.385 28.449999999999996 25.05 22.115000000000002 140-144 24.54 28.96 24.07 22.43 145-149 24.84 28.63 23.94 22.59 150-151 24.3125 28.762500000000003 24.712500000000002 22.2125 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 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 1.0 20 0.5 21 0.0 22 0.0 23 1.5 24 3.5 25 4.0 26 5.0 27 7.5 28 11.0 29 16.5 30 24.0 31 31.5 32 36.0 33 50.5 34 84.5 35 119.5 36 137.0 37 147.0 38 161.0 39 174.5 40 179.5 41 197.0 42 218.5 43 233.0 44 261.5 45 248.0 46 217.5 47 210.0 48 202.0 49 170.5 50 115.0 51 93.5 52 131.0 53 134.0 54 88.0 55 72.5 56 52.5 57 31.0 58 21.0 59 10.5 60 12.0 61 12.5 62 18.0 63 19.0 64 8.5 65 4.5 66 3.0 67 1.5 68 2.0 69 4.0 70 5.0 71 3.5 72 0.5 73 0.5 74 0.5 75 0.0 76 0.5 77 0.5 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 29.775000000000002 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 88.35 #Duplication Level Percentage of deduplicated Percentage of total 1 94.199207696661 83.22500000000001 2 4.102999434069043 7.249999999999999 3 0.8488964346349746 2.25 4 0.311262026032824 1.0999999999999999 5 0.08488964346349745 0.375 6 0.1414827391058291 0.75 7 0.028296547821165818 0.17500000000000002 8 0.0 0.0 9 0.056593095642331635 0.44999999999999996 >10 0.19807583474816073 3.1 >50 0.028296547821165818 1.325 >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 53 1.325 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 24 0.6 No Hit NTGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 24 0.6 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 21 0.525 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 17 0.42500000000000004 No Hit TATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCAT 14 0.35000000000000003 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 13 0.325 No Hit TAAAAAGCTCGTAGTTGGACTTTGGGTTGGGTCGGCCGGTCCGCCTCAGG 11 0.27499999999999997 No Hit CTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 9 0.22499999999999998 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 9 0.22499999999999998 No Hit CGGGCCGCCTTGAAGTACAATTCCCACCGAGCGGCGGGTAGAATCCTTTG 7 0.17500000000000002 No Hit AGGGACTATGGCCTTCCAGGCCAAGGAAGTTTGAGGCAATAACAGGTCTG 6 0.15 No Hit NATTAGATAAAAGGTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCAT 6 0.15 No Hit GCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCC 6 0.15 No Hit TGCAACAAACCCCGACTTCTGGAAGGGACGCATTTATTAGATAAAAGGTC 6 0.15 No Hit AACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGC 6 0.15 No Hit GAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGC 5 0.125 No Hit AATAGCGTATATTTAAGTTGTTGCAGTTAAAAAGCTCGTAGTTGGACTTT 5 0.125 No Hit AAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAAT 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 0.037500000000000006 0.0 0.0 0.0 0.0 14-15 0.0625 0.0 0.0 0.0 0.0 16-17 0.075 0.0 0.0 0.0 0.0 18-19 0.1 0.0 0.0 0.0 0.0 20-21 0.125 0.0 0.0 0.0 0.0 22-23 0.15 0.0 0.0 0.0 0.0 24-25 0.16249999999999998 0.0 0.0 0.0 0.0 26-27 0.175 0.0 0.0 0.0 0.0 28-29 0.225 0.0 0.0 0.0 0.0 30-31 0.25 0.0 0.0 0.0 0.0 32-33 0.2875 0.0 0.0 0.0 0.0 34-35 0.325 0.0 0.0 0.0 0.0 36-37 0.4 0.0 0.0 0.0 0.0 38-39 0.425 0.0 0.0 0.0 0.0 40-41 0.44999999999999996 0.0 0.0 0.0 0.0 42-43 0.5125 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 0.7125 0.0 0.0 0.0 0.0 50-51 0.8875 0.0 0.0 0.0 0.0 52-53 0.9875 0.0 0.0 0.0 0.0 54-55 1.125 0.0 0.0 0.0 0.0 56-57 1.25 0.0 0.0 0.0 0.0 58-59 1.425 0.0 0.0 0.0 0.0 60-61 1.5625 0.0 0.0 0.0 0.0 62-63 1.7 0.0 0.0 0.0 0.0 64-65 1.875 0.0 0.0 0.0 0.0 66-67 2.125 0.0 0.0 0.0 0.0 68-69 2.25 0.0 0.0 