Starting /dee2/code/volunteer_pipeline.sh SRR6322414 current disk space = 1543448317952 free memory = 1595592076 SRR6322414 SRAfilesize 0b298e05e8d0a60449beed7ed2635e2a SRR6322414.sra SRR6322414.sra file validated SRR6322414 is single end SRR6322414 is conventional basespace SRR6322414 read1 length is 50 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6322414_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 50 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.371 33.0 33.0 34.0 31.0 34.0 2 32.52325 33.0 33.0 34.0 31.0 34.0 3 32.52875 33.0 33.0 34.0 31.0 34.0 4 32.397 33.0 33.0 34.0 31.0 34.0 5 32.44725 33.0 33.0 34.0 31.0 34.0 6 35.91625 38.0 36.0 38.0 31.0 38.0 7 36.4005 38.0 37.0 38.0 34.0 38.0 8 36.564 38.0 38.0 38.0 34.0 38.0 9 36.54175 38.0 38.0 38.0 34.0 38.0 10 36.745 38.0 38.0 38.0 34.0 38.0 11 36.647 38.0 38.0 38.0 34.0 38.0 12 36.74175 38.0 38.0 38.0 34.0 38.0 13 36.66 38.0 38.0 38.0 34.0 38.0 14 36.74275 38.0 38.0 38.0 34.0 38.0 15 36.828 38.0 38.0 38.0 35.0 38.0 16 36.7345 38.0 38.0 38.0 35.0 38.0 17 36.77825 38.0 38.0 38.0 35.0 38.0 18 36.6645 38.0 38.0 38.0 34.0 38.0 19 36.6815 38.0 38.0 38.0 34.0 38.0 20 36.6255 38.0 38.0 38.0 34.0 38.0 21 36.6205 38.0 38.0 38.0 34.0 38.0 22 36.7435 38.0 38.0 38.0 34.0 38.0 23 36.73575 38.0 38.0 38.0 34.0 38.0 24 36.71625 38.0 38.0 38.0 34.0 38.0 25 36.77025 38.0 38.0 38.0 34.0 38.0 26 36.76975 38.0 38.0 38.0 34.0 38.0 27 36.57925 38.0 38.0 38.0 34.0 38.0 28 36.63925 38.0 38.0 38.0 34.0 38.0 29 36.677 38.0 38.0 38.0 34.0 38.0 30 36.6065 38.0 38.0 38.0 34.0 38.0 31 36.62925 38.0 38.0 38.0 34.0 38.0 32 36.6885 38.0 38.0 38.0 34.0 38.0 33 36.5395 38.0 38.0 38.0 34.0 38.0 34 36.58025 38.0 38.0 38.0 34.0 38.0 35 36.60275 38.0 38.0 38.0 34.0 38.0 36 36.61425 38.0 38.0 38.0 34.0 38.0 37 36.53575 38.0 38.0 38.0 34.0 38.0 38 36.436 38.0 38.0 38.0 34.0 38.0 39 36.44175 38.0 38.0 38.0 34.0 38.0 40 36.443 38.0 38.0 38.0 34.0 38.0 41 36.5655 38.0 38.0 38.0 34.0 38.0 42 36.44275 38.0 38.0 38.0 34.0 38.0 43 36.403 38.0 38.0 38.0 34.0 38.0 44 36.5175 38.0 38.0 38.0 34.0 38.0 45 36.41675 38.0 38.0 38.0 34.0 38.0 46 36.46125 38.0 38.0 38.0 34.0 38.0 47 36.3705 38.0 38.0 38.0 34.0 38.0 48 36.39425 38.0 38.0 38.0 34.0 38.0 49 36.28175 38.0 38.0 38.0 33.0 38.0 50 36.17225 38.0 38.0 38.0 34.0 38.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10 0.0 1101 11 0.0 1101 12 0.0 1101 13 0.0 1101 14 0.0 1101 15 0.0 1101 16 0.0 1101 17 0.0 1101 18 0.0 1101 19 0.0 1101 20 0.0 1101 21 0.0 1101 22 0.0 1101 23 0.0 1101 24 0.0 1101 25 0.0 1101 26 0.0 1101 27 0.0 1101 28 0.0 1101 29 0.0 1101 30 0.0 1101 31 0.0 1101 32 0.0 1101 33 0.0 1101 34 0.0 1101 35 0.0 1101 36 0.0 1101 37 0.0 1101 38 0.0 1101 39 0.0 1101 40 0.0 1101 41 0.0 1101 42 0.0 1101 43 0.0 1101 44 0.0 1101 45 0.0 1101 46 0.0 1101 47 0.0 1101 48 0.0 1101 49 0.0 1101 50 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 4.0 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 1.0 12 0.0 13 0.0 14 0.0 15 1.0 16 0.0 17 2.0 18 0.0 19 0.0 20 1.0 21 3.0 22 0.0 23 4.0 24 7.0 25 15.0 26 19.0 27 25.0 28 37.0 29 43.0 30 75.0 31 73.0 32 82.0 33 142.0 34 176.0 35 275.0 36 532.0 37 2483.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.25560312263914 14.656257869554267 7.831780407957694 42.2563585998489 2 25.25 20.825 33.95 19.975 3 22.125 25.025 22.75 30.099999999999998 4 26.974999999999998 31.225 18.7 23.1 5 26.400000000000002 31.974999999999998 20.825 20.8 6 20.200000000000003 30.7 23.5 25.6 7 19.05 14.7 39.2 27.05 8 20.65 19.125 26.8 33.425 9 20.575 18.875 29.75 30.8 10 23.849999999999998 32.25 19.75 24.15 11 28.725 20.225 17.025000000000002 34.025 12 26.85 17.75 23.474999999999998 31.924999999999997 13 23.225 23.325000000000003 24.224999999999998 29.225 14 24.9 23.95 26.075 25.074999999999996 15 24.349999999999998 24.25 23.775 27.625 16 25.374999999999996 22.8 23.200000000000003 28.625 17 23.325000000000003 24.775 24.375 27.525 18 23.400000000000002 24.75 26.075 25.775 19 25.1 23.400000000000002 24.175 27.325 20 24.75 24.9 25.3 25.05 21 23.75 23.849999999999998 25.3 