Starting /dee2/code/volunteer_pipeline.sh SRR522513 current disk space = 1543200124928 free memory = 1597639948 SRR522513 SRAfilesize c80d82f11fc07fceffb177e9114f6e46 SRR522513.sra SRR522513.sra file validated SRR522513 is single end SRR522513 is conventional basespace SRR522513 read1 length is 36 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR522513_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 46 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.2365 35.0 29.0 38.0 2.0 39.0 2 30.081 35.0 27.0 38.0 10.0 39.0 3 29.97775 35.0 27.0 38.0 9.0 39.0 4 30.08025 35.0 27.0 38.0 9.0 39.0 5 30.0775 35.0 27.0 38.0 9.0 39.0 6 30.6085 35.0 28.0 38.0 12.0 39.0 7 30.6255 35.0 28.0 38.0 13.0 39.0 8 30.09225 35.0 27.0 38.0 11.0 39.0 9 30.47025 35.0 27.0 38.0 12.0 39.0 10 30.33775 35.0 27.0 38.0 12.0 39.0 11 31.2645 35.0 29.0 38.0 18.0 39.0 12 31.1445 35.0 29.0 38.0 18.0 39.0 13 31.2385 35.0 29.0 38.0 18.0 39.0 14 31.06975 35.0 29.0 38.0 18.0 39.0 15 30.9965 35.0 28.0 38.0 18.0 39.0 16 31.17875 35.0 29.0 38.0 18.0 39.0 17 30.91375 35.0 28.0 38.0 18.0 39.0 18 30.9185 35.0 28.0 38.0 17.0 39.0 19 30.8335 35.0 28.0 38.0 18.0 39.0 20 30.66025 34.0 28.0 38.0 17.0 39.0 21 31.0985 35.0 29.0 38.0 17.0 39.0 22 30.8235 35.0 28.0 38.0 16.0 39.0 23 30.708 35.0 28.0 38.0 14.0 39.0 24 30.6325 35.0 28.0 38.0 16.0 39.0 25 30.3775 33.0 29.0 38.0 14.0 39.0 26 30.297 35.0 29.0 38.0 2.0 39.0 27 29.93175 35.0 27.0 38.0 2.0 39.0 28 29.67325 35.0 27.0 38.0 2.0 39.0 29 30.098 35.0 28.0 38.0 2.0 39.0 30 29.3315 35.0 27.0 38.0 2.0 39.0 31 29.91475 35.0 28.0 38.0 2.0 39.0 32 29.81125 35.0 28.0 38.0 2.0 39.0 33 29.56125 35.0 28.0 38.0 2.0 39.0 34 29.85175 35.0 29.0 38.0 2.0 39.0 35 29.7485 35.0 29.0 38.0 2.0 39.0 36 29.73575 35.0 29.0 38.0 2.0 39.0 >>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 pass #Quality Count 2 247.0 3 1.0 4 0.0 5 1.0 6 3.0 7 1.0 8 3.0 9 4.0 10 5.0 11 3.0 12 6.0 13 12.0 14 10.0 15 10.0 16 14.0 17 18.0 18 28.0 19 43.0 20 60.0 21 56.0 22 59.0 23 68.0 24 71.0 25 85.0 26 86.0 27 125.0 28 137.0 29 154.0 30 186.0 31 198.0 32 207.0 33 245.0 34 280.0 35 327.0 36 392.0 37 409.0 38 270.0 39 176.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 14.554794520547945 36.27283105022831 31.84931506849315 17.323059360730593 2 20.7 32.175 34.449999999999996 12.675 3 28.599999999999998 26.6 26.950000000000003 17.849999999999998 4 33.550000000000004 29.15 20.974999999999998 16.325 5 31.25 32.625 20.575 15.55 6 27.725 34.5 22.175 15.6 7 27.450000000000003 27.500000000000004 29.799999999999997 15.25 8 21.875 28.449999999999996 33.5 16.175 9 26.325 27.175 29.75 16.75 10 35.8 26.325 22.05 15.825 11 22.875 33.125 23.7 20.3 12 27.775 27.975 25.674999999999997 18.575 13 32.125 26.1 19.225 22.55 14 26.625 30.775000000000002 25.4 17.2 15 24.575 32.074999999999996 25.8 17.549999999999997 16 32.12409306980235 28.946710032524393 24.96872654490868 13.960470352764572 17 23.150000000000002 31.525 24.9 20.424999999999997 18 25.1 28.575 26.5 19.825 19 25.775 33.0 20.275000000000002 20.95 20 32.05 30.45 24.375 13.125 21 27.175 28.825 23.175 20.825 22 28.000000000000004 39.35 15.275 17.375 23 35.75 23.849999999999998 28.349999999999998 12.049999999999999 24 19.0 23.549999999999997 23.575 33.875 25 5.075 57.425000000000004 22.925 14.575 26 12.475 9.9 56.675 20.95 27 14.025000000000002 10.525 19.75 55.7 