Starting /dee2/code/volunteer_pipeline.sh SRR11462696 current disk space = 3050305400832 free memory = 1578659576 SRR11462696 SRAfilesize 58adac856d25749e879f1132f5af6f35 SRR11462696.sra SRR11462696.sra file validated SRR11462696 is single end SRR11462696 is conventional basespace SRR11462696 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462696_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 22.35 32.0 2.0 32.0 2.0 32.0 2 31.735 32.0 32.0 32.0 32.0 32.0 3 34.555 37.0 32.0 37.0 32.0 37.0 4 36.24875 37.0 37.0 37.0 32.0 37.0 5 36.38875 37.0 37.0 37.0 37.0 37.0 6 39.9715 41.0 41.0 41.0 37.0 41.0 7 40.13925 41.0 41.0 41.0 37.0 41.0 8 40.25325 41.0 41.0 41.0 41.0 41.0 9 40.213 41.0 41.0 41.0 37.0 41.0 10-14 40.3166 41.0 41.0 41.0 39.4 41.0 15-19 40.303450000000005 41.0 41.0 41.0 41.0 41.0 20-24 40.220349999999996 41.0 41.0 41.0 39.4 41.0 25-29 40.20495 41.0 41.0 41.0 40.2 41.0 30-34 40.0924 41.0 41.0 41.0 37.8 41.0 35-39 40.09025 41.0 41.0 41.0 37.8 41.0 40-44 40.10445 41.0 41.0 41.0 38.6 41.0 45-49 40.092850000000006 41.0 41.0 41.0 39.4 41.0 50-54 40.10215 41.0 41.0 41.0 38.6 41.0 55-59 40.036649999999995 41.0 41.0 41.0 37.0 41.0 60-64 39.98445 41.0 41.0 41.0 37.0 41.0 65-69 40.01135 41.0 41.0 41.0 37.0 41.0 70-74 39.80825 41.0 41.0 41.0 37.0 41.0 75-79 39.74375 41.0 40.2 41.0 37.0 41.0 80-84 40.18195 41.0 41.0 41.0 40.2 41.0 85-89 40.08749999999999 41.0 41.0 41.0 38.6 41.0 90-94 40.0657 41.0 41.0 41.0 37.8 41.0 95-99 40.0284 41.0 41.0 41.0 37.8 41.0 100-104 39.8135 41.0 41.0 41.0 37.0 41.0 105-109 39.77545 41.0 41.0 41.0 37.0 41.0 110-114 39.7509 41.0 41.0 41.0 37.0 41.0 115-119 39.69895 41.0 41.0 41.0 37.0 41.0 120-124 39.6018 41.0 41.0 41.0 37.0 41.0 125-129 39.3674 41.0 41.0 41.0 37.0 41.0 130-134 39.1261 41.0 41.0 41.0 37.0 41.0 135-139 38.7645 41.0 41.0 41.0 33.0 41.0 140-144 38.68135 41.0 41.0 41.0 32.0 41.0 145-149 38.278150000000004 41.0 41.0 41.0 32.0 41.0 150-151 37.24575 41.0 39.0 41.0 24.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 1.0 22 0.0 23 0.0 24 2.0 25 3.0 26 4.0 27 6.0 28 12.0 29 21.0 30 26.0 31 37.0 32 45.0 33 73.0 34 52.0 35 75.0 36 82.0 37 133.0 38 176.0 39 294.0 40 2958.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 5.985401459854015 37.372262773722625 42.007299270073 14.635036496350365 2 26.900000000000002 41.25 20.674999999999997 11.175 3 21.375 30.7 37.65 10.274999999999999 4 33.50837709427357 24.406101525381345 28.032008002000502 14.053513378344586 5 27.625 26.3 28.7 17.375 6 24.675 26.200000000000003 30.225 18.9 7 21.975 25.45 31.924999999999997 20.65 8 23.35 26.525 31.85 18.275 9 20.65 24.95 32.25 22.15 10-14 24.285 25.21 30.595 19.91 15-19 23.72 27.400000000000002 29.285 19.595000000000002 20-24 24.63 27.38 28.83 19.16 25-29 24.125 26.555 29.895 19.425 30-34 24.255 26.85 28.804999999999996 20.09 35-39 24.84 26.229999999999997 28.925 20.005 40-44 24.48 26.445 29.95 19.125 45-49 24.072407240724072 27.097709770977097 28.90789078907891 19.921992199219922 