Starting /dee2/code/volunteer_pipeline.sh SRR11462695 current disk space = 2824811917312 free memory = 1575820548 SRR11462695 SRAfilesize 0bca722f87ef147d57bce98298e56079 SRR11462695.sra SRR11462695.sra file validated SRR11462695 is single end SRR11462695 is conventional basespace SRR11462695 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462695_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 22.26 32.0 2.0 32.0 2.0 32.0 2 31.78375 32.0 32.0 32.0 32.0 32.0 3 34.46875 37.0 32.0 37.0 32.0 37.0 4 36.24125 37.0 37.0 37.0 32.0 37.0 5 36.49375 37.0 37.0 37.0 37.0 37.0 6 39.988 41.0 41.0 41.0 37.0 41.0 7 40.34725 41.0 41.0 41.0 37.0 41.0 8 40.1675 41.0 41.0 41.0 37.0 41.0 9 40.35125 41.0 41.0 41.0 41.0 41.0 10-14 40.39425 41.0 41.0 41.0 41.0 41.0 15-19 40.37445 41.0 41.0 41.0 41.0 41.0 20-24 40.33695 41.0 41.0 41.0 40.2 41.0 25-29 40.27815 41.0 41.0 41.0 39.4 41.0 30-34 40.36195 41.0 41.0 41.0 41.0 41.0 35-39 40.327299999999994 41.0 41.0 41.0 41.0 41.0 40-44 40.2577 41.0 41.0 41.0 41.0 41.0 45-49 40.27195 41.0 41.0 41.0 41.0 41.0 50-54 40.26315000000001 41.0 41.0 41.0 41.0 41.0 55-59 40.27745 41.0 41.0 41.0 39.4 41.0 60-64 40.1597 41.0 41.0 41.0 38.6 41.0 65-69 40.14685 41.0 41.0 41.0 37.8 41.0 70-74 40.083299999999994 41.0 41.0 41.0 37.0 41.0 75-79 39.7018 41.0 40.2 41.0 37.0 41.0 80-84 40.2452 41.0 41.0 41.0 41.0 41.0 85-89 40.262950000000004 41.0 41.0 41.0 41.0 41.0 90-94 40.19025 41.0 41.0 41.0 39.4 41.0 95-99 40.074149999999996 41.0 41.0 41.0 37.8 41.0 100-104 40.05375 41.0 41.0 41.0 38.6 41.0 105-109 39.967949999999995 41.0 41.0 41.0 37.0 41.0 110-114 40.0122 41.0 41.0 41.0 37.8 41.0 115-119 39.8866 41.0 41.0 41.0 37.0 41.0 120-124 39.673199999999994 41.0 41.0 41.0 37.0 41.0 125-129 39.504949999999994 41.0 41.0 41.0 37.0 41.0 130-134 39.50789999999999 41.0 41.0 41.0 37.0 41.0 135-139 39.3455 41.0 41.0 41.0 37.0 41.0 140-144 38.9744 41.0 41.0 41.0 37.0 41.0 145-149 38.7676 41.0 41.0 41.0 35.0 41.0 150-151 37.849374999999995 41.0 39.0 41.0 32.0 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 3.0 24 1.0 25 2.0 26 4.0 27 7.0 28 7.0 29 9.0 30 13.0 31 23.0 32 27.0 33 41.0 34 50.0 35 52.0 36 104.0 37 128.0 38 167.0 39 376.0 40 2986.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 6.087275394206087 37.33039970663733 39.75064173083975 16.831683168316832 2 26.55 42.575 19.05 11.825 3 22.2 29.549999999999997 38.05 10.2 4 35.75893973493373 25.03125781445361 26.25656414103526 12.953238309577394 5 28.875 26.825 26.375 17.925 6 25.974999999999998 26.650000000000002 29.275000000000002 18.099999999999998 7 22.2 27.900000000000002 29.525000000000002 20.375 8 24.95 26.200000000000003 30.4 18.45 9 22.25 23.75 31.3 22.7 10-14 25.205 25.335 29.705 19.755 15-19 25.35 26.41 28.835 19.405 20-24 24.77 27.445000000000004 27.965 19.82 25-29 24.955 27.025 28.455000000000002 19.564999999999998 30-34 24.325 26.445 29.099999999999998 20.13 35-39 