Starting /dee2/code/volunteer_pipeline.sh SRR522511 current disk space = 1543206989824 free memory = 1600973104 SRR522511 SRAfilesize 525b70796307ce550a8f50623a2e4037 SRR522511.sra SRR522511.sra file validated SRR522511 is single end SRR522511 is conventional basespace SRR522511 read1 length is 36 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR522511_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 36 %GC 45 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.635 35.0 29.0 38.0 2.0 39.0 2 29.8995 33.0 27.0 38.0 11.0 39.0 3 30.09225 35.0 27.0 38.0 11.0 39.0 4 30.1695 35.0 27.0 38.0 10.0 39.0 5 29.946 35.0 27.0 38.0 10.0 39.0 6 30.437 35.0 28.0 38.0 12.0 39.0 7 30.559 35.0 28.0 38.0 14.0 39.0 8 29.9135 33.0 27.0 38.0 12.0 39.0 9 30.2965 34.0 28.0 38.0 13.0 39.0 10 30.40325 35.0 28.0 38.0 13.0 39.0 11 30.73425 35.0 28.0 38.0 14.0 39.0 12 30.65375 35.0 28.0 38.0 14.0 39.0 13 30.40075 35.0 28.0 38.0 12.0 39.0 14 30.388 35.0 28.0 38.0 12.0 39.0 15 30.079 33.0 28.0 38.0 11.0 39.0 16 30.34825 35.0 28.0 38.0 2.0 39.0 17 29.93975 34.0 28.0 38.0 2.0 39.0 18 29.9305 34.0 28.0 38.0 2.0 39.0 19 29.74175 34.0 28.0 38.0 2.0 39.0 20 29.56875 34.0 28.0 38.0 2.0 39.0 21 29.2395 35.0 28.0 38.0 2.0 39.0 22 28.8385 34.0 27.0 38.0 2.0 39.0 23 28.67925 34.0 27.0 38.0 2.0 39.0 24 27.91325 33.0 26.0 38.0 2.0 39.0 25 26.7655 33.0 2.0 38.0 2.0 39.0 26 17.07525 2.0 2.0 33.0 2.0 36.0 27 16.52775 2.0 2.0 33.0 2.0 36.0 28 15.92 2.0 2.0 33.0 2.0 36.0 29 14.86675 2.0 2.0 33.0 2.0 36.0 30 2.29325 2.0 2.0 2.0 2.0 2.0 31 6.55425 2.0 2.0 2.0 2.0 28.0 32 5.9815 2.0 2.0 2.0 2.0 30.0 33 4.93575 2.0 2.0 2.0 2.0 23.0 34 2.18925 2.0 2.0 2.0 2.0 2.0 35 4.37725 2.0 2.0 2.0 2.0 2.0 36 2.96875 2.0 2.0 2.0 2.0 2.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1 1 0.0 1 2 0.0 1 3 0.0 1 4 0.0 1 5 0.0 1 6 0.0 1 7 0.0 1 8 0.0 1 9 0.0 1 10 0.0 1 11 0.0 1 12 0.0 1 13 0.0 1 14 0.0 1 15 0.0 1 16 0.0 1 17 0.0 1 18 0.0 1 19 0.0 1 20 0.0 1 21 0.0 1 22 0.0 1 23 0.0 1 24 0.0 1 25 0.0 1 26 0.0 1 27 0.0 1 28 0.0 1 29 0.0 1 30 0.0 1 31 0.0 1 32 0.0 1 33 0.0 1 34 0.0 1 35 0.0 1 36 0.0 >>END_MODULE >>Per sequence quality scores fail #Quality Count 2 304.0 3 3.0 4 3.0 5 7.0 6 7.0 7 3.0 8 14.0 9 16.0 10 17.0 11 15.0 12 18.0 13 34.0 14 48.0 15 60.0 16 86.0 17 98.0 18 116.0 19 128.0 20 171.0 21 190.0 22 199.0 23 216.0 24 260.0 25 253.0 26 212.0 27 197.0 28 236.0 29 271.0 30 281.0 31 236.0 32 124.0 33 89.0 34 61.0 35 26.0 36 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 17.885730057963016 35.41264145735578 31.76925200110406 14.932376483577144 2 24.175 30.925000000000004 32.95 11.95 3 27.700000000000003 28.599999999999998 23.200000000000003 20.5 4 33.85 28.749999999999996 19.1 18.3 5 27.975 34.425 20.549999999999997 17.05 6 28.4 33.825 21.15 16.625 7 28.975 26.974999999999998 27.875 16.175 8 21.075 28.299999999999997 33.25 17.375 9 22.925 28.799999999999997 31.075000000000003 