50-54 24.135 27.12 28.715000000000003 20.03 55-59 23.866193309665483 27.58137906895345 28.87644382219111 19.675983799189957 60-64 24.672467246724672 26.707670767076706 29.827982798279827 18.79187918791879 65-69 24.891244562228113 26.77133856692835 28.066403320166007 20.271013550677534 70-74 24.59868980347052 27.14407161074161 28.454268140221036 19.802970445566835 75-79 23.821191059552977 27.006350317515874 29.271463573178657 19.90099504975249 80-84 24.72 27.11 28.425 19.744999999999997 85-89 23.547354735473547 28.26282628262826 28.74787478747875 19.44194419441944 90-94 24.66246624662466 27.21272127212721 28.292829282928295 19.831983198319833 95-99 24.09240924092409 27.51775177517752 27.607760776077605 20.78207820782078 100-104 24.48 27.700000000000003 27.310000000000002 20.51 105-109 23.981199059953 27.951397569878495 26.826341317065854 21.241062053102656 110-114 23.82 27.534999999999997 26.57 22.075 115-119 24.04 27.315 27.189999999999998 21.455 120-124 23.775 27.465 26.77 21.990000000000002 125-129 24.044999999999998 27.12 25.835 23.0 130-134 23.02 27.765 25.83 23.385 135-139 22.825 27.52 25.7 23.955000000000002 140-144 22.805 28.21 24.745 24.240000000000002 145-149 22.96 27.950000000000003 24.94 24.15 150-151 21.912499999999998 28.1375 24.175 25.775 >>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 1.0 20 0.5 21 0.5 22 0.5 23 0.5 24 1.5 25 2.5 26 2.0 27 8.0 28 16.0 29 18.5 30 22.5 31 32.5 32 41.5 33 50.0 34 77.0 35 109.0 36 122.0 37 133.5 38 146.5 39 182.5 40 221.0 41 224.5 42 237.0 43 258.0 44 282.0 45 265.5 46 213.5 47 208.5 48 188.5 49 157.5 50 145.5 51 109.5 52 107.0 53 98.0 54 62.0 55 60.0 56 47.5 57 27.5 58 22.5 59 17.0 60 13.0 61 8.0 62 8.0 63 12.0 64 8.0 65 3.0 66 2.0 67 2.0 68 3.5 69 3.5 70 5.5 71 7.0 72 3.0 73 0.0 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 31.5 2 0.0 3 0.0 4 0.025 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 0.01 50-54 0.0 55-59 0.005 60-64 0.01 65-69 0.005 70-74 0.015 75-79 0.005 80-84 0.0 85-89 0.01 90-94 0.01 95-99 0.01 100-104 0.0 105-109 0.005 110-114 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 91.925 #Duplication Level Percentage of deduplicated Percentage of total 1 95.4854500951863 87.775 2 3.508294805548001 6.45 3 0.4895295077508839 1.35 4 0.19037258634756596 0.7000000000000001 5 0.08158825129181398 0.375 6 0.0 0.0 7 0.027196083763937992 0.17500000000000002 8 0.054392167527875984 0.4 9 0.027196083763937992 0.22499999999999998 >10 0.13598041881968997 2.55 >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 33 0.8250000000000001 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 32 0.8 No Hit TGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 15 0.375 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 11 0.27499999999999997 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 11 0.27499999999999997 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 9 0.22499999999999998 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 