Starting /dee2/code/volunteer_pipeline.sh SRR11462742 current disk space = 3051264344064 free memory = 1581836284 SRR11462742 SRAfilesize 233bc3fefeba3787698250f61efcdee7 SRR11462742.sra SRR11462742.sra file validated SRR11462742 is single end SRR11462742 is conventional basespace SRR11462742 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462742_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 20.735 32.0 2.0 32.0 2.0 32.0 2 31.77 32.0 32.0 32.0 32.0 32.0 3 34.31 32.0 32.0 37.0 32.0 37.0 4 36.13 37.0 37.0 37.0 32.0 37.0 5 36.4725 37.0 37.0 37.0 37.0 37.0 6 40.0025 41.0 41.0 41.0 37.0 41.0 7 40.12675 41.0 41.0 41.0 37.0 41.0 8 40.16075 41.0 41.0 41.0 37.0 41.0 9 40.309 41.0 41.0 41.0 41.0 41.0 10-14 40.289 41.0 41.0 41.0 37.8 41.0 15-19 40.25 41.0 41.0 41.0 37.0 41.0 20-24 40.210150000000006 41.0 41.0 41.0 37.0 41.0 25-29 40.159 41.0 41.0 41.0 37.0 41.0 30-34 40.083600000000004 41.0 41.0 41.0 37.8 41.0 35-39 39.996950000000005 41.0 41.0 41.0 37.0 41.0 40-44 40.0201 41.0 41.0 41.0 37.0 41.0 45-49 40.05050000000001 41.0 41.0 41.0 37.0 41.0 50-54 39.93885 41.0 41.0 41.0 37.0 41.0 55-59 39.886900000000004 41.0 41.0 41.0 37.0 41.0 60-64 39.904300000000006 41.0 41.0 41.0 37.0 41.0 65-69 39.8695 41.0 41.0 41.0 37.0 41.0 70-74 39.7582 41.0 41.0 41.0 37.0 41.0 75-79 39.6819 41.0 40.2 41.0 37.0 41.0 80-84 40.025549999999996 41.0 41.0 41.0 37.0 41.0 85-89 39.99505 41.0 41.0 41.0 37.0 41.0 90-94 39.91185 41.0 41.0 41.0 37.0 41.0 95-99 39.7736 41.0 41.0 41.0 37.0 41.0 100-104 39.7436 41.0 41.0 41.0 37.0 41.0 105-109 39.7623 41.0 41.0 41.0 37.0 41.0 110-114 39.62815 41.0 41.0 41.0 37.0 41.0 115-119 39.64835000000001 41.0 41.0 41.0 37.0 41.0 120-124 39.52795 41.0 41.0 41.0 37.0 41.0 125-129 39.32345 41.0 41.0 41.0 37.0 41.0 130-134 39.0774 41.0 41.0 41.0 35.0 41.0 135-139 38.984300000000005 41.0 41.0 41.0 34.0 41.0 140-144 38.832249999999995 41.0 41.0 41.0 33.0 41.0 145-149 38.498250000000006 41.0 41.0 41.0 32.0 41.0 150-151 37.775125 41.0 39.0 41.0 29.5 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 1.0 22 0.0 23 0.0 24 4.0 25 3.0 26 5.0 27 8.0 28 10.0 29 20.0 30 19.0 31 37.0 32 48.0 33 65.0 34 63.0 35 87.0 36 101.0 37 135.0 38 169.0 39 321.0 40 2903.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 6.547619047619048 37.976190476190474 39.56349206349206 15.912698412698411 2 26.150000000000002 42.775 19.025 12.049999999999999 3 21.125 30.225 38.175 10.475 4 34.675 23.599999999999998 26.275 15.45 5 27.375 27.150000000000002 28.1 17.375 6 26.35 26.1 29.275000000000002 18.275 7 22.475 26.75 28.499999999999996 22.275 8 26.950000000000003 24.5 31.15 17.4 9 22.475 23.525 33.324999999999996 20.674999999999997 10-14 25.645 25.27 29.23 19.855 15-19 25.355 27.05 28.52 19.075 20-24 24.83 28.18 27.650000000000002 19.34 25-29 24.21 26.855 29.485 19.45 30-34 23.865 25.869999999999997 29.020000000000003 21.245 35-39 24.255 26.615 28.494999999999997 20.635 40-44 24.0 26.634999999999998 28.845 20.52 45-49 24.355 26.474999999999998 28.610000000000003 20.560000000000002 50-54 24.099999999999998 26.224999999999998 28.415000000000003 21.26 