Starting /dee2/code/volunteer_pipeline.sh SRR11462735 current disk space = 3051303723008 free memory = 1581904220 SRR11462735 SRAfilesize cdf39ac945a3249f8d77e9daa59aac99 SRR11462735.sra SRR11462735.sra file validated SRR11462735 is single end SRR11462735 is conventional basespace SRR11462735 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11462735_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 20.50875 32.0 2.0 32.0 2.0 32.0 2 31.73625 32.0 32.0 32.0 32.0 32.0 3 34.2875 37.0 32.0 37.0 32.0 37.0 4 36.265 37.0 37.0 37.0 32.0 37.0 5 36.3475 37.0 37.0 37.0 37.0 37.0 6 39.97725 41.0 41.0 41.0 37.0 41.0 7 40.17725 41.0 41.0 41.0 37.0 41.0 8 40.22175 41.0 41.0 41.0 37.0 41.0 9 40.287 41.0 41.0 41.0 37.0 41.0 10-14 40.347 41.0 41.0 41.0 41.0 41.0 15-19 40.29709999999999 41.0 41.0 41.0 40.2 41.0 20-24 40.2193 41.0 41.0 41.0 39.4 41.0 25-29 40.20479999999999 41.0 41.0 41.0 38.6 41.0 30-34 40.1142 41.0 41.0 41.0 37.8 41.0 35-39 40.16055 41.0 41.0 41.0 39.4 41.0 40-44 40.1512 41.0 41.0 41.0 39.4 41.0 45-49 40.1193 41.0 41.0 41.0 39.4 41.0 50-54 40.102599999999995 41.0 41.0 41.0 38.6 41.0 55-59 40.049249999999994 41.0 41.0 41.0 37.0 41.0 60-64 39.947950000000006 41.0 41.0 41.0 37.0 41.0 65-69 40.005449999999996 41.0 41.0 41.0 37.0 41.0 70-74 39.8027 41.0 41.0 41.0 37.0 41.0 75-79 39.808099999999996 41.0 40.2 41.0 37.0 41.0 80-84 40.19024999999999 41.0 41.0 41.0 40.2 41.0 85-89 40.14015 41.0 41.0 41.0 39.4 41.0 90-94 40.14925 41.0 41.0 41.0 38.6 41.0 95-99 40.02875 41.0 41.0 41.0 37.8 41.0 100-104 39.894400000000005 41.0 41.0 41.0 37.0 41.0 105-109 39.79565000000001 41.0 41.0 41.0 37.0 41.0 110-114 39.84565 41.0 41.0 41.0 37.0 41.0 115-119 39.797200000000004 41.0 41.0 41.0 37.0 41.0 120-124 39.748850000000004 41.0 41.0 41.0 37.0 41.0 125-129 39.5715 41.0 41.0 41.0 37.0 41.0 130-134 39.4263 41.0 41.0 41.0 37.0 41.0 135-139 39.161649999999995 41.0 41.0 41.0 37.0 41.0 140-144 39.28545 41.0 41.0 41.0 37.0 41.0 145-149 38.9461 41.0 41.0 41.0 36.0 41.0 150-151 38.191625 41.0 39.0 41.0 32.0 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 2.0 25 4.0 26 2.0 27 5.0 28 11.0 29 15.0 30 22.0 31 28.0 32 42.0 33 64.0 34 49.0 35 62.0 36 84.0 37 134.0 38 153.0 39 298.0 40 3024.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 6.0072086503804565 36.44373247897477 41.85022026431718 15.698838606327591 2 25.424999999999997 43.275000000000006 20.225 11.075 3 23.075000000000003 28.999999999999996 37.7 10.225 4 33.57518138603953 24.043032274205654 28.071053289967473 14.310733049787341 5 27.85 27.375 27.375 17.4 6 25.3 27.425 29.799999999999997 17.474999999999998 7 23.525 26.275 29.45 20.75 8 25.25 25.6 30.725 18.425 9 21.3 24.55 34.0 20.150000000000002 10-14 24.68 25.655 29.335 20.330000000000002 15-19 23.96 27.325 28.939999999999998 19.775000000000002 20-24 24.11 27.775 28.46 19.655 25-29 23.695 26.75 30.195 19.36 30-34 23.755000000000003 25.96 29.465000000000003 20.82 35-39 24.455 26.075 29.220000000000002 20.25 40-44 23.755000000000003 26.75 28.860000000000003 20.635 45-49 24.02 27.525 28.235 20.22 50-54 23.905 27.16 28.125 20.810000000000002 55-59 24.33 27.284999999999997 27.815 20.57 60-64 24.785 26.015 29.354999999999997 19.845 65-69 