25.130000000000003 26.25 28.53 20.09 40-44 24.735 26.3 29.12 19.845 45-49 24.25 26.605 28.98 20.165 50-54 24.41 26.915 28.815 19.86 55-59 24.465 26.815 28.59 20.13 60-64 24.779999999999998 26.55 28.955 19.715 65-69 24.765 26.445 28.555000000000003 20.235 70-74 25.245 26.025 28.62 20.11 75-79 23.695 27.6 28.249999999999996 20.455000000000002 80-84 24.34 27.165 28.425 20.07 85-89 24.474999999999998 26.915 27.994999999999997 20.615 90-94 24.48 26.674999999999997 28.845 20.0 95-99 24.345 27.55 27.88 20.225 100-104 24.529999999999998 27.185 28.095 20.19 105-109 23.315 27.435 28.389999999999997 20.86 110-114 24.16 27.965 27.72 20.155 115-119 24.34 28.035 27.47 20.155 120-124 23.544999999999998 28.299999999999997 27.325 20.830000000000002 125-129 24.175 28.57 26.195 21.060000000000002 130-134 24.2 28.735 26.27 20.794999999999998 135-139 23.665 29.035 25.505 21.795 140-144 23.165 28.485 25.480000000000004 22.869999999999997 145-149 22.585 28.67 26.125 22.62 150-151 22.3375 28.499999999999996 25.4625 23.7 >>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 0.5 8 0.5 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 0.0 22 0.5 23 0.5 24 0.0 25 2.5 26 3.5 27 3.0 28 5.5 29 7.0 30 8.0 31 15.0 32 30.5 33 46.5 34 70.5 35 92.0 36 99.5 37 104.0 38 131.5 39 169.5 40 199.5 41 215.5 42 227.5 43 261.5 44 287.0 45 277.0 46 245.5 47 225.0 48 233.0 49 205.0 50 164.5 51 135.0 52 105.0 53 101.5 54 77.0 55 59.0 56 50.5 57 40.0 58 30.5 59 15.0 60 11.0 61 11.5 62 7.0 63 7.0 64 6.5 65 1.0 66 0.5 67 2.0 68 3.0 69 2.5 70 1.5 71 0.5 72 0.0 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 31.825 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 0.0 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 92.925 #Duplication Level Percentage of deduplicated Percentage of total 1 94.67312348668281 87.97500000000001 2 4.277643260694108 7.95 3 0.8071025020177561 2.25 4 0.053806833467850416 0.2 5 0.053806833467850416 0.25 6 0.026903416733925208 0.15 7 0.0 0.0 8 0.026903416733925208 0.2 9 0.0 0.0 >10 0.08071025020177562 1.0250000000000001 >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 17 0.42500000000000004 No Hit TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 14 0.35000000000000003 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 10 0.25 No Hit TTTGATGATCTGGAGGGCTTGCAGGAGTATCTTGATTCTTCGGTTGTTGC 8 0.2 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 6 0.15 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 5 0.125 No Hit AGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTA 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 0.025 0.0 0.0 0.0 0.0 18-19 0.037500000000000006 0.0 0.0 0.0 0.0 20-21 0.0625 0.0 0.0 0.0 0.0 22-23 0.075 0.0 0.0 0.0 0.0 24-25 0.1125 0.0 0.0 0.0 0.0 26-27 0.125 0.0 0.0 0.0 0.0 28-29 0.175 0.0 0.0 0.0 0.0 30-31 0.23750000000000002 0.0 0.0 0.0 0.0 32-33 0.3 0.0 0.0 0.0 0.0 34-35 0.3625 0.0 0.0 0.0 0.0 36-37 0.4375 