17.2 10 34.9 26.05 21.275 17.775 11 22.375 33.074999999999996 23.674999999999997 20.875 12 26.575 26.35 29.549999999999997 17.525 13 30.7 25.374999999999996 17.375 26.55 14 26.575 31.624999999999996 22.975 18.825 15 26.0 31.5 25.75 16.75 16 31.374999999999996 29.125 23.125 16.375 17 22.55 30.275000000000002 24.725 22.45 18 24.675 26.85 25.674999999999997 22.8 19 26.125 33.800000000000004 18.525 21.55 20 32.550000000000004 29.65 24.025 13.775 21 24.85 29.125 25.575 20.45 22 25.5 39.525 17.65 17.325 23 33.074999999999996 23.849999999999998 28.549999999999997 14.524999999999999 24 17.599999999999998 23.175 28.025 31.2 25 7.675 49.35 23.45 19.525000000000002 26 15.475 10.75 51.449999999999996 22.325 27 14.35 11.5 23.95 50.2 28 8.4 17.349999999999998 57.45 16.8 29 14.2 15.55 22.025 48.225 30 49.122807017543856 12.280701754385964 28.07017543859649 10.526315789473683 31 15.925 13.3 51.324999999999996 19.45 32 10.875 45.875 18.075 25.174999999999997 33 19.254813703425857 9.077269317329332 53.23830957739435 18.42960740185046 34 55.81395348837209 6.976744186046512 11.627906976744185 25.581395348837212 35 10.8 6.35 21.5 61.35 36 14.524999999999999 5.1499999999999995 23.05 57.275 >>END_MODULE >>Per sequence GC content fail #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 0.0 19 0.0 20 0.0 21 2.5 22 5.0 23 5.0 24 11.0 25 17.0 26 35.0 27 53.0 28 53.0 29 72.0 30 91.0 31 91.0 32 186.5 33 282.0 34 282.0 35 344.0 36 406.0 37 406.0 38 462.0 39 518.0 40 550.5 41 583.0 42 583.0 43 545.0 44 507.0 45 507.0 46 555.0 47 603.0 48 603.0 49 581.0 50 559.0 51 389.0 52 219.0 53 219.0 54 154.0 55 89.0 56 89.0 57 61.5 58 34.0 59 34.0 60 25.5 61 17.0 62 17.0 63 11.5 64 6.0 65 6.0 66 6.0 67 6.0 68 5.5 69 5.0 70 5.0 71 2.5 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 9.425 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 98.575 31 0.0 32 0.0 33 0.025 34 98.925 35 0.0 36 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 36 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 79.325 #Duplication Level Percentage of deduplicated Percentage of total 1 95.27261266939804 75.575 2 2.4897573274503624 3.95 3 0.6618342262842736 1.575 4 0.3781909864481563 1.2 5 0.34667507091080996 1.375 6 0.12606366214938544 0.6 7 0.0 0.0 8 0.06303183107469272 0.4 9 0.03151591553734636 0.22499999999999998 >10 0.5672864796722344 7.875 >50 0.0 0.0 >100 0.06303183107469272 7.225 >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 TACCTGGTTGATCCTGCCAGTAGTCGTATNCCGNCT 183 4.575 No Hit TTTGGATTGAAGGGAGCTCTGATCTCGTANGCCNTC 106 2.65 No Hit ATCTCGTATGCCGTCTTCTGCTTGAAAAANAAANAA 50 1.25 Illumina Single End Adapter 1 (95% over 24bp) CTAACGAACGAACGATTTGAACATCTCGTNTGCNGT 30 0.75 No Hit GGGGACGTAGCTCATAATCTCGTATGCCGNCTTNTG 24 0.6 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACNCGTNTG 23 0.575 No Hit GGGGATGTAGCTCAAAATCTCGTATGCCGNCTTNTG 20 0.5 No Hit