0.0 0.0 70-71 2.4375 0.0 0.0 0.0 0.0 72-73 2.7375 0.0 0.0 0.0 0.0 74-75 3.0250000000000004 0.0 0.0 0.0 0.0 76-77 3.3875 0.0 0.0 0.0 0.0 78-79 3.7625 0.0 0.0 0.0 0.0 80-81 4.1875 0.0 0.0 0.0 0.0 82-83 4.6 0.0 0.0 0.0 0.0 84-85 5.0625 0.0 0.0 0.0 0.0 86-87 5.5375 0.0 0.0 0.0 0.0 88-89 6.175 0.0 0.0 0.0 0.0 90-91 7.300000000000001 0.0 0.0 0.0 0.0 92-93 8.25 0.0 0.0 0.0 0.0 94-95 8.9125 0.0 0.0 0.0 0.0 96-97 9.5625 0.0 0.0 0.0 0.0 98-99 10.375 0.0 0.0 0.0 0.0 100-101 11.1875 0.0 0.0 0.0 0.0 102-103 12.0 0.0 0.0 0.0 0.0 104-105 12.9875 0.0 0.0 0.0 0.0 106-107 14.1125 0.0 0.0 0.0 0.0 108-109 15.1875 0.0 0.0 0.0 0.0 110-111 16.8125 0.0 0.0 0.0 0.0 112-113 18.875 0.0 0.0 0.0 0.0 114-115 20.75 0.0 0.0 0.0 0.0 116-117 22.387500000000003 0.0 0.0 0.0 0.0 118-119 23.85 0.0 0.0 0.0 0.0 120-121 25.3125 0.0 0.0 0.0 0.0 122-123 26.8375 0.0 0.0 0.0 0.0 124-125 28.5375 0.0 0.0 0.0 0.0 126-127 30.4875 0.0 0.0 0.0 0.0 128-129 32.3125 0.0 0.0 0.0 0.0 130-131 34.175 0.0 0.0 0.0 0.0 132-133 35.95 0.0 0.0 0.0 0.0 134-135 38.35 0.0 0.0 0.0 0.0 136-137 40.325 0.0 0.0 0.0 0.0 138-139 41.9375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGTTTTC 10 0.006871484 144.71251 8 TGGCATC 15 0.008254925 135.40352 1 TGGTTTT 20 3.6161486E-4 108.53438 7 >>END_MODULE Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758201 READS because READLEN < 1 Read 1758201 spots for SRR11462731.sra Written 1758201 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra Rejected 1758186 READS because READLEN < 1 Read 1758186 spots for SRR11462731.sra Written 1758186 spots for SRR11462731.sra SRR ids: ['SRR11462731.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_rh7ynv87 SRR11462731.sra spots: 35163735 blocks: [[1, 1758186], [1758187, 3516372], [3516373, 5274558], [5274559, 7032744], [7032745, 8790930], [8790931, 10549116], [10549117, 12307302], [12307303, 14065488], [14065489, 15823674], [15823675, 17581860], [17581861, 19340046], [19340047, 21098232], [21098233, 22856418], [22856419, 24614604], [24614605, 26372790], [26372791, 28130976], [28130977, 29889162], [29889163, 31647348], [31647349, 33405534], [33405535, 35163735]] SRR11462731 file size 11928475 SRR11462731 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 SRR11462731 SRR11462731_1.fastq Input file: SRR11462731_1.fastq trimmed: SRR11462731-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 10:04:50 2025 >> started Wed Feb 12 10:05:11 2025 >> done (21.484s) 35163735 reads processed; of these: 11782 ( 0.03%) short reads filtered out after trimming by size control 748 ( 0.00%) empty reads filtered out after trimming by size control 35151205 (99.96%) reads available; of these: 8880818 (25.26%) trimmed reads available after processing 26270387 (74.74%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2716 0.01% 19 3027 0.01% 20 3298 0.01% 21 3722 0.01% 22 4272 0.01% 23 4506 0.01% 24 4940 0.01% 25 5082 0.01% 26 5208 0.01% 27 6886 0.02% 28 6205 0.02% 29 6592 0.02% 30 7134 0.02% 31 7066 0.02% 32 7147 0.02% 33 7577 0.02% 34 8680 0.02% 35 8411 0.02% 36 8918 0.03% 37 10662 0.03% 38 9476 0.03% 39 10014 0.03% 40 10785 0.03% 41 10760 0.03% 42 12900 0.04% 43 13344 0.04% 44 12319 0.04% 45 13567 0.04% 46 14304 0.04% 47 19120 0.05% 48 16980 0.05% 49 20585 0.06% 50 16424 0.05% 51 18147 0.05% 52 18262 0.05% 53 19854 0.06% 54 22140 0.06% 55 21469 0.06% 56 22700 0.06% 57 25896 0.07% 58 25857 0.07% 59 26414 0.08% 60 30022 0.09% 61 29557 0.08% 62 68281 0.19% 63 31852 0.09% 64 36601 0.10% 65 33644 0.10% 66 35562 0.10% 67 38118 0.11% 68 38448 0.11% 69 51065 0.15% 70 43833 