55-59 24.945 26.889999999999997 28.03 20.135 60-64 24.59 26.33 28.79 20.29 65-69 25.36 26.534999999999997 27.765 20.34 70-74 25.218782817422614 26.64899734960244 28.104215632344854 20.028004200630097 75-79 24.37 26.68 28.970000000000002 19.98 80-84 24.675 27.37 28.02 19.935 85-89 24.36 27.025 28.73 19.885 90-94 25.06 25.985000000000003 28.720000000000002 20.235 95-99 24.635 26.724999999999998 28.015 20.625 100-104 25.080000000000002 26.505000000000003 27.794999999999998 20.62 105-109 23.805 26.640000000000004 28.33 21.224999999999998 110-114 24.845 26.75 28.89 19.515 115-119 24.565 26.8 27.950000000000003 20.685000000000002 120-124 23.474999999999998 27.245 28.52 20.76 125-129 24.94 28.07 26.93 20.06 130-134 24.205 29.020000000000003 26.97 19.805 135-139 23.494999999999997 29.054999999999996 26.47 20.979999999999997 140-144 23.965 28.04 26.939999999999998 21.055 145-149 23.880000000000003 27.755000000000003 26.790000000000003 21.575 150-151 23.375 28.225 26.687499999999996 21.712500000000002 >>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 0.0 17 0.0 18 0.5 19 0.5 20 0.5 21 1.0 22 2.0 23 2.0 24 2.0 25 2.0 26 1.0 27 3.0 28 6.5 29 10.5 30 15.0 31 19.0 32 24.5 33 32.0 34 47.5 35 80.5 36 96.5 37 101.0 38 136.0 39 169.0 40 186.5 41 233.5 42 260.0 43 247.5 44 271.0 45 294.0 46 267.5 47 238.5 48 225.0 49 178.5 50 151.5 51 128.0 52 99.0 53 93.5 54 73.0 55 73.5 56 60.5 57 34.5 58 35.5 59 23.5 60 15.0 61 15.0 62 8.0 63 8.5 64 7.0 65 4.0 66 1.5 67 0.5 68 2.0 69 2.5 70 1.0 71 4.0 72 4.0 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 37.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 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 0.015 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 87.725 #Duplication Level Percentage of deduplicated Percentage of total 1 91.87802792818466 80.60000000000001 2 6.355086919350242 11.15 3 0.8549444286121403 2.25 4 0.3419777714448561 1.2 5 0.17098888572242804 0.75 6 0.08549444286121402 0.44999999999999996 7 0.08549444286121402 0.525 8 0.0 0.0 9 0.05699629524080935 0.44999999999999996 >10 0.17098888572242804 2.625 >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 TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 26 0.65 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 26 0.65 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 18 0.44999999999999996 No Hit TGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 14 0.35000000000000003 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 11 0.27499999999999997 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 10 0.25 No Hit TAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACAC 9 0.22499999999999998 No Hit CTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACAAACCCC 9 0.22499999999999998 No Hit CGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGA 7 0.17500000000000002 No Hit CTATGATGGACGCTACTGGACTATGTGGAAACTACCCATGTTTGGATGCA 7 0.17500000000000002 No Hit NAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACAC 7 0.17500000000000002 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 6 0.15 