TGACAGAAGAGAGTGAGCACATCTCGTATNCCGNCT 18 0.44999999999999996 No Hit NTTGGATTGAAGGGAGCTCTGATCTCGTANGCCNTC 18 0.44999999999999996 No Hit NACCTGGTTGATCCTGCCAGTAGTCGTATNCCGNCT 18 0.44999999999999996 No Hit TAACGAACGAACGATTTGAACATCTCGTANGCCNTC 14 0.35000000000000003 No Hit GGGCCTGTAGCTCAGAGGAATCTCGTATGNCGTNTT 13 0.325 No Hit TGGGCCTGTAGCTCAGAGGAATCTCGTATNCCGNCT 13 0.325 No Hit TAGATATTTCAGGTTGTGTGGAATCTCGTNTGCNGT 12 0.3 No Hit TTGACAGAAGAGAGTGAGCACATCTCGTANGCCNTC 11 0.27499999999999997 No Hit TAGTAAATCGTAGTGGACATAAGCATCTCNTATNCC 11 0.27499999999999997 No Hit GGGGATGTAGCTCAGAATCTCGTATGCCGNCTTNTG 10 0.25 RNA PCR Primer, Index 40 (95% over 23bp) CCTAACGAACGAACGATTTGAACATCTCGNATGNCG 10 0.25 No Hit CACGACTCTCGGCAACGGATATCTCGGCTNTCGNAT 10 0.25 No Hit AAGGAAGCTATAAGATCTCGTATGCCGTCNTCTNCT 10 0.25 RNA PCR Primer, Index 28 (95% over 22bp) GACACGACTCTCGGCAACGGATATCTCGTNTGCNGT 9 0.22499999999999998 No Hit AACGAACGATTTGAACATCTCGTATGCCGNCTTNTG 8 0.2 No Hit GTATGCCGTCTTCTGCTTGAAAAAAAAAANAAANAA 8 0.2 No Hit AGGTCATGCTGGAGTTTCATCATCTCGTANGCCNTC 6 0.15 No Hit ATCTCGTATGCCGTCTTCTGCTTGAAAAANAAANAT 6 0.15 Illumina Single End Adapter 1 (95% over 24bp) AAGGAAGCTATAAGTATCTCGTATGCCGTNTTCNGC 6 0.15 No Hit GTGCAGTGATTATAAAAACATTCCTCGTANGCCNTC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATNATCNCG 5 0.125 No Hit NTAACGAACGAACGATTTGAACATCTCGTNTGCNGT 5 0.125 No Hit GCATCCTAACGAACGAACGATTTGAACATNTCGNAT 5 0.125 No Hit NTATGCCGTCTTCTGCTTGAAAAAAAAAANAAANAA 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCGGNTCTNGT 5 0.125 No Hit TTCATGGACGTTGATAAGATCCTTCATCTNGTANGC 5 0.125 No Hit GGCGGATGTAGCCAAGTGGAATCTCGTATNCCGNCT 5 0.125 No Hit CAACATGATGGCCTCAATTCTGAACATCTNGTANGC 5 0.125 No Hit CGAACGATTTGAACATCTCGTATGCCGTCNTCTNCT 5 0.125 RNA PCR Primer, Index 39 (95% over 21bp) GGACGGTGAAGATTGATATTTGGTCTCGTNTGCNGT 5 0.125 No Hit CACGACTCTCGGCAACGGATATCTCGTATNCCGNCT 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 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTATGCC 40 0.0 230.875 30 CGTATGC 45 0.0 205.22221 29 TCGTATG 45 0.0 205.22221 28 CTCGTAT 65 0.0 142.07692 27 TCTCGTA 90 0.0 102.61111 26 ATCTCGT 100 0.0 92.35 25 TACCTGG 25 9.397E-4 25.30137 1 ATCCTGC 25 0.0016321454 23.087502 11 GTTGATC 25 0.0016321454 23.087502 7 TGGTTGA 25 0.0016321454 23.087502 5 GGTTGAT 25 0.0016321454 23.087502 6 AGTAGTC 25 0.0016321454 23.087502 19 CCAGTAG 25 0.0016321454 23.087502 17 CCTGCCA 25 0.0016321454 23.087502 13 GTCGTAT 25 0.0016321454 23.087502 23 CAGTAGT 25 0.0016321454 23.087502 18 TGATCCT 25 0.0016321454 23.087502 9 TAGTCGT 25 0.0016321454 23.087502 21 GCCAGTA 25 0.0016321454 23.087502 16 CTGGTTG 25 0.0016321454 23.087502 4 >>END_MODULE Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Read 1259417 spots for SRR522511.sra Written 1259417 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra Read 1259416 spots for SRR522511.sra Written 1259416 spots for SRR522511.sra SRR ids: ['SRR522511.