0.12% 71 48846 0.14% 72 54562 0.16% 73 66520 0.19% 74 63754 0.18% 75 58462 0.17% 76 56161 0.16% 77 75656 0.22% 78 63847 0.18% 79 80971 0.23% 80 69629 0.20% 81 72238 0.21% 82 80672 0.23% 83 84314 0.24% 84 92170 0.26% 85 90862 0.26% 86 94134 0.27% 87 108602 0.31% 88 100789 0.29% 89 156190 0.44% 90 113552 0.32% 91 127245 0.36% 92 118743 0.34% 93 124518 0.35% 94 133636 0.38% 95 135905 0.39% 96 156411 0.44% 97 172188 0.49% 98 154723 0.44% 99 161519 0.46% 100 164814 0.47% 101 174935 0.50% 102 205528 0.58% 103 186943 0.53% 104 193687 0.55% 105 196892 0.56% 106 204310 0.58% 107 209343 0.60% 108 229264 0.65% 109 249262 0.71% 110 233706 0.66% 111 240678 0.68% 112 640060 1.82% 113 257072 0.73% 114 255554 0.73% 115 251450 0.72% 116 269335 0.77% 117 283527 0.81% 118 281411 0.80% 119 295867 0.84% 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 12 0.00% 151 26270387 74.74% 35151205 reads passed initial QC criterion=sequence-density sequence-density=17.89 sequence-density-rank=1 fanout-score=38.66 fanout-score-rank=1 prefix-density=20.87 prefix-fanout=33.1 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGATCTCGTATGCCGTCTTCTGCTTGAAA criterion=fanout-score sequence-density=17.89 sequence-density-rank=1 fanout-score=38.66 fanout-score-rank=1 prefix-density=20.87 prefix-fanout=33.1 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGATCTCGTATGCCGTCTTCTGCTTGAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGATCTCGTATGCCGTCTTCTGCTTGAAA -o SRR11462731 - Input file: STDIN trimmed: SRR11462731-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGTGGATCTCGTATGCCGTCTTCTGCTTG -- 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 10:06:26 2025 >> started Wed Feb 12 10:07:06 2025 >> done (40.457s) 31245516 reads processed; of these: 389 ( 0.00%) short reads filtered out after trimming by size control 6 ( 0.00%) empty reads filtered out after trimming by size control 31245121 (100.00%) reads available; of these: 9501689 (30.41%) trimmed reads available after processing 21743432 (69.59%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2472 0.01% 19 2755 0.01% 20 2963 0.01% 21 3378 0.01% 22 3802 0.01% 23 4045 0.01% 24 4385 0.01% 25 4627 0.01% 26 4723 0.02% 27 6182 0.02% 28 5574 0.02% 29 5935 0.02% 30 6383 0.02% 31 6358 0.02% 32 6348 0.02% 33 6794 0.02% 34 7786 0.02% 35 7601 0.02% 36 7939 0.03% 37 9590 0.03% 38 8605 0.03% 39 9050 0.03% 40 9661 0.03% 41 9605 0.03% 42 11568 0.04% 43 11960 0.04% 44 11038 0.04% 45 12155 0.04% 46 12957 0.04% 47 17052 0.05% 48 15163 0.05% 49 18390 0.06% 50 14750 0.05% 51 16213 0.05% 52 16347 0.05% 53 18029 0.06% 54 19805 0.06% 55 19322 0.06% 56 20056 0.06% 57 23269 0.07% 58 23212 0.07% 59 23536 0.08% 60 27087 0.09% 61 26532 0.08% 62 61054 0.20% 63 28709 0.09% 64 32864 0.11% 65 30092 0.10% 66 31973 0.10% 67 34148 0.11% 68 34618 0.11% 69 45724 0.15% 70 40045 0.13% 71 43749 0.14% 72 48988 0.16% 73 59450 0.19% 74 57351 0.18% 75 51865 0.17% 76 50440 0.16% 77 67657 0.22% 78 57356 0.18% 79 72622 0.23% 80 62267 0.20% 81 65243 0.21% 82 72268 0.23% 83 75811 0.24% 84 82040 0.26% 85 81560 0.26% 86 84149 0.27% 87 97322 0.31% 88 90586 0.29% 89 139728 0.45% 90 102169 0.33% 91 114357 0.37% 92 106594 0.34% 93 111219 0.36% 94 119593 0.38% 95 121861 0.39% 96 140237 0.45% 97 154059 0.49% 98 138500 0.44% 99 145239 0.46% 100 147545 0.47% 101 157756 0.50% 102 183652 0.59% 103 167686 0.54% 104 172791 0.55% 105 175771 0.56% 106 182646 0.58% 107 186991 0.60% 108 205763 0.66% 109 223326 0.71% 110 209457 0.67% 111 215157 0.69% 112 573410 1.84% 113 228863 0.73% 114 228390 0.73% 115 