No Hit NGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTA 6 0.15 No Hit TATTGACTATGATCAGCTGGAGAAAAGTGCCACTCTTTTCAGACCAAAAT 6 0.15 No Hit TGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 5 0.125 No Hit AATCCGGGCTAGATGCGACGCGTGCGCCCGCCGTCCGATTGCCGACCTGC 5 0.125 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 5 0.125 No Hit NGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 5 0.125 No Hit AAAAGGAATCTTTTCTTGGTTAAGGCTGTGGATGAGGACGAGGGGAGTCC 5 0.125 No Hit NGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTG 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.037500000000000006 0.0 0.0 0.0 0.0 12-13 0.05 0.0 0.0 0.0 0.0 14-15 0.075 0.0 0.0 0.0 0.0 16-17 0.075 0.0 0.0 0.0 0.0 18-19 0.1 0.0 0.0 0.0 0.0 20-21 0.125 0.0 0.0 0.0 0.0 22-23 0.125 0.0 0.0 0.0 0.0 24-25 0.125 0.0 0.0 0.0 0.0 26-27 0.125 0.0 0.0 0.0 0.0 28-29 0.15 0.0 0.0 0.0 0.0 30-31 0.1875 0.0 0.0 0.0 0.0 32-33 0.2625 0.0 0.0 0.0 0.0 34-35 0.275 0.0 0.0 0.0 0.0 36-37 0.275 0.0 0.0 0.0 0.0 38-39 0.3 0.0 0.0 0.0 0.0 40-41 0.325 0.0 0.0 0.0 0.0 42-43 0.325 0.0 0.0 0.0 0.0 44-45 0.375 0.0 0.0 0.0 0.0 46-47 0.4 0.0 0.0 0.0 0.0 48-49 0.4375 0.0 0.0 0.0 0.0 50-51 0.4875 0.0 0.0 0.0 0.0 52-53 0.5 0.0 0.0 0.0 0.0 54-55 0.575 0.0 0.0 0.0 0.0 56-57 0.6125 0.0 0.0 0.0 0.0 58-59 0.6875 0.0 0.0 0.0 0.0 60-61 0.7749999999999999 0.0 0.0 0.0 0.0 62-63 0.9750000000000001 0.0 0.0 0.0 0.0 64-65 1.15 0.0 0.0 0.0 0.0 66-67 1.275 0.0 0.0 0.0 0.0 68-69 1.3624999999999998 0.0 0.0 0.0 0.0 70-71 1.5 0.0 0.0 0.0 0.0 72-73 1.7125 0.0 0.0 0.0 0.0 74-75 1.975 0.0 0.0 0.0 0.0 76-77 2.0625 0.0 0.0 0.0 0.0 78-79 2.2 0.0 0.0 0.0 0.0 80-81 2.35 0.0 0.0 0.0 0.0 82-83 2.4749999999999996 0.0 0.0 0.0 0.0 84-85 2.5875000000000004 0.0 0.0 0.0 0.0 86-87 2.7375 0.0 0.0 0.0 0.0 88-89 3.0999999999999996 0.0 0.0 0.0 0.0 90-91 3.6500000000000004 0.0 0.0 0.0 0.0 92-93 3.9000000000000004 0.0 0.0 0.0 0.0 94-95 4.2625 0.0 0.0 0.0 0.0 96-97 4.5875 0.0 0.0 0.0 0.0 98-99 4.85 0.0 0.0 0.0 0.0 100-101 5.3125 0.0 0.0 0.0 0.0 102-103 5.737500000000001 0.0 0.0 0.0 0.0 104-105 6.2625 0.0 0.0 0.0 0.0 106-107 6.6625 0.0 0.0 0.0 0.0 108-109 6.9875 0.0 0.0 0.0 0.0 110-111 7.375 0.0 0.0 0.0 0.0 112-113 7.9125 0.0 0.0 0.0 0.0 114-115 8.5875 0.0 0.0 0.0 0.0 116-117 9.2875 0.0 0.0 0.0 0.0 118-119 10.225 0.0 0.0 0.0 0.0 120-121 11.3625 0.0 0.0 0.0 0.0 122-123 12.274999999999999 0.0 0.0 0.0 0.0 124-125 13.4625 0.0 0.0 0.0 0.0 126-127 14.2625 0.0 0.0 0.0 0.0 128-129 15.175 0.0 0.0 0.0 0.0 130-131 16.0 0.0 0.0 0.0 0.0 132-133 16.825 0.0 0.0 0.0 0.0 134-135 17.575 0.0 0.0 0.0 0.0 136-137 18.65 0.0 0.0 0.0 0.0 138-139 19.9 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGTTGAC 10 0.0017509761 226.88235 1 GTTGACT 10 0.006882143 144.6375 2 ACGTCCC 10 0.006882143 144.6375 9 TACGTCC 10 0.006882143 144.6375 8 AGGCAAA 10 0.006882143 144.6375 7 ACTACGT 10 0.006882143 144.6375 6 >>END_MODULE Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080454 READS because READLEN < 1 Read 2080454 spots for SRR11462742.sra Written 2080454 spots for SRR11462742.sra Rejected 2080471 READS because READLEN < 1 Read 2080471 spots for SRR11462742.sra Written 2080471 spots for SRR11462742.sra SRR ids: ['SRR11462742.