0.0 0.0 0.0 0.0 38-39 0.525 0.0 0.0 0.0 0.0 40-41 0.55 0.0 0.0 0.0 0.0 42-43 0.65 0.0 0.0 0.0 0.0 44-45 0.75 0.0 0.0 0.0 0.0 46-47 0.775 0.0 0.0 0.0 0.0 48-49 0.8125 0.0 0.0 0.0 0.0 50-51 0.9125 0.0 0.0 0.0 0.0 52-53 1.0375 0.0 0.0 0.0 0.0 54-55 1.2000000000000002 0.0 0.0 0.0 0.0 56-57 1.2375 0.0 0.0 0.0 0.0 58-59 1.3624999999999998 0.0 0.0 0.0 0.0 60-61 1.475 0.0 0.0 0.0 0.0 62-63 1.6749999999999998 0.0 0.0 0.0 0.0 64-65 1.8125 0.0 0.0 0.0 0.0 66-67 1.975 0.0 0.0 0.0 0.0 68-69 2.1375 0.0 0.0 0.0 0.0 70-71 2.25 0.0 0.0 0.0 0.0 72-73 2.4000000000000004 0.0 0.0 0.0 0.0 74-75 2.5625 0.0 0.0 0.0 0.0 76-77 2.7875 0.0 0.0 0.0 0.0 78-79 3.05 0.0 0.0 0.0 0.0 80-81 3.325 0.0 0.0 0.0 0.0 82-83 3.6125 0.0 0.0 0.0 0.0 84-85 3.9125 0.0 0.0 0.0 0.0 86-87 4.15 0.0 0.0 0.0 0.0 88-89 4.4125 0.0 0.0 0.0 0.0 90-91 4.7375 0.0 0.0 0.0 0.0 92-93 5.1625 0.0 0.0 0.0 0.0 94-95 5.4875 0.0 0.0 0.0 0.0 96-97 5.85 0.0 0.0 0.0 0.0 98-99 6.6 0.0 0.0 0.0 0.0 100-101 7.3375 0.0 0.0 0.0 0.0 102-103 7.9375 0.0 0.0 0.0 0.0 104-105 8.6875 0.0 0.0 0.0 0.0 106-107 9.45 0.0 0.0 0.0 0.0 108-109 10.175 0.0 0.0 0.0 0.0 110-111 11.1625 0.0 0.0 0.0 0.0 112-113 12.3 0.0 0.0 0.0 0.0 114-115 13.3875 0.0 0.0 0.0 0.0 116-117 14.3625 0.0 0.0 0.0 0.0 118-119 15.3875 0.0 0.0 0.0 0.0 120-121 16.299999999999997 0.0 0.0 0.0 0.0 122-123 17.525 0.0 0.0 0.0 0.0 124-125 19.4125 0.0 0.0 0.0 0.0 126-127 20.6 0.0 0.0 0.0 0.0 128-129 22.125 0.0 0.0 0.0 0.0 130-131 23.8 0.0 0.0 0.0 0.0 132-133 25.0625 0.0 0.0 0.0 0.0 134-135 26.2625 0.0 0.0 0.0 0.0 136-137 27.275 0.0 0.0 0.0 0.0 138-139 28.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACAAACC 10 0.006875036 144.6875 5 AAACCCC 10 0.006875036 144.6875 7 AACAAAC 10 0.006875036 144.6875 4 AACCCCG 10 0.006875036 144.6875 8 GCAACAA 10 0.006875036 144.6875 2 ACCCCGA 10 0.006875036 144.6875 9 CAAACCC 10 0.006875036 144.6875 6 GGTATGA 10 0.006875036 144.6875 5 >>END_MODULE Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253194 READS because READLEN < 1 Read 2253194 spots for SRR11462695.sra Written 2253194 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra Rejected 2253192 READS because READLEN < 1 Read 2253192 spots for SRR11462695.sra Written 2253192 spots for SRR11462695.sra SRR ids: ['SRR11462695.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_80i9jhug SRR11462695.sra spots: 45063842 blocks: [[1, 2253192], [2253193, 4506384], [4506385, 6759576], [6759577, 9012768], [9012769, 11265960], [11265961, 13519152], [13519153, 15772344], [15772345, 18025536], [18025537, 20278728], [20278729, 22531920], [22531921, 24785112], [24785113, 27038304], [27038305, 29291496], [29291497, 31544688], [31544689, 33797880], [33797881, 36051072], [36051073, 38304264], [38304265, 40557456], [40557457, 42810648], [42810649, 45063842]] SRR11462695 file size 15292964 SRR11462695 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 SRR11462695 SRR11462695_1.fastq