27.1 22 24.525 25.224999999999998 24.025 26.224999999999998 23 23.075000000000003 26.075 24.45 26.400000000000002 24 23.974999999999998 24.05 25.775 26.200000000000003 25 23.799999999999997 23.625 23.5 29.075 26 23.825 23.599999999999998 24.725 27.85 27 23.95 24.0 25.324999999999996 26.724999999999998 28 23.825 24.65 23.95 27.575 29 24.025 24.575 25.3 26.1 30 24.2 22.225 26.125 27.450000000000003 31 24.0 23.375 24.875 27.750000000000004 32 24.875 25.25 24.325 25.55 33 22.775000000000002 24.95 24.675 27.6 34 24.825 25.0 22.975 27.200000000000003 35 23.125 25.45 25.074999999999996 26.35 36 23.400000000000002 25.025 24.95 26.625 37 25.174999999999997 23.05 24.375 27.400000000000002 38 23.400000000000002 24.95 25.05 26.6 39 23.974999999999998 23.075000000000003 25.8 27.150000000000002 40 24.7 23.45 25.224999999999998 26.625 41 24.0 25.4 24.85 25.75 42 24.125 22.75 25.75 27.375 43 23.599999999999998 24.3 24.349999999999998 27.750000000000004 44 23.525 25.474999999999998 24.825 26.174999999999997 45 23.200000000000003 23.875 26.5 26.424999999999997 46 24.0 23.625 25.424999999999997 26.950000000000003 47 23.525 24.325 25.1 27.05 48 23.275000000000002 23.775 25.15 27.800000000000004 49 24.925 22.725 24.55 27.800000000000004 50 24.325 22.95 24.275 28.449999999999996 >>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 0.5 16 1.0 17 0.5 18 0.0 19 0.0 20 0.0 21 2.5 22 5.0 23 2.5 24 0.0 25 4.5 26 9.0 27 12.0 28 15.0 29 19.5 30 24.0 31 39.5 32 55.0 33 65.0 34 75.0 35 98.5 36 122.0 37 125.0 38 128.0 39 164.0 40 200.0 41 223.5 42 247.0 43 256.5 44 266.0 45 266.5 46 267.0 47 279.0 48 291.0 49 297.5 50 304.0 51 304.0 52 304.0 53 300.0 54 296.0 55 273.0 56 250.0 57 232.0 58 214.0 59 195.5 60 177.0 61 166.5 62 156.0 63 141.5 64 127.0 65 116.0 66 105.0 67 104.5 68 104.0 69 86.0 70 68.0 71 64.0 72 60.0 73 58.5 74 57.0 75 39.0 76 21.0 77 25.5 78 30.0 79 22.0 80 14.0 81 9.0 82 4.0 83 4.0 84 4.0 85 2.0 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 pass #Base N-Count 1 0.7250000000000001 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 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.0 34 0.0 35 0.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 50 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.675 #Duplication Level Percentage of deduplicated Percentage of total 1 96.07686148919136 90.0 2 2.695489725113424 5.050000000000001 3 0.6138243928476115 1.725 4 0.373632239124633 1.4000000000000001 5 0.10675206832132372 0.5 6 0.02668801708033093 0.15 7 0.02668801708033093 0.17500000000000002 8 0.02668801708033093 0.2 9 0.0 0.0 >10 0.05337603416066186 0.8 >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 GGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTT 18 0.44999999999999996 No Hit CAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCT 14 0.35000000000000003 No Hit GTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGAC 8 0.2 No Hit GCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTC 7 0.17500000000000002 No Hit GTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCAAAGACTTTGATTTC 6 0.15 No Hit GTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATT 5 0.125 No Hit CTTCGAGCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAA 5 0.125 No Hit GTGCAGTCGGCGCACTTGGCCAAGCCGACCACGACGGACGCCGCCTCGGC 5 0.125 No Hit CAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATC 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #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 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384719 spots for SRR6322414.sra Written 1384719 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra Read 1384707 spots for SRR6322414.sra Written 1384707 spots for SRR6322414.sra SRR ids: ['SRR6322414.