Starting /dee2/code/volunteer_pipeline.sh SRR5423539 current disk space = 3051728490496 free memory = 1580380448 SRR5423539 SRAfilesize f6e37652e7b29655b545cf3e675f48d7 SRR5423539.sra SRR5423539.sra file validated SRR5423539 is single end SRR5423539 is conventional basespace SRR5423539 read1 length is 52 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR5423539_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 52 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.00625 33.0 31.0 34.0 30.0 34.0 2 32.14 34.0 31.0 34.0 30.0 34.0 3 32.0935 34.0 31.0 34.0 30.0 34.0 4 35.45525 37.0 35.0 37.0 33.0 37.0 5 35.556 37.0 35.0 37.0 33.0 37.0 6 35.63175 37.0 35.0 37.0 33.0 37.0 7 35.70425 37.0 35.0 37.0 33.0 37.0 8 35.8205 37.0 35.0 37.0 35.0 37.0 9 37.36225 39.0 37.0 39.0 35.0 39.0 10 37.229 39.0 37.0 39.0 33.0 39.0 11 37.2155 39.0 37.0 39.0 33.0 39.0 12 37.22875 39.0 37.0 39.0 34.0 39.0 13 36.78575 39.0 37.0 39.0 32.0 39.0 14 38.39725 40.0 38.0 41.0 34.0 41.0 15 38.4915 40.0 38.0 41.0 34.0 41.0 16 38.54725 40.0 38.0 41.0 34.0 41.0 17 38.4815 40.0 38.0 41.0 34.0 41.0 18 38.2915 40.0 38.0 41.0 33.0 41.0 19 38.43925 40.0 38.0 41.0 34.0 41.0 20 38.3545 40.0 38.0 41.0 34.0 41.0 21 38.207 40.0 38.0 41.0 33.0 41.0 22 38.49825 40.0 38.0 41.0 34.0 41.0 23 38.33925 40.0 38.0 41.0 34.0 41.0 24 38.20625 40.0 38.0 41.0 33.0 41.0 25 38.2095 40.0 38.0 41.0 33.0 41.0 26 38.128 40.0 38.0 41.0 33.0 41.0 27 38.38725 40.0 38.0 41.0 34.0 41.0 28 38.306 40.0 38.0 41.0 34.0 41.0 29 37.904 40.0 37.0 41.0 32.0 41.0 30 38.123 40.0 38.0 41.0 33.0 41.0 31 37.9 40.0 37.0 41.0 33.0 41.0 32 37.87475 40.0 37.0 41.0 33.0 41.0 33 37.9235 40.0 37.0 41.0 33.0 41.0 34 37.854 40.0 37.0 41.0 32.0 41.0 35 37.91025 40.0 37.0 41.0 33.0 41.0 36 37.67425 40.0 37.0 41.0 32.0 41.0 37 36.86375 39.0 36.0 41.0 30.0 41.0 38 37.30475 39.0 36.0 41.0 31.0 41.0 39 37.37275 39.0 37.0 41.0 31.0 41.0 40 37.4405 40.0 37.0 41.0 31.0 41.0 41 37.317 39.0 36.0 41.0 31.0 41.0 42 37.22125 39.0 36.0 41.0 31.0 41.0 43 37.054 39.0 36.0 41.0 30.0 41.0 44 37.054 39.0 36.0 41.0 31.0 41.0 45 36.702 39.0 35.0 41.0 30.0 41.0 46 36.7745 39.0 35.0 41.0 30.0 41.0 47 36.90975 39.0 35.0 41.0 30.0 41.0 48 36.6625 39.0 35.0 41.0 30.0 41.0 49 36.36625 39.0 35.0 41.0 29.0 41.0 50 36.56775 39.0 35.0 41.0 30.0 41.0 51 36.486 39.0 35.0 41.0 30.0 41.0 52 35.55575 38.0 34.0 40.0 28.0 41.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1313 1 0.0 1313 2 0.0 1313 3 0.0 1313 4 0.0 1313 5 0.0 1313 6 0.0 1313 7 0.0 1313 8 0.0 1313 9 0.0 1313 10 0.0 1313 11 0.0 1313 12 0.0 1313 13 0.0 1313 14 0.0 1313 15 0.0 1313 16 0.0 1313 17 0.0 1313 18 0.0 1313 19 0.0 1313 20 0.0 1313 21 0.0 1313 22 0.0 1313 23 0.0 1313 24 0.0 1313 25 0.0 1313 26 0.0 1313 27 0.0 1313 28 0.0 1313 29 0.0 1313 30 0.0 1313 31 0.0 1313 32 0.0 1313 33 0.0 1313 34 0.0 1313 35 0.0 1313 36 0.0 1313 37 0.0 1313 38 0.0 1313 39 0.0 1313 40 0.0 1313 41 0.0 1313 42 0.0 1313 43 0.0 1313 44 0.0 1313 45 0.0 1313 46 0.0 1313 47 0.0 1313 48 0.0 1313 49 0.0 1313 50 0.0 1313 51 0.0 1313 52 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 5.0 22 3.0 23 5.0 24 8.0 25 14.0 26 14.0 27 29.0 28 39.0 29 53.0 30 68.0 31 104.0 32 103.0 33 156.0 34 194.0 35 226.0 36 329.0 37 489.0 38 765.0 39 1394.0 40 1.