Input file: SRR11462695_1.fastq trimmed: SRR11462695-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 Thu Apr 10 11:49:29 2025 >> started Thu Apr 10 11:49:59 2025 >> done (29.569s) 45063842 reads processed; of these: 21462 ( 0.05%) short reads filtered out after trimming by size control 3274 ( 0.01%) empty reads filtered out after trimming by size control 45039106 (99.95%) reads available; of these: 7035271 (15.62%) trimmed reads available after processing 38003835 (84.38%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 4892 0.01% 19 5219 0.01% 20 5998 0.01% 21 6364 0.01% 22 7338 0.02% 23 7378 0.02% 24 8375 0.02% 25 8390 0.02% 26 8492 0.02% 27 9465 0.02% 28 9560 0.02% 29 9988 0.02% 30 10172 0.02% 31 10539 0.02% 32 10431 0.02% 33 11025 0.02% 34 11360 0.03% 35 12028 0.03% 36 11983 0.03% 37 15114 0.03% 38 12315 0.03% 39 13215 0.03% 40 13447 0.03% 41 13761 0.03% 42 15511 0.03% 43 15504 0.03% 44 15291 0.03% 45 16771 0.04% 46 17150 0.04% 47 22376 0.05% 48 18980 0.04% 49 20530 0.05% 50 19371 0.04% 51 20658 0.05% 52 21305 0.05% 53 21623 0.05% 54 24305 0.05% 55 24606 0.05% 56 24824 0.06% 57 27355 0.06% 58 26264 0.06% 59 31178 0.07% 60 29560 0.07% 61 29657 0.07% 62 46584 0.10% 63 31966 0.07% 64 34681 0.08% 65 33146 0.07% 66 33930 0.08% 67 38963 0.09% 68 36637 0.08% 69 41322 0.09% 70 40586 0.09% 71 44544 0.10% 72 46112 0.10% 73 49002 0.11% 74 58123 0.13% 75 51057 0.11% 76 48635 0.11% 77 53014 0.12% 78 56037 0.12% 79 62842 0.14% 80 58156 0.13% 81 63294 0.14% 82 63893 0.14% 83 66154 0.15% 84 73501 0.16% 85 75917 0.17% 86 80972 0.18% 87 81453 0.18% 88 82457 0.18% 89 111033 0.25% 90 87932 0.20% 91 93120 0.21% 92 91014 0.20% 93 98978 0.22% 94 107955 0.24% 95 107242 0.24% 96 121968 0.27% 97 121025 0.27% 98 117185 0.26% 99 122240 0.27% 100 123999 0.28% 101 133318 0.30% 102 160934 0.36% 103 144558 0.32% 104 145053 0.32% 105 151129 0.34% 106 159612 0.35% 107 165872 0.37% 108 171940 0.38% 109 203138 0.45% 110 183917 0.41% 111 183843 0.41% 112 247591 0.55% 113 204603 0.45% 114 202276 0.45% 115 211466 0.47% 116 213749 0.47% 117 231399 0.51% 118 241209 0.54% 119 243327 0.54% 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 38003835 84.38% 45039106 reads passed initial QC criterion=sequence-density sequence-density=12.29 sequence-density-rank=1 fanout-score=40.64 fanout-score-rank=1 prefix-density=14.65 prefix-fanout=34.1 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACTCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=12.29 sequence-density-rank=1 fanout-score=40.64 fanout-score-rank=1 prefix-density=14.65 prefix-fanout=34.1 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACTCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACTCAATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR11462695 - Input file: STDIN trimmed: SRR11462695-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACCACTCAATCTCGTATGCCGTCTTCTGCTTG -- 