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_v0sca4op SRR6322414.sra spots: 27694152 blocks: [[1, 1384707], [1384708, 2769414], [2769415, 4154121], [4154122, 5538828], [5538829, 6923535], [6923536, 8308242], [8308243, 9692949], [9692950, 11077656], [11077657, 12462363], [12462364, 13847070], [13847071, 15231777], [15231778, 16616484], [16616485, 18001191], [18001192, 19385898], [19385899, 20770605], [20770606, 22155312], [22155313, 23540019], [23540020, 24924726], [24924727, 26309433], [26309434, 27694152]] SRR6322414 file size 4816396 SRR6322414 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 SRR6322414 SRR6322414_1.fastq Input file: SRR6322414_1.fastq trimmed: SRR6322414-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 Sat Dec 7 10:34:01 2024 >> started Sat Dec 7 10:34:18 2024 >> done (17.358s) 27694152 reads processed; of these: 7732 ( 0.03%) short reads filtered out after trimming by size control 25513 ( 0.09%) empty reads filtered out after trimming by size control 27660907 (99.88%) reads available; of these: 430227 ( 1.56%) trimmed reads available after processing 27230680 (98.44%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 388 0.00% 19 400 0.00% 20 459 0.00% 21 587 0.00% 22 638 0.00% 23 775 0.00% 24 984 0.00% 25 1230 0.00% 26 1283 0.00% 27 1309 0.00% 28 1401 0.01% 29 1599 0.01% 30 1628 0.01% 31 1963 0.01% 32 2178 0.01% 33 2569 0.01% 34 2896 0.01% 35 3335 0.01% 36 3947 0.01% 37 4647 0.02% 38 5643 0.02% 39 6506 0.02% 40 8130 0.03% 41 9888 0.04% 42 12925 0.05% 43 15744 0.06% 44 19780 0.07% 45 27158 0.10% 46 38077 0.14% 47 51847 0.19% 48 81972 0.30% 49 118341 0.43% 50 27230680 98.44% 27660907 reads passed initial QC criterion=sequence-density sequence-density=0.08 sequence-density-rank=1 fanout-score=2.30 fanout-score-rank=22 prefix-density=0.08 prefix-fanout=2.3 sequence=CCTCCTTGTCCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=28.65 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=1.0 sequence=GGCTGCTGGAGGGTAGGAGCGTCTGCTGGCATCGGAGAAGGTGAAGAAGAGAAGGTTCAGGGCCAGAAGCGCAACGATCAGTTCCACTTTCT Started job on | Dec 07 10:34:35 Started mapping on | Dec 07 10:34:35 Finished on | Dec 07 10:35:12 Mapping speed, Million of reads per hour | 2691.33 Number of input reads | 27660907 Average input read length | 49 UNIQUE READS: Uniquely mapped reads number | 21287988 Uniquely mapped reads % | 76.96% Average mapped length | 49.84 Number of splices: Total | 3256158 Number of splices: Annotated (sjdb) | 3141540 Number of splices: GT/AG | 3213073 Number of splices: GC/AG | 36557 Number of splices: AT/AC | 1948 Number of splices: Non-canonical | 4580 Mismatch rate per base, % | 0.16% Deletion rate per base | 0.01% Deletion average length | 1.62 Insertion rate per base | 0.00% Insertion average length | 1.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1179501 % of reads mapped to multiple loci | 4.26% Number of reads mapped to too many loci | 5002999 % of reads mapped to too many loci | 18.09% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.47% % of reads unmapped: other | 0.22% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5193418 5193418 5193418 N_multimapping 1179501 1179501 1179501 N_noFeature 832228 20490406 992238 N_ambiguous 668397 1345 31329 UnstrandedReadsAssigned:19787363 PositiveStrandReadsAssigned:796237 NegativeStrandReadsAssigned:20264421 Dataset is classified negative stranded MeadianReadLen=50 20thPercentileLength=50 echo kmer=45 SRR6322414 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: SRR6322414-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 27,660,907 reads, 20,564,021 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,182 rounds 52973 SRR6322414.ke.tsv 35125 SRR6322414.se.tsv 88098 total ==> SRR6322414.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 125.864 11.17 PNS24247 1044 945 9.11791 0.716708 PNS24249 1928 1829 66.7283 2.71003 PNS24246 1044 945 9.11791 0.716708 PNS24248 1044 945 9.11791 0.716708 PNS24244 1471 1372 153.054 8.28647 PNS24243 293 194 0 0 KQK14069 1603 1504 1274 62.9218 KQK14071 474 375 415.755 82.354 ==> SRR6322414.se.tsv <== BRADI_1g14170v3 1878 BRADI_1g53295v3 111 BRADI_1g59795v3 309 BRADI_1g07683v3 0 BRADI_1g00485v3 9 BRADI_1g20270v3 1481 BRADI_1g74790v3 105 BRADI_1g09890v3 23 BRADI_1g77505v3 330 BRADI_1g48960v3 2 SRR6322414 completed mapping pipeline successfully