28 7.074999999999999 14.899999999999999 62.5 15.525 29 13.206603301650826 15.907953976988495 17.858929464732366 53.02651325662831 30 55.716787590693016 10.307730798098575 24.843632724543408 9.131848886664999 31 14.98623967975982 13.41005754315737 56.99274455841882 14.610958218663997 32 8.98173630222667 52.464348261195894 17.28796597448086 21.26594946209657 33 16.400000000000002 7.7 57.85 18.05 34 60.25 6.45 15.35 17.95 35 9.7024256064016 5.7514378594648665 19.679919979995 64.86621655413853 36 14.000000000000002 4.25 17.925 63.824999999999996 >>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 0.5 8 1.0 9 1.0 10 0.5 11 0.0 12 0.0 13 0.5 14 1.0 15 0.5 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.5 22 1.0 23 1.0 24 1.5 25 2.0 26 11.5 27 21.0 28 21.0 29 30.0 30 39.0 31 39.0 32 81.5 33 124.0 34 124.0 35 136.5 36 149.0 37 149.0 38 250.5 39 352.0 40 424.5 41 497.0 42 497.0 43 561.5 44 626.0 45 626.0 46 593.0 47 560.0 48 560.0 49 624.5 50 689.0 51 612.5 52 536.0 53 536.0 54 366.5 55 197.0 56 197.0 57 154.0 58 111.0 59 111.0 60 84.0 61 57.0 62 57.0 63 40.0 64 23.0 65 14.5 66 6.0 67 6.0 68 6.0 69 6.0 70 6.0 71 4.0 72 2.0 73 2.0 74 1.0 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 warn #Base N-Count 1 12.4 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 0.075 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 0.05 30 0.075 31 0.075 32 0.075 33 0.0 34 0.0 35 0.025 36 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 36 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.6 #Duplication Level Percentage of deduplicated Percentage of total 1 95.30871670702179 78.725 2 2.754237288135593 4.55 3 0.8777239709443099 2.175 4 0.24213075060532688 0.8 5 0.18159806295399517 0.75 6 0.1513317191283293 0.75 7 0.03026634382566586 0.17500000000000002 8 0.06053268765133172 0.4 9 0.06053268765133172 0.44999999999999996 >10 0.2723970944309927 4.7 >50 0.0 0.0 >100 0.06053268765133172 6.525 >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 TTTGGATTGAAGGGAGCTCTGATCTCGTATGCCGTC 133 3.325 No Hit TACCTGGTTGATCCTGCCAGTAGTCGTATGCCGTCT 128 3.2 No Hit ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAA 48 1.2 Illumina Single End Adapter 1 (95% over 24bp) GGGGATGTAGCTCAAAATCTCGTATGCCGTCTTCTG 24 0.6 RNA PCR Primer, Index 40 (96% over 26bp) CTAACGAACGAACGATTTGAACATCTCGTATGCCGT 22 0.5499999999999999 No Hit GGGGACGTAGCTCATAATCTCGTATGCCGTCTTCTG 22 0.5499999999999999 RNA PCR Primer, Index 40 (96% over 26bp) NTTGGATTGAAGGGAGCTCTGATCTCGTATGCCGTC 20 0.5 No Hit NACCTGGTTGATCCTGCCAGTAGTCGTATGCCGTCT 19 0.475 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATATCTCGT 13 0.325 No Hit GGGGATGTAGCTCAGAATCTCGTATGCCGTCTTCTG 10 0.25 RNA PCR Primer, Index 40 (100% over 26bp) TAGATATTTCAGGTTGTGTGGAATCTCGTATGCCGT 10 0.25 No Hit TAGTAAATCGTAGTGGACATAAGCATCTCGTATGCC 9 0.22499999999999998 No Hit TGGGCCTGTAGCTCAGAGGAATCTCGTATGCCGTCT 9 0.22499999999999998 No Hit AGGGCTATAGCTCAGTTCGGTAGAGCAACTCGTATG 8 0.2 No Hit NTCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAAAA 8 0.2 Illumina Paired End PCR Primer 2 (95% over 24bp) CGACACGACTCTCGGCAACGGATATCATCTCGTATG 7 0.17500000000000002 No Hit TGGAACAATGTAGGCAAGGGAAGTCGGATCTCGTAT 6 0.15 No Hit TGACAGAAGAGAGTGAGCACATCTCGTATGCCGTCT 6 0.15 No Hit TTGACAGAAGAGAGTGAGCACATCTCGTATGCCGTC 6 0.15 No Hit ATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAAGCC 6 0.15 Illumina Single End Adapter 1 (95% over 24bp) TAACGAACGAACGATTTGAACATCTCGTATGCCGTC 6 0.15 No Hit CATCGAGTAGACCTTGTTATTGTGAGAATTATCTCG 5 0.125 No Hit GGGCCTGTAGCTCAGAGGAATCTCGTATGCCGTCTT 5 0.125 No Hit GACACGACTCTCGGCAACGGATATCTCGTATGCCGT 5 0.125 No Hit AGTAGTTGGTATAGGTGAATAGGCATCTCGTATGCC 5 0.125 No Hit ATGGAACAATGTAGGCAAGGGAAGTCGATCTCGTAT 5 0.125 No Hit GTATGCCGTCTTCTGCTTGAAAAAAAAAAAAAAAAA 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATCCTGC 20 0.0046587866 29.874998 11 GTTGATC 20 0.0046587866 29.874998 7 TGGTTGA 20 0.0046587866 29.874998 5 GGTTGAT 20 0.0046587866 29.874998 6 AGTAGTC 20 0.0046587866 29.874998 19 CCAGTAG 20 0.0046587866 29.874998 17 CCTGCCA 20 0.0046587866 29.874998 13 GTCGTAT 20 0.0046587866 29.874998 23 CAGTAGT 20 0.0046587866 29.874998 18 TGATCCT 20 0.0046587866 29.874998 9 TAGTCGT 20 0.0046587866 29.874998 21 CTGGTTG 20 0.0046587866 29.874998 4 ACCTGGT 20 0.0046587866 29.874998 2 GATCCTG 20 0.0046587866 29.874998 10 AGTCGTA 20 0.0046587866 29.874998 22 TGCCAGT 20 0.0046587866 29.874998 15 TTGATCC 20 0.0046587866 29.874998 8 CTGCCAG 20 0.0046587866 29.874998 14 TCCTGCC 20 0.0046587866 29.874998 12 CCTGGTT 20 0.0046587866 29.874998 3 >>END_MODULE Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350354 spots for SRR522513.sra Written 1350354 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra Read 1350343 spots for SRR522513.sra Written 1350343 spots for SRR522513.sra SRR ids: ['SRR522513.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_525kllek SRR522513.sra spots: 27006871 blocks: [[1, 1350343], [1350344, 2700686], [2700687, 4051029], [4051030, 5401372], [5401373, 6751715], [6751716, 8102058], [8102059, 9452401], [9452402, 10802744], [10802745, 12153087], [12153088, 13503430], [13503431, 14853773], [14853774, 16204116], [16204117, 17554459], [17554460, 18904802], [18904803, 20255145], [20255146, 21605488], [21605489, 22955831], [22955832, 24306174], [24306175, 25656517], [25656518, 27006871]] SRR522513 file size 3791801 SRR522513 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 SRR522513 SRR522513_1.fastq Input file: SRR522513_1.fastq trimmed: SRR522513-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 11:11:19 2024 >> started Sat Dec 7 11:11:34 2024 >> done (15.158s) 27006871 reads processed; of these: 184045 ( 0.68%) short reads filtered out after trimming by size control 83270 ( 0.31%) empty reads filtered out after trimming by size control 26739556 (99.01%) reads available; of these: 2290997 ( 8.57%) trimmed reads available after processing 24448559 (91.43%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 30921 0.12% 19 52713 0.20% 20 92958 0.35% 21 28049 0.10% 22 49304 0.18% 23 79492 0.30% 24 161827 0.61% 25 210073 0.79% 26 33205 0.12% 27 61038 0.23% 28 86331 0.32% 29 145142 0.54% 30 420345 1.57% 31 117877 0.44% 32 63705 0.24% 33 254366 0.95% 34 177468 0.66% 35 226183 0.85% 36 24448559 91.43% 26739556 reads passed initial QC criterion=sequence-density sequence-density=29.44 sequence-density-rank=1 fanout-score=77.63 fanout-score-rank=1 prefix-density=76.21 prefix-fanout=30.0 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAA criterion=fanout-score sequence-density=29.44 sequence-density-rank=1 fanout-score=77.63 fanout-score-rank=1 prefix-density=76.21 prefix-fanout=30.0 sequence=ATCTCGTATGCCGTCTTCTGCTTGAAAAA 