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_dst91atf SRR11462742.sra spots: 41609097 blocks: [[1, 2080454], [2080455, 4160908], [4160909, 6241362], [6241363, 8321816], [8321817, 10402270], [10402271, 12482724], [12482725, 14563178], [14563179, 16643632], [16643633, 18724086], [18724087, 20804540], [20804541, 22884994], [22884995, 24965448], [24965449, 27045902], [27045903, 29126356], [29126357, 31206810], [31206811, 33287264], [33287265, 35367718], [35367719, 37448172], [37448173, 39528626], [39528627, 41609097]] SRR11462742 file size 14118891 SRR11462742 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 SRR11462742 SRR11462742_1.fastq Input file: SRR11462742_1.fastq trimmed: SRR11462742-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 12:52:08 2025 >> started Wed Feb 12 12:52:33 2025 >> done (24.240s) 41609097 reads processed; of these: 16767 ( 0.04%) short reads filtered out after trimming by size control 3568 ( 0.01%) empty reads filtered out after trimming by size control 41588762 (99.95%) reads available; of these: 5143490 (12.37%) trimmed reads available after processing 36445272 (87.63%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 3326 0.01% 19 3248 0.01% 20 4652 0.01% 21 4203 0.01% 22 4749 0.01% 23 5588 0.01% 24 6044 0.01% 25 5601 0.01% 26 6606 0.02% 27 6930 0.02% 28 6655 0.02% 29 7227 0.02% 30 6900 0.02% 31 7340 0.02% 32 7143 0.02% 33 7607 0.02% 34 7825 0.02% 35 8639 0.02% 36 8225 0.02% 37 12229 0.03% 38 8727 0.02% 39 9983 0.02% 40 8924 0.02% 41 9479 0.02% 42 10957 0.03% 43 10694 0.03% 44 10645 0.03% 45 13747 0.03% 46 12357 0.03% 47 18107 0.04% 48 14037 0.03% 49 17825 0.04% 50 14214 0.03% 51 15105 0.04% 52 16083 0.04% 53 15802 0.04% 54 17582 0.04% 55 17872 0.04% 56 19496 0.05% 57 20585 0.05% 58 19447 0.05% 59 21524 0.05% 60 22327 0.05% 61 22466 0.05% 62 50664 0.12% 63 23744 0.06% 64 27591 0.07% 65 24499 0.06% 66 25378 0.06% 67 29241 0.07% 68 28730 0.07% 69 34671 0.08% 70 30438 0.07% 71 35058 0.08% 72 36486 0.09% 73 38998 0.09% 74 53818 0.13% 75 37858 0.09% 76 35080 0.08% 77 40982 0.10% 78 42186 0.10% 79 52522 0.13% 80 42585 0.10% 81 45927 0.11% 82 45297 0.11% 83 48267 0.12% 84 56688 0.14% 85 55217 0.13% 86 60887 0.15% 87 58476 0.14% 88 57435 0.14% 89 125294 0.30% 90 63421 0.15% 91 68968 0.17% 92 66468 0.16% 93 70537 0.17% 94 79038 0.19% 95 76895 0.18% 96 93233 0.22% 97 86718 0.21% 98 81322 0.20% 99 83279 0.20% 100 84423 0.20% 101 93534 0.22% 102 140692 0.34% 103 101050 0.24% 104 99601 0.24% 105 102926 0.25% 106 108054 0.26% 107 119301 0.29% 108 115353 0.28% 109 147909 0.36% 110 125666 0.30% 111 126041 0.30% 112 199675 0.48% 113 137061 0.33% 114 141758 0.34% 115 143207 0.34% 116 147829 0.36% 117 159786 0.38% 118 168497 0.41% 119 168488 0.41% 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 21 0.00% 151 36445272 87.63% 41588762 reads passed initial QC criterion=sequence-density sequence-density=9.66 sequence-density-rank=1 fanout-score=41.92 fanout-score-rank=2 prefix-density=11.58 prefix-fanout=35.0 