8 0.2 No Hit NTGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 8 0.2 No Hit NACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 7 0.17500000000000002 No Hit NGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 5 0.125 No Hit AGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGAT 5 0.125 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 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 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.0875 0.0 0.0 0.0 0.0 28-29 0.15 0.0 0.0 0.0 0.0 30-31 0.16249999999999998 0.0 0.0 0.0 0.0 32-33 0.2 0.0 0.0 0.0 0.0 34-35 0.275 0.0 0.0 0.0 0.0 36-37 0.3125 0.0 0.0 0.0 0.0 38-39 0.3375 0.0 0.0 0.0 0.0 40-41 0.3875 0.0 0.0 0.0 0.0 42-43 0.48750000000000004 0.0 0.0 0.0 0.0 44-45 0.65 0.0 0.0 0.0 0.0 46-47 0.725 0.0 0.0 0.0 0.0 48-49 0.7625 0.0 0.0 0.0 0.0 50-51 0.825 0.0 0.0 0.0 0.0 52-53 0.925 0.0 0.0 0.0 0.0 54-55 0.9874999999999999 0.0 0.0 0.0 0.0 56-57 1.1375000000000002 0.0 0.0 0.0 0.0 58-59 1.3125 0.0 0.0 0.0 0.0 60-61 1.525 0.0 0.0 0.0 0.0 62-63 1.85 0.0 0.0 0.0 0.0 64-65 2.1625 0.0 0.0 0.0 0.0 66-67 2.4375 0.0 0.0 0.0 0.0 68-69 2.7249999999999996 0.0 0.0 0.0 0.0 70-71 3.1125 0.0 0.0 0.0 0.0 72-73 3.4749999999999996 0.0 0.0 0.0 0.0 74-75 4.1125 0.0 0.0 0.0 0.0 76-77 4.575 0.0 0.0 0.0 0.0 78-79 5.025 0.0 0.0 0.0 0.0 80-81 5.625 0.0 0.0 0.0 0.0 82-83 6.3125 0.0 0.0 0.0 0.0 84-85 7.0 0.0 0.0 0.0 0.0 86-87 7.625 0.0 0.0 0.0 0.0 88-89 8.125 0.0 0.0 0.0 0.0 90-91 9.412500000000001 0.0 0.0 0.0 0.0 92-93 10.1625 0.0 0.0 0.0 0.0 94-95 11.0625 0.0 0.0 0.0 0.0 96-97 12.1125 0.0 0.0 0.0 0.0 98-99 13.4375 0.0 0.0 0.0 0.0 100-101 14.662500000000001 0.0 0.0 0.0 0.0 102-103 15.8625 0.0 0.0 0.0 0.0 104-105 17.012500000000003 0.0 0.0 0.0 0.0 106-107 18.3875 0.0 0.0 0.0 0.0 108-109 19.875 0.0 0.0 0.0 0.0 110-111 21.6 0.0 0.0 0.0 0.0 112-113 23.0875 0.0 0.0 0.0 0.0 114-115 25.1125 0.0 0.0 0.0 0.0 116-117 26.75 0.0 0.0 0.0 0.0 118-119 28.5125 0.0 0.0 0.0 0.0 120-121 29.9875 0.0 0.0 0.0 0.0 122-123 31.775000000000002 0.0 0.0 0.0 0.0 124-125 33.375 0.0 0.0 0.0 0.0 126-127 34.9875 0.0 0.0 0.0 0.0 128-129 36.2875 0.0 0.0 0.0 0.0 130-131 37.900000000000006 0.0 0.0 0.0 0.0 132-133 39.3875 0.0 0.0 0.0 0.0 134-135 41.025000000000006 0.0 0.0 0.0 0.0 136-137 42.7875 0.0 0.0 0.0 0.0 138-139 44.2 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGTTTTG 10 0.006875036 144.6875 4 TGATCCT 10 0.006875036 144.6875 9 TTTTGTT 15 0.007408205 140.30302 1 CACGTCC 85 0.003225104 11.915441 140-144 TCACGTC 85 0.003225104 11.915441 140-144 >>END_MODULE Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871454 READS because READLEN < 1 Read 1871454 spots for SRR11462696.sra Written 1871454 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra Rejected 1871447 READS because READLEN < 1 Read 1871447 spots for SRR11462696.sra Written 1871447 spots for SRR11462696.sra SRR ids: ['SRR11462696.