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 ATCTCGTATGCCGTCTTCTGCTTGAAAAA -o SRR522513 - Input file: STDIN trimmed: SRR522513-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): ATCTCGTATGCCGTCTTCTGCTTGAAAAA -- 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 11:12:17 2024 >> started Sat Dec 7 11:12:45 2024 >> done (28.483s) 24956919 reads processed; of these: 881287 ( 3.53%) short reads filtered out after trimming by size control 893214 ( 3.58%) empty reads filtered out after trimming by size control 23182418 (92.89%) reads available; of these: 20219190 (87.22%) trimmed reads available after processing 2963228 (12.78%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 253247 1.09% 19 396731 1.71% 20 678692 2.93% 21 2615002 11.28% 22 758688 3.27% 23 1801976 7.77% 24 11489085 49.56% 25 956096 4.12% 26 422233 1.82% 27 366665 1.58% 28 304995 1.32% 29 294728 1.27% 30 252089 1.09% 31 145589 0.63% 32 101037 0.44% 33 91231 0.39% 34 11131 0.05% 35 23580 0.10% 36 2219623 9.57% criterion=sequence-density sequence-density=5.22 sequence-density-rank=1 fanout-score=1.33 fanout-score-rank=10 prefix-density=0.05 prefix-fanout=1.3 sequence=TTTGGATTGAAGGGAGCTCTG criterion=fanout-score sequence-density=0.40 sequence-density-rank=7 fanout-score=90.14 fanout-score-rank=1 prefix-density=1.05 prefix-fanout=34.7 sequence=ATTCGTATGCCGT Started job on | Dec 07 11:13:04 Started mapping on | Dec 07 11:13:04 Finished on | Dec 07 11:14:02 Mapping speed, Million of reads per hour | 1549.56 Number of input reads | 24965055 Average input read length | 25 UNIQUE READS: Uniquely mapped reads number | 14684506 Uniquely mapped reads % | 58.82% Average mapped length | 24.46 Number of splices: Total | 92624 Number of splices: Annotated (sjdb) | 17549 Number of splices: GT/AG | 81435 Number of splices: GC/AG | 5657 Number of splices: AT/AC | 47 Number of splices: Non-canonical | 5485 Mismatch rate per base, % | 0.68% 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 | 5538324 % of reads mapped to multiple loci | 22.18% Number of reads mapped to too many loci | 3220193 % of reads mapped to too many loci | 12.90% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.93% % of reads unmapped: other | 2.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 4742225 4742225 4742225 N_multimapping 5538324 5538324 5538324 N_noFeature 10502769 11202098 13935686 N_ambiguous 97362 45351 3858 UnstrandedReadsAssigned:4084375 PositiveStrandReadsAssigned:3437057 NegativeStrandReadsAssigned:744962 Dataset is classified unstranded MeadianReadLen=24 20thPercentileLength=22 echo kmer=19 SRR522513 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: SRR522513-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 24,965,055 reads, 8,251,287 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,334 rounds 52973 SRR522513.ke.tsv 35125 SRR522513.se.tsv 88098 total ==> SRR522513.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 11.5155 0.951438 PNS24243 293 194 0 0 KQK14069 1603 1504 28.6905 2.16243 KQK14071 474 375 1.30945 0.395832 ==> SRR522513.se.tsv <== BRADI_1g14170v3 31 BRADI_1g53295v3 8 BRADI_1g59795v3 4 BRADI_1g07683v3 0 BRADI_1g00485v3 4 BRADI_1g20270v3 84 BRADI_1g74790v3 103 BRADI_1g09890v3 6 BRADI_1g77505v3 6 BRADI_1g48960v3 0 SRR522513 completed mapping pipeline successfully