24.515 27.155 27.555000000000003 20.775 70-74 24.709999999999997 26.685 28.22 20.385 75-79 23.955000000000002 26.26 29.665000000000003 20.119999999999997 80-84 24.09 27.67 28.235 20.005 85-89 23.595 27.675 28.799999999999997 19.93 90-94 25.21 25.295 29.39 20.105 95-99 24.575 26.52 28.32 20.585 100-104 24.740000000000002 26.445 28.694999999999997 20.119999999999997 105-109 23.44 26.625 28.18 21.755 110-114 24.465 26.619999999999997 28.505000000000003 20.41 115-119 23.665 26.735 29.015 20.585 120-124 24.154999999999998 26.955000000000002 29.21 19.68 125-129 24.305 27.52 28.275 19.900000000000002 130-134 23.225 27.905 28.144999999999996 20.724999999999998 135-139 23.925 27.83 26.99 21.255 140-144 24.27 27.76 27.375 20.595 145-149 24.915000000000003 26.650000000000002 27.034999999999997 21.4 150-151 23.4125 26.1125 28.299999999999997 22.175 >>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 1.0 21 1.0 22 0.0 23 1.0 24 2.0 25 4.5 26 4.5 27 4.0 28 8.0 29 11.0 30 17.0 31 25.0 32 35.0 33 40.5 34 59.0 35 93.5 36 112.5 37 133.0 38 159.5 39 172.0 40 205.5 41 218.5 42 232.5 43 268.0 44 302.0 45 280.0 46 234.5 47 217.5 48 187.5 49 161.5 50 133.5 51 117.0 52 106.0 53 80.5 54 56.5 55 84.0 56 72.0 57 33.0 58 28.0 59 17.0 60 17.0 61 13.5 62 10.0 63 13.5 64 7.0 65 2.5 66 2.5 67 1.5 68 1.5 69 3.0 70 3.0 71 2.5 72 1.5 73 0.5 74 0.5 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 37.574999999999996 2 0.0 3 0.0 4 0.075 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 0.0 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 88.94999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 94.32265317594154 83.89999999999999 2 4.0472175379426645 7.199999999999999 3 0.6464305789769533 1.725 4 0.5059021922428331 1.7999999999999998 5 0.11242270938729623 0.5 6 0.056211354693648116 0.3 7 0.028105677346824058 0.17500000000000002 8 0.08431703204047217 0.6 9 0.0 0.0 >10 0.19673974142776843 3.8 >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 fail #Sequence Count Percentage Possible Source TGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 43 1.075 No Hit NATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 28 0.7000000000000001 No Hit TATTTGCTACTCGGATAACCGTAGTAATTCTAGAGCTAATACGTGCAACA 27 0.675 No Hit NGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGG 19 0.475 No Hit AGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTA 14 0.35000000000000003 No Hit AAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAA 11 0.27499999999999997 No Hit NGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTA 10 0.25 No Hit ATGCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTT 8 0.2 No Hit AACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 8 0.2 No Hit TATTTTACTTATTCCGTGAATCGGAGGCGGGGCGCTGCCCCTCTTTTTGG 8 0.2 No Hit NGGAACAAAAGGGTAAAAGCTCGTTTGATTCTGATTTCCAGTACGAATAC 7 0.17500000000000002 No Hit TGTTGGCCTTCGGGATCGGAGTAATGATTAACAGGGACAGTCGGGGGCAT 6 0.15 No Hit TAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAA 6 0.15 No Hit TGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTT 5 0.125 No Hit AGACTGTGAAACTGCGAATGGCTCATTAAATCAGTTATAGTTTGTTTGAT 5 0.125 No Hit NACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCT 5 