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.92740926157697 12.315394242803505 6.157697121401752 39.59949937421777 2 22.55 14.924999999999999 35.325 27.200000000000003 3 19.875 19.3 25.775 35.05 4 24.275 27.85 21.475 26.400000000000002 5 24.474999999999998 32.175 21.85 21.5 6 20.25 31.7 23.674999999999997 24.375 7 16.55 19.0 42.4 22.05 8 18.6 19.8 28.775000000000002 32.824999999999996 9 18.825 19.5 31.775 29.9 10 20.625 34.175 22.1 23.1 11 24.375 23.125 20.75 31.75 12 23.625 20.325 24.349999999999998 31.7 13 21.275 23.35 27.700000000000003 27.675 14 22.475 24.65 26.0 26.875 15 23.75 22.925 25.324999999999996 28.000000000000004 16 23.95 23.825 25.85 26.375 17 23.724999999999998 23.175 26.075 27.025 18 23.425 22.650000000000002 25.75 28.175 19 23.925 23.200000000000003 25.6 27.275 20 22.975 23.95 24.975 28.1 21 22.75 22.775000000000002 27.025 27.450000000000003 22 22.175 24.425 25.1 28.299999999999997 23 22.236118059029515 23.486743371685844 25.46273136568284 28.8144072036018 24 22.175 23.849999999999998 24.099999999999998 29.875 25 23.875 22.75 25.75 27.625 26 22.5 22.35 26.3 28.849999999999998 27 22.0 22.85 26.625 28.525 28 23.625 21.775 26.650000000000002 27.950000000000003 29 22.025 23.974999999999998 25.324999999999996 28.675 30 22.625 22.475 25.4 29.5 31 23.525 22.975 24.525 28.975 32 23.724999999999998 23.45 26.125 26.700000000000003 33 23.075000000000003 22.7 25.35 28.875 34 22.375 24.3 25.124999999999996 28.199999999999996 35 23.599999999999998 23.875 25.575 26.950000000000003 36 24.575 22.675 24.2 28.549999999999997 37 24.0 23.799999999999997 25.25 26.950000000000003 38 24.224999999999998 22.75 25.275 27.750000000000004 39 22.25 23.849999999999998 24.15 29.75 40 24.775 21.7 24.625 28.9 41 22.650000000000002 23.5 25.2 28.65 42 24.05 22.35 25.4 28.199999999999996 43 24.8 21.8 26.424999999999997 26.974999999999998 44 24.45 23.325000000000003 25.825 26.400000000000002 45 24.175 22.425 24.375 29.025000000000002 46 23.36168084042021 24.212106053026513 24.637318659329665 27.788894447223612 47 23.724999999999998 22.7 24.55 29.025000000000002 48 22.166624968726545 23.042281711283465 25.39404553415061 29.39704778583938 49 23.65 23.45 25.775 27.125 50 23.036518259129565 23.536768384192097 25.437718859429715 27.988994497248626 51 24.418313735301474 21.966474856142106 24.7935951963973 28.821616212159118 52 23.9 22.05 25.674999999999997 28.375 >>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 0.5 17 1.0 18 1.5 19 2.0 20 1.5 21 1.0 22 2.0 23 3.0 24 3.5 25 4.0 26 6.0 27 8.0 28 12.5 29 17.0 30 19.5 31 22.0 32 26.0 33 30.0 34 40.0 35 50.0 36 57.5 37 65.0 38 85.0 39 123.5 40 142.0 41 150.5 42 159.0 43 205.0 44 251.0 45 270.5 46 290.0 47 313.0 48 336.0 49 343.5 50 351.0 51 381.5 52 412.0 53 389.5 54 367.0 55 369.5 56 372.0 57 348.0 58 324.0 59 263.5 60 203.0 61 177.5 62 152.0 63 112.5 64 80.5 65 88.0 66 70.0 67 52.0 68 46.5 69 41.0 70 36.0 71 31.0 72 29.5 73 28.0 74 19.5 75 11.0 76 7.0 77 3.0 78 3.5 79 4.0 80 2.5 81 1.0 82 0.5 83 0.0 84 0.5 85 1.0 86 0.5 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 0.125 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 0.05 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 0.05 47 0.0 48 0.075 49 0.0 50 0.05 51 0.075 52 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 52 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 