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_fvwtonrt SRR11462696.sra spots: 37428947 blocks: [[1, 1871447], [1871448, 3742894], [3742895, 5614341], [5614342, 7485788], [7485789, 9357235], [9357236, 11228682], [11228683, 13100129], [13100130, 14971576], [14971577, 16843023], [16843024, 18714470], [18714471, 20585917], [20585918, 22457364], [22457365, 24328811], [24328812, 26200258], [26200259, 28071705], [28071706, 29943152], [29943153, 31814599], [31814600, 33686046], [33686047, 35557493], [35557494, 37428947]] SRR11462696 file size 12698293 SRR11462696 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 SRR11462696 SRR11462696_1.fastq Input file: SRR11462696_1.fastq trimmed: SRR11462696-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 06:43:20 2025 >> started Wed Feb 12 06:43:41 2025 >> done (21.464s) 37428947 reads processed; of these: 8186 ( 0.02%) short reads filtered out after trimming by size control 595 ( 0.00%) empty reads filtered out after trimming by size control 37420166 (99.98%) reads available; of these: 11257132 (30.08%) trimmed reads available after processing 26163034 (69.92%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1992 0.01% 19 2222 0.01% 20 2520 0.01% 21 2626 0.01% 22 3102 0.01% 23 3432 0.01% 24 3666 0.01% 25 3739 0.01% 26 3936 0.01% 27 4919 0.01% 28 4630 0.01% 29 5163 0.01% 30 5454 0.01% 31 5425 0.01% 32 5814 0.02% 33 6162 0.02% 34 7027 0.02% 35 7275 0.02% 36 7189 0.02% 37 9922 0.03% 38 8471 0.02% 39 8947 0.02% 40 9403 0.03% 41 9775 0.03% 42 11722 0.03% 43 12121 0.03% 44 11587 0.03% 45 13618 0.04% 46 14800 0.04% 47 18366 0.05% 48 18180 0.05% 49 24015 0.06% 50 17847 0.05% 51 19608 0.05% 52 20748 0.06% 53 22069 0.06% 54 25916 0.07% 55 25493 0.07% 56 27237 0.07% 57 33179 0.09% 58 30961 0.08% 59 33587 0.09% 60 38274 0.10% 61 38766 0.10% 62 73878 0.20% 63 43330 0.12% 64 48137 0.13% 65 47738 0.13% 66 51215 0.14% 67 56346 0.15% 68 56984 0.15% 69 75839 0.20% 70 67243 0.18% 71 72718 0.19% 72 82216 0.22% 73 105544 0.28% 74 98245 0.26% 75 92976 0.25% 76 90013 0.24% 77 113133 0.30% 78 103187 0.28% 79 130795 0.35% 80 111204 0.30% 81 117317 0.31% 82 127998 0.34% 83 131699 0.35% 84 143401 0.38% 85 144387 0.39% 86 152784 0.41% 87 165678 0.44% 88 160938 0.43% 89 290431 0.78% 90 181059 0.48% 91 195530 0.52% 92 180908 0.48% 93 191880 0.51% 94 205217 0.55% 95 198996 0.53% 96 219226 0.59% 97 237066 0.63% 98 218279 0.58% 99 228073 0.61% 100 223192 0.60% 101 237892 0.64% 102 267938 0.72% 103 247834 0.66% 104 243613 0.65% 105 251714 0.67% 106 253250 0.68% 107 259104 0.69% 108 274419 0.73% 109 307940 0.82% 110 276197 0.74% 111 283572 0.76% 112 488192 1.30% 113 287256 0.77% 114 285449 0.76% 115 277544 0.74% 116 284788 0.76% 117 304154 0.81% 118 295371 0.79% 119 305086 0.82% 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% 150 114 0.00% 151 26163034 69.92% 37420166 reads passed initial QC criterion=sequence-density sequence-density=15.22 sequence-density-rank=1 fanout-score=38.77 fanout-score-rank=1 prefix-density=17.75 prefix-fanout=33.