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA criterion=fanout-score sequence-density=0.01 sequence-density-rank=17 fanout-score=110.86 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=6.5 sequence=CTTCCTCCTCTATGATCTCATCGGCAGCCGTTGCCACCGTCAACCGCACCCCGGCACAAGCCAACATGGTGGCACCATTCAATGGTCTCAAGTCTGCCGCAGCTTTCCCAGTCAGTACCAGAAAGGCTAATGACATTACTTCCATTGCAAGCAATGGTGGACGAGTTCAATGCATGCAGGTGTGGCCACCAACTGGATTGAAGAAGTTCGAGACTCTTTCTTACCTTCCAGATCTCACAGAGGAGGAATTGGCCAAGGAAATTGATTACCTTCTTCGCTCGAAGTGGGTTCCTTGCTTGGAATTCGAGTTGGAGAAAGGTTGGGTCTACCGTGAGCACCACAGCTCACCAGGGTACTATGATGGACGCTACTGGACTATGTGGAA 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTGAAAAAAAAA -o SRR11462742 - Input file: STDIN trimmed: SRR11462742-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTGATATCTCGTATGCCGTCTTCTGCTTG -- 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 Wed Feb 12 12:54:01 2025 >> started Wed Feb 12 12:54:39 2025 >> done (37.767s) 33271010 reads processed; of these: 535 ( 0.00%) short reads filtered out after trimming by size control 17 ( 0.00%) empty reads filtered out after trimming by size control 33270458 (100.00%) reads available; of these: 6510989 (19.57%) trimmed reads available after processing 26759469 (80.43%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 2712 0.01% 19 2659 0.01% 20 3728 0.01% 21 3470 0.01% 22 3843 0.01% 23 4467 0.01% 24 4830 0.01% 25 4533 0.01% 26 5408 0.02% 27 5618 0.02% 28 5406 0.02% 29 5902 0.02% 30 5619 0.02% 31 6010 0.02% 32 5799 0.02% 33 6128 0.02% 34 6227 0.02% 35 7046 0.02% 36 6649 0.02% 37 9873 0.03% 38 6983 0.02% 39 7983 0.02% 40 7157 0.02% 41 7567 0.02% 42 8879 0.03% 43 8541 0.03% 44 8536 0.03% 45 11088 0.03% 46 9969 0.03% 47 14490 0.04% 48 11358 0.03% 49 14488 0.04% 50 11717 0.04% 51 12226 0.04% 52 12847 0.04% 53 12925 0.04% 54 14200 0.04% 55 14487 0.04% 56 15337 0.05% 57 16621 0.05% 58 15516 0.05% 59 17326 0.05% 60 17902 0.05% 61 18310 0.06% 62 40902 0.12% 63 19249 0.06% 64 22126 0.07% 65 19970 0.06% 66 20452 0.06% 67 23693 0.07% 68 23374 0.07% 69 27960 0.08% 70 24617 0.07% 71 27940 0.08% 72 29410 0.09% 73 31365 0.09% 74 43521 0.13% 75 30587 0.09% 76 28788 0.09% 77 33289 0.10% 78 33821 0.10% 79 41936 0.13% 80 33943 0.10% 81 40762 0.12% 82 36445 0.11% 83 38896 0.12% 84 42061 0.13% 85 44750 0.13% 86 49233 0.15% 87 47555 0.14% 88 46542 0.14% 89 100749 0.30% 90 51979 0.16% 91 55677 0.17% 92 54447 0.16% 93 56267 0.17% 94 63870 0.19% 95 60966 0.18% 96 75449 0.23% 97 69352 0.21% 98 65813 0.20% 99 67559 0.20% 100 68103 0.20% 101 75563 0.23% 102 113170 0.34% 103 81965 0.25% 104 80697 0.24% 105 83203 0.25% 106 86757 0.26% 107 95270 0.29% 108 93162 0.28% 109 118885 0.36% 110 101418 0.30% 111 101063 0.30% 112 162284 0.49% 113 109981 0.33% 114 114843 0.35% 115 114087 0.34% 116 119460 0.36% 117 123768 0.37% 118 130439 0.39% 119 132203 0.40% 120 145655 0.44% 121 147698 0.44% 122 146547 0.44% 123 230984 0.69% 124 181891 0.55% 125 154907 0.47% 126 167392 0.50% 127 183353 0.55% 128 175277 0.53% 129 164453 0.49% 130 168258 0.51% 131 194122 0.58% 132 203510 0.61% 133 216935 0.65% 134 189994 0.57% 135 210202 