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 Thu Apr 10 11:51:45 2025 >> started Thu Apr 10 11:52:38 2025 >> done (53.466s) 38110013 reads processed; of these: 636 ( 0.00%) short reads filtered out after trimming by size control 17 ( 0.00%) empty reads filtered out after trimming by size control 38109360 (100.00%) reads available; of these: 8875946 (23.29%) trimmed reads available after processing 29233414 (76.71%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 4211 0.01% 19 4460 0.01% 20 5143 0.01% 21 5459 0.01% 22 6254 0.02% 23 6327 0.02% 24 7105 0.02% 25 7176 0.02% 26 7232 0.02% 27 8018 0.02% 28 8186 0.02% 29 8515 0.02% 30 8623 0.02% 31 8968 0.02% 32 8888 0.02% 33 9321 0.02% 34 9737 0.03% 35 10287 0.03% 36 10281 0.03% 37 12850 0.03% 38 10459 0.03% 39 11122 0.03% 40 11445 0.03% 41 11664 0.03% 42 13148 0.03% 43 13241 0.03% 44 12931 0.03% 45 14337 0.04% 46 14620 0.04% 47 19077 0.05% 48 16172 0.04% 49 17469 0.05% 50 16605 0.04% 51 17571 0.05% 52 18133 0.05% 53 18537 0.05% 54 20742 0.05% 55 20906 0.05% 56 20889 0.05% 57 23292 0.06% 58 22200 0.06% 59 26412 0.07% 60 25155 0.07% 61 25366 0.07% 62 39781 0.10% 63 27306 0.07% 64 29646 0.08% 65 28400 0.07% 66 28862 0.08% 67 33178 0.09% 68 31416 0.08% 69 35020 0.09% 70 34868 0.09% 71 37728 0.10% 72 39486 0.10% 73 41475 0.11% 74 49509 0.13% 75 43060 0.11% 76 41835 0.11% 77 45315 0.12% 78 47777 0.13% 79 53543 0.14% 80 49638 0.13% 81 56598 0.15% 82 54167 0.14% 83 56162 0.15% 84 59715 0.16% 85 64726 0.17% 86 69338 0.18% 87 69438 0.18% 88 70728 0.19% 89 94872 0.25% 90 75854 0.20% 91 79348 0.21% 92 77610 0.20% 93 84374 0.22% 94 91781 0.24% 95 91108 0.24% 96 103587 0.27% 97 102652 0.27% 98 99669 0.26% 99 104756 0.27% 100 105849 0.28% 101 113953 0.30% 102 137052 0.36% 103 123774 0.32% 104 123763 0.32% 105 128726 0.34% 106 135610 0.36% 107 140532 0.37% 108 146895 0.39% 109 173209 0.45% 110 156216 0.41% 111 156121 0.41% 112 211873 0.56% 113 173976 0.46% 114 172787 0.45% 115 178114 0.47% 116 181719 0.48% 117 189062 0.50% 118 197816 0.52% 119 202979 0.53% 120 216485 0.57% 121 219952 0.58% 122 219494 0.58% 123 293135 0.77% 124 267158 0.70% 125 232851 0.61% 126 242785 0.64% 127 256429 0.67% 128 245748 0.64% 129 253706 0.67% 130 251120 0.66% 131 265786 0.70% 132 278936 0.73% 133 300845 0.79% 134 269043 0.71% 135 290167 0.76% 136 275927 0.72% 137 299518 0.79% 138 327133 0.86% 139 292743 0.77% 140 320314 0.84% 141 284450 0.75% 142 297567 0.78% 143 308443 0.81% 144 297714 0.78% 145 305017 0.80% 146 308533 0.81% 147 429869 1.13% 148 804995 2.11% 149 0 0.00% 150 0 0.00% 151 23480611 61.61% criterion=sequence-density sequence-density=0.51 sequence-density-rank=1 fanout-score=2.19 fanout-score-rank=31 prefix-density=0.53 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGT criterion=fanout-score sequence-density=0.04 sequence-density-rank=31 fanout-score=34.85 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=6.8 