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9j4df7w4 SRR522511.sra spots: 25188321 blocks: [[1, 1259416], [1259417, 2518832], [2518833, 3778248], [3778249, 5037664], [5037665, 6297080], [6297081, 7556496], [7556497, 8815912], [8815913, 10075328], [10075329, 11334744], [11334745, 12594160], [12594161, 13853576], [13853577, 15112992], [15112993, 16372408], [16372409, 17631824], [17631825, 18891240], [18891241, 20150656], [20150657, 21410072], [21410073, 22669488], [22669489, 23928904], [23928905, 25188321]] SRR522511 file size 3535975 SRR522511 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 SRR522511 SRR522511_1.fastq Input file: SRR522511_1.fastq trimmed: SRR522511-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 11:11:46 2024 >> started Sat Dec 7 11:11:57 2024 >> done (11.492s) 25188321 reads processed; of these: 233524 ( 0.93%) short reads filtered out after trimming by size control 89866 ( 0.36%) empty reads filtered out after trimming by size control 24864931 (98.72%) reads available; of these: 2729854 (10.98%) trimmed reads available after processing 22135077 (89.02%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 40486 0.16% 19 66609 0.27% 20 113411 0.46% 21 34052 0.14% 22 61191 0.25% 23 105651 0.42% 24 218561 0.88% 25 324996 1.31% 26 52799 0.21% 27 94237 0.38% 28 109118 0.44% 29 184689 0.74% 30 449078 1.81% 31 99017 0.40% 32 82553 0.33% 33 161269 0.65% 34 229703 0.92% 35 302434 1.22% 36 22135077 89.02% 24864931 reads passed initial QC criterion=sequence-density sequence-density=30.78 sequence-density-rank=1 fanout-score=74.85 fanout-score-rank=1 prefix-density=70.38 prefix-fanout=32.7 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAACAAAC criterion=fanout-score sequence-density=30.78 sequence-density-rank=1 fanout-score=74.85 fanout-score-rank=1 prefix-density=70.38 prefix-fanout=32.7 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAACAAAC 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 ATCTCGTATGCCGTCTTCTGCTTGAAAAACAAAC -o SRR522511 - Input file: STDIN trimmed: SRR522511-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): ATCTCGTATGCCGTCTTCTGCTTGAAAAACAAAC -- 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 Sat Dec 7 11:12:23 2024 >> started Sat Dec 7 11:12:47 2024 >> done (23.502s) 23260742 reads processed; of these: 1604626 ( 6.90%) short reads filtered out after trimming by size control 615659 ( 2.65%) empty reads filtered out after trimming by size control 21040457 (90.45%) reads available; of these: 16740918 (79.57%) trimmed reads available after processing 4299539 (20.43%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 304491 1.45% 19 469549 2.23% 20 807484 3.84% 21 2278249 10.83% 22 768253 3.65% 23 1523634 7.24% 24 9095114 43.23% 25 878775 4.18% 26 389540 1.85% 27 323252 1.54% 28 224961 1.07% 29 259477 1.23% 30 284644 1.35% 31 116243 0.55% 