87.725 #Duplication Level Percentage of deduplicated Percentage of total 1 91.67854089484183 80.425 2 5.329153605015674 9.35 3 1.6813907096038756 4.425 4 0.6839555428897122 2.4 5 0.17098888572242804 0.75 6 0.28498147620404674 1.5 7 0.1139925904816187 0.7000000000000001 8 0.028498147620404674 0.2 9 0.0 0.0 >10 0.028498147620404674 0.25 >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 CGATAGAACTCGCACCGAGCTCCAGCTATCCTGAGGGAAACTTCGGAGGGAA 10 0.25 No Hit GCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACAGCACCGGAGGCACGAC 8 0.2 No Hit GTCGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAAT 7 0.17500000000000002 No Hit GGGCTTACTACTTAGATGCTTTCAGCAGTTATCCGCTCCGCACTTGGCTACC 7 0.17500000000000002 No Hit CCCGTGTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGT 7 0.17500000000000002 No Hit CCTATACCCAAGTCAGACGAACGATTTGCACGTCAGTATCGCTGCGGGCCTC 7 0.17500000000000002 No Hit CGCGTATTTAAGTCGTCTGCAAAGGATTCTACCCGCCGCTCGGTGGGAATTG 6 0.15 No Hit GTCAGGATTGGGTAATTTGCGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCG 6 0.15 No Hit GTCGAATCCAATGATACGGATAAAGGAGTTAGGGTAAGCTTTCTTCGCCTCC 6 0.15 No Hit CGGCAATCGGACGGCGGGCGCACGCGTCGCATCTAGCCCGGATTCTGACTTA 6 0.15 No Hit CTCATCTTGGGGTGGGCTTACTACTTAGATGCTTTCAGCAGTTATCCGCTCC 6 0.15 No Hit CCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAAAG 6 0.15 No Hit GTCAGTATCGCTGCGGGCCTCCACCAGAGTTTCCTCTGGCTTCGCCCCGCTC 6 0.15 No Hit GTCGGCAATCGGACGGCGGGCGCACGCGTCGCATCTAGCCCGGATTCTGACT 6 0.15 No Hit GATAGAACTCGCACCGAGCTCCAGCTATCCTGAGGGAAACTTCGGAGGGAAC 6 0.15 No Hit CTTGTCCGTACCAGTTCTGAGTCGACTGTTCGACGCCCGGGGAAGGCCCCCG 6 0.15 No Hit GTACAAGGCCCGGGAACGAATTCACCGCCGTATGGCTGACCGGCGATTACTA 5 0.125 No Hit CAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAAAGC 5 0.125 No Hit CTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCG 5 0.125 No Hit GCAAAGGATTCTACCCGCCGCTCGGTGGGAATTGTACTTCAAGGCGGCCCGC 5 0.125 No Hit GGGAAACTTCGGAGGGAACCAGCTACTAGACGGTTCGATTAGTCTTTCGCCC 5 0.125 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAA 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 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra Read 200000 spots for SRR5423539.sra Written 200000 spots for SRR5423539.sra SRR ids: ['SRR5423539.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_a81b3do4 SRR5423539.sra spots: 4000000 blocks: [[1, 200000], [200001, 400000], [400001, 600000], [600001, 800000], [800001, 1000000], [1000001, 1200000], [1200001, 1400000], [1400001, 1600000], [1600001, 1800000], [1800001, 2000000], [2000001, 2200000], [2200001, 2400000], [2400001, 2600000], [2600001, 2800000], [2800001, 3000000], [3000001, 3200000], [3200001, 3400000], [3400001, 3600000], [3600001, 3800000], [3800001, 4000000]] SRR5423539 file size 703996 SRR5423539 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 SRR5423539 SRR5423539_1.fastq Input file: SRR5423539_1.fastq trimmed: SRR5423539-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 17:29:33 2025 >> started Wed Feb 12 17:29:34 2025 >> done (1.949s) 4000000 reads processed; of these: 310 ( 0.01%) short reads filtered out after trimming by size control 171 ( 0.00%) empty reads filtered out after trimming by size control 3999519 (99.99%) reads available; of these: 95211 ( 2.38%) trimmed reads available after processing 3904308 (97.62%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 10 0.00% 20 13 0.00% 21 0 0.00% 22 5 0.00% 23 8 0.00% 24 14 0.00% 25 27 0.00% 26 23 0.00% 27 44 0.00% 28 82 0.00% 29 69 0.00% 30 85 0.00% 31 124 0.00% 32 201 0.01% 33 200 0.01% 34 177 0.00% 35 160 0.00% 36 241 0.01% 37 294 0.01% 38 341 0.01% 39 314 0.01% 40 417 0.01% 41 624 0.02% 42 559 0.01% 43 725 0.02% 44 991 0.02% 45 1804 0.05% 46 2401 0.06% 47 2507 0.06% 48 3110 0.08% 49 5623 0.14% 50 12242 0.31% 51 61765 1.54% 52 3904308 97.62% 3999519 reads passed initial QC criterion=sequence-density sequence-density=0.59 sequence-density-rank=1 fanout-score=1.95 fanout-score-rank=33 prefix-density=0.57 prefix-fanout=2.0 sequence=CCGTCAATTCCTTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=18.49 fanout-score-rank=1 prefix-density=0.20 prefix-fanout=1.0 sequence=GCCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCACAAGCCAGTTATCCCTGTGGTAACTTTTCTGACACCTCTAGCTTCAAATTCCGAAGGTCTAAAGGATCGATAGGCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGT Started job on | Feb 12 17:29:45 Started mapping on | Feb 12 17:29:45 Finished on | Feb 12 17:29:52 Mapping speed, Million of reads per hour | 2056.90 Number of input reads | 3999519 Average input read length | 51 UNIQUE READS: Uniquely mapped reads number | 2709724 Uniquely mapped reads % | 67.75% Average mapped length | 51.82 Number of splices: Total | 317326 Number of splices: Annotated (sjdb) | 313540 Number of splices: GT/AG | 310545 Number of splices: GC/AG | 6255 Number of splices: AT/AC | 215 Number of splices: Non-canonical | 311 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.00% Deletion average length | 1.55 Insertion rate per base | 0.00% Insertion average length | 1.19 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 275906 % of reads mapped to multiple loci | 6.90% Number of reads mapped to too many loci | 993017 % of reads mapped to too many loci | 24.83% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.52% % of reads unmapped: other | 0.00% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1013889 1013889 1013889 N_multimapping 275906 275906 275906 N_noFeature 406230 2644754 421261 N_ambiguous 60654 39 10690 UnstrandedReadsAssigned:2242840 PositiveStrandReadsAssigned:64931 NegativeStrandReadsAssigned:2277773 Dataset is classified negative stranded MeadianReadLen=52 20thPercentileLength=52 echo kmer=47 SRR5423539 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: SRR5423539-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 3,999,519 reads, 2,971,179 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,064 rounds 52401 SRR5423539.ke.tsv 34699 SRR5423539.se.tsv 87100 total ==> SRR5423539.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 59 10.2667 Potri.005G024800.1.v4.1 1035 936 17 6.06492 Potri.004G059700.1.v4.1 961 862 13 5.03603 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 17 1.99605 Potri.016G087400.1.v4.1 270 171 83 162.082 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 1 0.199479 Potri.012G127500.1.v4.1 977 878 28 10.6492 ==> SRR5423539.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 3 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 48 Potri.001G212900.v4.1 2 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 1 SRR5423539 completed mapping pipeline successfully