0.63% 136 199555 0.60% 137 210812 0.63% 138 237064 0.71% 139 210549 0.63% 140 231859 0.70% 141 201675 0.61% 142 218184 0.66% 143 225926 0.68% 144 217029 0.65% 145 230194 0.69% 146 227500 0.68% 147 345312 1.04% 148 715918 2.15% 149 0 0.00% 150 12 0.00% 151 22783675 68.48% criterion=sequence-density sequence-density=0.72 sequence-density-rank=1 fanout-score=2.15 fanout-score-rank=30 prefix-density=0.74 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=38 fanout-score=303.15 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=6.4 sequence=GAAAGATGGCCTCGGCATCATTTCTCAAGTCATCACCAGTTCTAGACAAGTCTGAGTTTGTTAAGGGTCAGACCCTCCGCTTGCCTTCTGCCTCCATTGTCCGGTGCCGCTCCACCGCCCCTTCTGCTCTTACCGTTCGTGCTGGTTCCTATGCTGAGGAGCTTGTCAAAACCGCGAAAAC Started job on | Feb 12 12:55:16 Started mapping on | Feb 12 12:55:16 Finished on | Feb 12 12:56:29 Mapping speed, Million of reads per hour | 2050.93 Number of input reads | 41588210 Average input read length | 141 UNIQUE READS: Uniquely mapped reads number | 36795945 Uniquely mapped reads % | 88.48% Average mapped length | 140.09 Number of splices: Total | 17210732 Number of splices: Annotated (sjdb) | 16879515 Number of splices: GT/AG | 16870522 Number of splices: GC/AG | 260877 Number of splices: AT/AC | 10320 Number of splices: Non-canonical | 69013 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.02% Deletion average length | 2.13 Insertion rate per base | 0.01% Insertion average length | 1.87 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 989956 % of reads mapped to multiple loci | 2.38% Number of reads mapped to too many loci | 2336597 % of reads mapped to too many loci | 5.62% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.42% % of reads unmapped: other | 0.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3802309 3802309 3802309 N_multimapping 989956 989956 989956 N_noFeature 1771451 2418560 35634753 N_ambiguous 653575 139429 796 UnstrandedReadsAssigned:34370919 PositiveStrandReadsAssigned:34237956 NegativeStrandReadsAssigned:1160396 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=134 echo kmer=129 SRR11462742 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: SRR11462742-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 41,588,210 reads, 35,049,777 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,247 rounds 52401 SRR11462742.ke.tsv 34699 SRR11462742.se.tsv 87100 total ==> SRR11462742.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 3908 60.4786 Potri.005G024800.1.v4.1 1035 936 509 16.1497 Potri.004G059700.1.v4.1 961 862 86 2.96288 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 3287.45 34.3282 Potri.016G087400.1.v4.1 270 171 2258 392.148 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 142.945 2.53592 Potri.012G127500.1.v4.1 977 878 193 6.52807 ==> SRR11462742.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 223 Potri.001G233950.v4.1 4 Potri.001G122700.v4.1 193 Potri.001G212900.v4.1 4 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 2 Potri.001G416900.v4.1 2 Potri.001G452600.v4.1 50 SRR11462742 completed mapping pipeline successfully