0.125 No Hit AATGATCGTGACCGTGTGGTTGAAGCTAGGGATGAGCTGCACCGGATGTT 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 0.0 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 10-11 0.0125 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.037500000000000006 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.0625 0.0 0.0 0.0 0.0 26-27 0.1 0.0 0.0 0.0 0.0 28-29 0.125 0.0 0.0 0.0 0.0 30-31 0.15 0.0 0.0 0.0 0.0 32-33 0.2 0.0 0.0 0.0 0.0 34-35 0.25 0.0 0.0 0.0 0.0 36-37 0.25 0.0 0.0 0.0 0.0 38-39 0.30000000000000004 0.0 0.0 0.0 0.0 40-41 0.35 0.0 0.0 0.0 0.0 42-43 0.35 0.0 0.0 0.0 0.0 44-45 0.35 0.0 0.0 0.0 0.0 46-47 0.3625 0.0 0.0 0.0 0.0 48-49 0.375 0.0 0.0 0.0 0.0 50-51 0.375 0.0 0.0 0.0 0.0 52-53 0.3875 0.0 0.0 0.0 0.0 54-55 0.4625 0.0 0.0 0.0 0.0 56-57 0.5125 0.0 0.0 0.0 0.0 58-59 0.55 0.0 0.0 0.0 0.0 60-61 0.6 0.0 0.0 0.0 0.0 62-63 0.7125 0.0 0.0 0.0 0.0 64-65 0.825 0.0 0.0 0.0 0.0 66-67 0.925 0.0 0.0 0.0 0.0 68-69 0.9875 0.0 0.0 0.0 0.0 70-71 1.1125 0.0 0.0 0.0 0.0 72-73 1.1375 0.0 0.0 0.0 0.0 74-75 1.275 0.0 0.0 0.0 0.0 76-77 1.4625 0.0 0.0 0.0 0.0 78-79 1.5875 0.0 0.0 0.0 0.0 80-81 1.6625 0.0 0.0 0.0 0.0 82-83 1.7625 0.0 0.0 0.0 0.0 84-85 1.8125 0.0 0.0 0.0 0.0 86-87 1.9375 0.0 0.0 0.0 0.0 88-89 2.0625 0.0 0.0 0.0 0.0 90-91 2.375 0.0 0.0 0.0 0.0 92-93 2.6125 0.0 0.0 0.0 0.0 94-95 2.7875 0.0 0.0 0.0 0.0 96-97 3.0125 0.0 0.0 0.0 0.0 98-99 3.3875 0.0 0.0 0.0 0.0 100-101 3.5375 0.0 0.0 0.0 0.0 102-103 3.8375000000000004 0.0 0.0 0.0 0.0 104-105 4.2125 0.0 0.0 0.0 0.0 106-107 4.5625 0.0 0.0 0.0 0.0 108-109 4.9625 0.0 0.0 0.0 0.0 110-111 5.55 0.0 0.0 0.0 0.0 112-113 6.2375 0.0 0.0 0.0 0.0 114-115 6.8375 0.0 0.0 0.0 0.0 116-117 7.375 0.0 0.0 0.0 0.0 118-119 7.8625 0.0 0.0 0.0 0.0 120-121 8.5875 0.0 0.0 0.0 0.0 122-123 9.4375 0.0 0.0 0.0 0.0 124-125 10.075 0.0 0.0 0.0 0.0 126-127 10.6625 0.0 0.0 0.0 0.0 128-129 11.35 0.0 0.0 0.0 0.0 130-131 11.899999999999999 0.0 0.0 0.0 0.0 132-133 12.8375 0.0 0.0 0.0 0.0 134-135 13.825 0.0 0.0 0.0 0.0 136-137 14.8125 0.0 0.0 0.0 0.0 138-139 15.875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACCCTAA 10 0.006883923 144.625 8 >>END_MODULE Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213978 READS because READLEN < 1 Read 2213978 spots for SRR11462735.sra Written 2213978 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra Rejected 2213976 READS because READLEN < 1 Read 2213976 spots for SRR11462735.sra Written 2213976 spots for SRR11462735.sra SRR ids: ['SRR11462735.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_l_2ovd0f SRR11462735.sra spots: 44279522 blocks: [[1, 2213976], [2213977, 4427952], [4427953, 6641928], [6641929, 8855904], [8855905, 11069880], [11069881, 13283856], [13283857, 15497832], [15497833, 17711808], [17711809, 19925784], [19925785, 22139760], [22139761, 24353736], [24353737, 26567712], [26567713, 28781688], [28781689, 30995664], [30995665, 33209640], [33209641, 35423616], [35423617, 37637592], [37637593, 39851568], [39851569, 42065544], [42065545, 44279522]] SRR11462735 file size 15026418 SRR11462735 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 SRR11462735 SRR11462735_1.fastq Input file: SRR11462735_1.fastq trimmed: SRR11462735-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 11:54:30 2025 >> started Wed Feb 12 11:54:54 2025 >> done (23.578s) 44279522 reads processed; of these: 7997 ( 0.02%) short reads filtered out after trimming by size control 942 ( 0.00%) empty reads filtered out after trimming by size control 44270583 (99.98%) reads available; of these: 3765869 ( 8.51%) trimmed reads available after processing 40504714 (91.49%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1854 0.00% 19 2098 0.00% 20 2170 0.00% 21 2312 0.01% 22 2713 0.01% 23 2923 0.01% 24 3131 0.01% 25 2930 0.01% 26 3172 0.01% 27 4241 0.01% 28 3496 0.01% 29 3698 0.01% 30 3882 0.01% 31 3877 0.01% 32 3855 0.01% 33 4046 0.01% 34 4409 0.01% 35 4409 0.01% 36 4362 0.01% 37 6903 0.02% 38 4741 0.01% 39 5040 0.01% 40 4898 0.01% 41 4995 0.01% 42 5780 0.01% 43 5778 0.01% 44 5712 0.01% 45 8041 0.02% 46 7012 0.02% 47 10854 0.02% 48 8575 0.02% 49 12417 0.03% 50 7801 0.02% 51 8841 0.02% 52 8699 0.02% 53 9004 0.02% 54 10701 0.02% 55 9570 0.02% 56 11365 0.03% 57 12369 0.03% 58 10911 0.02% 59 11690 0.03% 60 13474 0.03% 61 12987 0.03% 62 37848 0.09% 63 13923 0.03% 64 15982 0.04% 65 14568 0.03% 66 15255 0.03% 67 17123 0.04% 68 16503 0.04% 69 24139 0.05% 70 17994 0.04% 71 20248 0.05% 72 22856 0.05% 73 27978 0.06% 74 36829 0.08% 75 24845 0.06% 76 22333 0.05% 77 28408 0.06% 78 26327 0.06% 79 35191 0.08% 80 27760 0.06% 81 28762 0.06% 82 31308 0.07% 83 31908 0.07% 84 34980 0.08% 85 36120 0.08% 86 40311 0.09% 87 41584 0.09% 88 39696 0.09% 89 121461 0.27% 90 45901 0.10% 91 52526 0.12% 92 45503 0.10% 93 50566 0.11% 94 55017 0.12% 95 52312 0.12% 96 59914 0.14% 97 63181 0.14% 98 58806 0.13% 99 61142 0.14% 100 61484 0.14% 101 67749 0.15% 102 120694 0.27% 103 74371 0.17% 104 74091 0.17% 105 76387 0.17% 106 80962 0.18% 107 86873 0.20% 108 92374 0.21% 109 124033 0.28% 110 100338 0.23% 111 100597 0.23% 112 184035 0.42% 113 114705 0.26% 114 109471 0.25% 115 111713 0.25% 116 113689 0.26% 117 125140 0.28% 118 132355 0.30% 119 135807 0.31% 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% 150 157 0.00% 151 40504714 91.49% 44270583 reads passed initial QC criterion=sequence-density sequence-density=7.50 sequence-density-rank=1 fanout-score=41.29 fanout-score-rank=1 prefix-density=9.16 prefix-fanout=33.8 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCTTCTGCTTG criterion=fanout-score sequence-density=7.50 sequence-density-rank=1 fanout-score=41.29 fanout-score-rank=1 prefix-density=9.16 prefix-fanout=33.8 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCTTCTGCTTG 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCTTCTGCTTG -o SRR11462735 - Input file: STDIN trimmed: SRR11462735-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTGGCCATCTCGTATGCCGTCTTCTGCTTG -- 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 11:56:25 2025 >> started Wed Feb 12 11:57:02 2025 >> done (37.278s) 33202937 reads processed; of these: 247 ( 0.00%) short reads filtered out after trimming by size control 7 ( 0.00%) empty reads filtered out after trimming by size control 33202683 (100.00%) reads available; of these: 5469571 (16.47%) trimmed reads available after processing 27733112 (83.53%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 