222435 0.71% 116 239647 0.77% 117 244508 0.78% 118 242710 0.78% 119 258794 0.83% 120 289622 0.93% 121 284389 0.91% 122 277435 0.89% 123 298965 0.96% 124 323418 1.04% 125 273554 0.88% 126 297572 0.95% 127 308494 0.99% 128 297496 0.95% 129 315974 1.01% 130 280053 0.90% 131 284228 0.91% 132 444593 1.42% 133 346246 1.11% 134 296466 0.95% 135 315320 1.01% 136 292557 0.94% 137 307685 0.98% 138 349646 1.12% 139 314176 1.01% 140 304099 0.97% 141 286283 0.92% 142 322747 1.03% 143 312566 1.00% 144 271634 0.87% 145 358921 1.15% 146 275929 0.88% 147 350784 1.12% 148 548112 1.75% 149 0 0.00% 150 6 0.00% 151 14090344 45.10% criterion=sequence-density sequence-density=1.03 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=29 prefix-density=1.02 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTACTCTGCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=19.50 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=4.5 sequence=GAAGCCATGAAAGCTGTAGAAACCACTGTCAATCTGGGTCCAATTGCAACTGCTTAATCTTCTTCGAGGAGGATTTGGAGTCGTCTTATTTTTATTTTTTAAGAGTCGTCCAAGGTCTTTCTAGTAGATTCTGTTGCTTCCATAAAGATATCAGTTTCGTGTAGTACCGAGTGTCAATTTGTTCCATGTAGAAAATTACCTTGATTACTATATTATAAATAAACATTATTTCACAGAAATAATTT Started job on | Feb 12 10:07:43 Started mapping on | Feb 12 10:07:43 Finished on | Feb 12 10:10:28 Mapping speed, Million of reads per hour | 766.93 Number of input reads | 35150810 Average input read length | 133 UNIQUE READS: Uniquely mapped reads number | 26751003 Uniquely mapped reads % | 76.10% Average mapped length | 129.62 Number of splices: Total | 10793686 Number of splices: Annotated (sjdb) | 10524551 Number of splices: GT/AG | 10625612 Number of splices: GC/AG | 129027 Number of splices: AT/AC | 5266 Number of splices: Non-canonical | 33781 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.02% Deletion average length | 2.16 Insertion rate per base | 0.01% Insertion average length | 1.80 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 834650 % of reads mapped to multiple loci | 2.37% Number of reads mapped to too many loci | 5032453 % of reads mapped to too many loci | 14.32% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.04% % of reads unmapped: other | 0.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 7565157 7565157 7565157 N_multimapping 834650 834650 834650 N_noFeature 1909135 2336289 25988970 N_ambiguous 440405 105907 667 UnstrandedReadsAssigned:24401463 PositiveStrandReadsAssigned:24308807 NegativeStrandReadsAssigned:761366 Dataset is classified positive stranded MeadianReadLen=145 20thPercentileLength=112 echo kmer=107 SRR11462731 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: SRR11462731-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 35,150,810 reads, 25,612,968 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,060 rounds 52401 SRR11462731.ke.tsv 34699 SRR11462731.se.tsv 87100 total ==> SRR11462731.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 2202.99 45.8252 Potri.005G024800.1.v4.1 1035 936 1370 58.4268 Potri.004G059700.1.v4.1 961 862 0 0 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 2565.15 36.0039 Potri.016G087400.1.v4.1 270 171 1018 237.64 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 2048.89 48.8574 Potri.012G127500.1.v4.1 977 878 45 2.0459 ==> SRR11462731.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 0 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 308 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 5 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 78 SRR11462731 completed mapping pipeline successfully