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTGAAAA criterion=fanout-score sequence-density=15.22 sequence-density-rank=1 fanout-score=38.77 fanout-score-rank=1 prefix-density=17.75 prefix-fanout=33.2 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTGAAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTGAAAA -o SRR11462696 - Input file: STDIN trimmed: SRR11462696-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCCGCATCTCGTATGCCGTCTTCTGCTTG -- 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 06:45:01 2025 >> started Wed Feb 12 06:45:37 2025 >> done (36.127s) 32742645 reads processed; of these: 310 ( 0.00%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 32742328 (100.00%) reads available; of these: 8649676 (26.42%) trimmed reads available after processing 24092652 (73.58%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1776 0.01% 19 2010 0.01% 20 2290 0.01% 21 2394 0.01% 22 2720 0.01% 23 3064 0.01% 24 3242 0.01% 25 3321 0.01% 26 3496 0.01% 27 4336 0.01% 28 4080 0.01% 29 4586 0.01% 30 4835 0.01% 31 4803 0.01% 32 5149 0.02% 33 5477 0.02% 34 6260 0.02% 35 6424 0.02% 36 6386 0.02% 37 8788 0.03% 38 7484 0.02% 39 7859 0.02% 40 8366 0.03% 41 8659 0.03% 42 10388 0.03% 43 10750 0.03% 44 10352 0.03% 45 12208 0.04% 46 13191 0.04% 47 16282 0.05% 48 15998 0.05% 49 21227 0.06% 50 15985 0.05% 51 17517 0.05% 52 18378 0.06% 53 19528 0.06% 54 22909 0.07% 55 22604 0.07% 56 24089 0.07% 57 29560 0.09% 58 27418 0.08% 59 29839 0.09% 60 33898 0.10% 61 34340 0.10% 62 65472 0.20% 63 38491 0.12% 64 42595 0.13% 65 42239 0.13% 66 45404 0.14% 67 49822 0.15% 68 50803 0.16% 69 67138 0.21% 70 60365 0.18% 71 64463 0.20% 72 72792 0.22% 73 93092 0.28% 74 86639 0.26% 75 81520 0.25% 76 79702 0.24% 77 100091 0.31% 78 90905 0.28% 79 115709 0.35% 80 98140 0.30% 81 104570 0.32% 82 112909 0.34% 83 116474 0.36% 84 125691 0.38% 85 127873 0.39% 86 134843 0.41% 87 146109 0.45% 88 142067 0.43% 89 255545 0.78% 90 161284 0.49% 91 172539 0.53% 92 160337 0.49% 93 168750 0.52% 94 180514 0.55% 95 175225 0.54% 96 193591 0.59% 97 208712 0.64% 98 192523 0.59% 99 202005 0.62% 100 196747 0.60% 101 210308 0.64% 102 235107 0.72% 103 218098 0.67% 104 214421 0.65% 105 221507 0.68% 106 222804 0.68% 107 227284 0.69% 108 242205 0.74% 109 270993 0.83% 110 243930 0.74% 111 249617 0.76% 112 431489 1.32% 113 251019 0.77% 114 250883 0.77% 115 241840 0.74% 116 249985 0.76% 117 257254 0.79% 118 249665 0.76% 119 262502 0.80% 120 278911 0.85% 121 285062 0.87% 122 266577 0.81% 123 296265 0.90% 124 295264 0.90% 125 260379 0.80% 126 272964 0.83% 127 282914 0.86% 128 271263 0.83% 129 267854 0.82% 130 258745 0.79% 131 260958 0.80% 132 330277 1.01% 133 302636 0.92% 134 263574 0.80% 135 288049 0.88% 136 259408 0.79% 137 268507 0.82% 138 276938 0.85% 139 259608 0.79% 140 287599 0.88% 141 252666 0.77% 142 260629 0.80% 143 261709 0.80% 144 247521 0.76% 145 295539 0.90% 146 254171 0.78% 147 324474 0.99% 148 544109 1.66% 149 0 0.00% 150 66 0.00% 151 14568825 44.50% criterion=sequence-density