32 76378 0.36% 33 82489 0.39% 34 38978 0.19% 35 50817 0.24% 36 3068129 14.58% criterion=sequence-density sequence-density=6.46 sequence-density-rank=1 fanout-score=0.00 fanout-score-rank=13 prefix-density=0.00 prefix-fanout=1.0 sequence=TACCTGGTTGATCCTGCCAGTAGTCGTATGCCGTCTTCTGCTTGAAAAA criterion=fanout-score sequence-density=0.76 sequence-density-rank=4 fanout-score=67.42 fanout-score-rank=1 prefix-density=1.22 prefix-fanout=42.1 sequence=ATCGTATGCCGT Started job on | Dec 07 11:13:04 Started mapping on | Dec 07 11:13:04 Finished on | Dec 07 11:13:52 Mapping speed, Million of reads per hour | 1698.35 Number of input reads | 22644646 Average input read length | 26 UNIQUE READS: Uniquely mapped reads number | 12631504 Uniquely mapped reads % | 55.78% Average mapped length | 25.15 Number of splices: Total | 144353 Number of splices: Annotated (sjdb) | 14963 Number of splices: GT/AG | 131338 Number of splices: GC/AG | 8605 Number of splices: AT/AC | 41 Number of splices: Non-canonical | 4369 Mismatch rate per base, % | 1.12% Deletion rate per base | 0.00% Deletion average length | 1.24 Insertion rate per base | 0.00% Insertion average length | 1.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 5258067 % of reads mapped to multiple loci | 23.22% Number of reads mapped to too many loci | 2859496 % of reads mapped to too many loci | 12.63% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.33% % of reads unmapped: other | 2.04% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4755075 4755075 4755075 N_multimapping 5258067 5258067 5258067 N_noFeature 8480646 9065796 11993456 N_ambiguous 124552 69469 3378 UnstrandedReadsAssigned:4026306 PositiveStrandReadsAssigned:3496239 NegativeStrandReadsAssigned:634670 Dataset is classified positive stranded MeadianReadLen=24 20thPercentileLength=22 echo kmer=19 SRR522511 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=19 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 19 [index] number of targets: 52,972 [index] number of k-mers: 65,492,969 [index] number of equivalence classes: 320,172 [quant] running in single-end mode [quant] will process file 1: SRR522511-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22,644,646 reads, 4,392,194 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,184 rounds 52973 SRR522511.ke.tsv 35125 SRR522511.se.tsv 88098 total ==> SRR522511.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0 0 PNS24247 1044 945 0 0 PNS24249 1928 1829 0 0 PNS24246 1044 945 0 0 PNS24248 1044 945 0 0 PNS24244 1471 1372 8 0.921272 PNS24243 293 194 2 1.62885 KQK14069 1603 1504 8 0.840416 KQK14071 474 375 0 0 ==> SRR522511.se.tsv <== BRADI_1g14170v3 8 BRADI_1g53295v3 5 BRADI_1g59795v3 0 BRADI_1g07683v3 0 BRADI_1g00485v3 5 BRADI_1g20270v3 67 BRADI_1g74790v3 72 BRADI_1g09890v3 3 BRADI_1g77505v3 3 BRADI_1g48960v3 0 SRR522511 completed mapping pipeline successfully