sequence=GCTCTTGGATGCGTCTTCCCCGAGCTCTTGTCCCGCAACGGTGTCAAGTTCGGCGAGGCTGTATGGTTCAAGGCTGGAGCCCAGATCTTCAGCGAGGGTGGACTTGACTACTTGGGCAACCCAAGCTTGATCCACGCACAAAGCATCTTGGCCATCTGGGCTACACAGGTGGTCTTGATGGGTGCCGTTGAGGGTTACAGAATTGCTGGCGGGCCACTCGGTGAGGTAACTGACCCAATCTACCCAGGTGGAAGCTTCGACCCACTGGGCTTGGCTGACGATCCCGAAGCATTCGCTGAGTTGAAGGTGAAGGAACTCAAGAATGGTAGGTTGGCTATGTTCTCAATGTTCGGATTCTTTGTCCAGGCCATTGTGACCGGAAAGGGACCACTGGAGAACCTGGCTGACCACCTTTCTGACCCAGTAAACAACAACGCCTGGGCATATGCCACAAACTTCGTTCCCGGAAAGTGAGCAACAAAAGAGTTTTTTCTGTGCTGGGACTATTGGC Started job on | Apr 10 11:53:16 Started mapping on | Apr 10 11:53:17 Finished on | Apr 10 11:54:52 Mapping speed, Million of reads per hour | 1706.72 Number of input reads | 45038453 Average input read length | 139 UNIQUE READS: Uniquely mapped reads number | 39934531 Uniquely mapped reads % | 88.67% Average mapped length | 137.44 Number of splices: Total | 17857829 Number of splices: Annotated (sjdb) | 17496547 Number of splices: GT/AG | 17528802 Number of splices: GC/AG | 249413 Number of splices: AT/AC | 10507 Number of splices: Non-canonical | 69107 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.02% Deletion average length | 2.17 Insertion rate per base | 0.01% Insertion average length | 1.97 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1458983 % of reads mapped to multiple loci | 3.24% Number of reads mapped to too many loci | 1871312 % of reads mapped to too many loci | 4.15% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.85% % of reads unmapped: other | 0.09% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3644939 3644939 3644939 N_multimapping 1458983 1458983 1458983 N_noFeature 1739258 2371703 38852460 N_ambiguous 609339 159888 843 UnstrandedReadsAssigned:37585934 PositiveStrandReadsAssigned:37402940 NegativeStrandReadsAssigned:1081228 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=126 echo kmer=121 SRR11462695 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: SRR11462695-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 45,038,453 reads, 38,836,672 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,220 rounds 52401 SRR11462695.ke.tsv 34699 SRR11462695.se.tsv 87100 total ==> SRR11462695.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 1457.47 21.7076 Potri.005G024800.1.v4.1 1035 936 413 12.6113 Potri.004G059700.1.v4.1 961 862 83 2.75206 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 3368 33.8477 Potri.016G087400.1.v4.1 270 171 3997 668.074 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 251 4.28553 Potri.012G127500.1.v4.1 977 878 179 5.827 ==> SRR11462695.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 453 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 279 Potri.001G212900.v4.1 799 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 10 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 50 SRR11462695 completed mapping pipeline successfully