sequence-density=0.72 sequence-density-rank=1 fanout-score=2.14 fanout-score-rank=34 prefix-density=0.72 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTACTCTGCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=35 fanout-score=359.77 fanout-score-rank=1 prefix-density=0.33 prefix-fanout=13.4 sequence=TTGGATTTGATTAGATCCACCAATAAAAAGGGCTTGCCTTACACTCTTGGTCTTAATCAATTTGCTGATTGGACATGGCAAGAGTTCCAAAAGTACAGACTGGGAGCTGCCCAAAATTGCTCTGCAACCACAAGGGGCAATCACAAGCTTACGAACGCTCTTCTTCCTGAAACGAAAGACTGGAGGGAAGAAGGCATAGTCAGTCCCGTTAAGAATCAAGGTCACTGTGGATCTTGCTGGACTTTCAGCACCACTGGAGCTCTAGAGGCTGCTTACCACCAGGCTTTTGGGAAAGGAATCTCTCTGTCTGAACAGCAGCTTGTGGACTGTGCTAGAGCATTTAATAACTTTGGCTGCAATG Started job on | Feb 12 06:46:55 Started mapping on | Feb 12 06:46:55 Finished on | Feb 12 06:48:06 Mapping speed, Million of reads per hour | 1897.34 Number of input reads | 37419849 Average input read length | 122 UNIQUE READS: Uniquely mapped reads number | 30664905 Uniquely mapped reads % | 81.95% Average mapped length | 119.99 Number of splices: Total | 11689164 Number of splices: Annotated (sjdb) | 11412012 Number of splices: GT/AG | 11494165 Number of splices: GC/AG | 156905 Number of splices: AT/AC | 6644 Number of splices: Non-canonical | 31450 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.02% Deletion average length | 2.08 Insertion rate per base | 0.01% Insertion average length | 1.78 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 973260 % of reads mapped to multiple loci | 2.60% Number of reads mapped to too many loci | 3478805 % of reads mapped to too many loci | 9.30% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.06% % of reads unmapped: other | 0.09% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5781684 5781684 5781684 N_multimapping 973260 973260 973260 N_noFeature 2048817 2546185 29813232 N_ambiguous 458470 104549 615 UnstrandedReadsAssigned:28157618 PositiveStrandReadsAssigned:28014171 NegativeStrandReadsAssigned:851058 Dataset is classified positive stranded MeadianReadLen=135 20thPercentileLength=99 echo kmer=95 SRR11462696 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: SRR11462696-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 37,419,849 reads, 29,265,766 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,140 rounds 52401 SRR11462696.ke.tsv 34699 SRR11462696.se.tsv 87100 total ==> SRR11462696.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 2746 59.9388 Potri.005G024800.1.v4.1 1035 936 686.244 30.7103 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 4938.28 72.7324 Potri.016G087400.1.v4.1 270 171 1530 374.781 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 1530.98 38.3086 Potri.012G127500.1.v4.1 977 878 118 5.6295 ==> SRR11462696.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 2 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 370 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 22 SRR11462696 completed mapping pipeline successfully