1434 0.00% 19 1607 0.00% 20 1641 0.00% 21 1727 0.01% 22 2069 0.01% 23 2274 0.01% 24 2339 0.01% 25 2229 0.01% 26 2382 0.01% 27 3219 0.01% 28 2651 0.01% 29 2806 0.01% 30 2928 0.01% 31 2894 0.01% 32 2897 0.01% 33 3052 0.01% 34 3356 0.01% 35 3381 0.01% 36 3284 0.01% 37 5140 0.02% 38 3590 0.01% 39 3733 0.01% 40 3728 0.01% 41 3778 0.01% 42 4422 0.01% 43 4442 0.01% 44 4371 0.01% 45 6098 0.02% 46 5250 0.02% 47 8243 0.02% 48 6417 0.02% 49 9264 0.03% 50 5985 0.02% 51 6703 0.02% 52 6590 0.02% 53 6844 0.02% 54 8037 0.02% 55 7253 0.02% 56 8492 0.03% 57 9358 0.03% 58 8245 0.02% 59 8794 0.03% 60 10210 0.03% 61 9837 0.03% 62 28578 0.09% 63 10517 0.03% 64 11963 0.04% 65 11032 0.03% 66 11663 0.04% 67 12933 0.04% 68 12496 0.04% 69 18247 0.05% 70 13809 0.04% 71 15289 0.05% 72 17393 0.05% 73 21052 0.06% 74 27777 0.08% 75 18459 0.06% 76 16884 0.05% 77 21668 0.07% 78 19991 0.06% 79 26709 0.08% 80 20899 0.06% 81 22284 0.07% 82 23504 0.07% 83 24189 0.07% 84 26008 0.08% 85 27322 0.08% 86 30578 0.09% 87 31414 0.09% 88 30199 0.09% 89 91164 0.27% 90 35172 0.11% 91 40334 0.12% 92 34916 0.11% 93 37926 0.11% 94 41529 0.13% 95 39013 0.12% 96 45329 0.14% 97 47434 0.14% 98 44717 0.13% 99 46908 0.14% 100 46326 0.14% 101 51702 0.16% 102 90593 0.27% 103 56572 0.17% 104 55917 0.17% 105 57793 0.17% 106 60807 0.18% 107 65707 0.20% 108 70058 0.21% 109 93610 0.28% 110 75882 0.23% 111 75869 0.23% 112 139123 0.42% 113 85992 0.26% 114 82387 0.25% 115 84274 0.25% 116 85542 0.26% 117 90876 0.27% 118 95061 0.29% 119 99958 0.30% 120 109407 0.33% 121 114251 0.34% 122 109258 0.33% 123 162854 0.49% 124 138690 0.42% 125 120893 0.36% 126 124790 0.38% 127 148329 0.45% 128 134191 0.40% 129 133896 0.40% 130 135581 0.41% 131 139066 0.42% 132 164503 0.50% 133 188129 0.57% 134 153789 0.46% 135 169549 0.51% 136 158945 0.48% 137 165570 0.50% 138 199427 0.60% 139 170084 0.51% 140 208443 0.63% 141 174296 0.52% 142 181017 0.55% 143 194182 0.58% 144 189813 0.57% 145 224255 0.68% 146 209823 0.63% 147 325587 0.98% 148 718123 2.16% 149 0 0.00% 150 98 0.00% 151 25001502 75.30% criterion=sequence-density sequence-density=1.03 sequence-density-rank=1 fanout-score=2.14 fanout-score-rank=32 prefix-density=1.05 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAGTGTAGTACTCTGCT criterion=fanout-score sequence-density=0.01 sequence-density-rank=38 fanout-score=563.84 fanout-score-rank=1 prefix-density=0.32 prefix-fanout=17.7 sequence=TTGGATTTGATTAGATCCACCAATAAAAAGGGCTTGCCTTACACTCTTGGTCTTAATCAATTTGCTGATTGGACATGGCAAGAGTTCCAAAAGTACAGACTGGGAGCTGCCCAAAATTGCTCTGCAACCACAAGGGGCAATCACAAGCTTACGAACGCTCTTCTTCCTGAAACGAAAGACTGGAGGGAAGAAGGCATAGTCAGTCCCGTTAAGAATCAAGGTCACTGTGGATCTTGCTGGACTTTCAGCACCACTGGAGCTCTAGAGGCTGCTTACCACCAGGCTTTTGGGAAAGGAATCTCTCTGTCTGAACAGCAGCTTGTGGACTGTGCTAGAGCATTTAATAACTTTGGCTGCAATG Started job on | Feb 12 11:57:41 Started mapping on | Feb 12 11:57:41 Finished on | Feb 12 11:59:34 Mapping speed, Million of reads per hour | 1410.38 Number of input reads | 44270329 Average input read length | 144 UNIQUE READS: Uniquely mapped reads number | 36908190 Uniquely mapped reads % | 83.37% Average mapped length | 142.89 Number of splices: Total | 17011425 Number of splices: Annotated (sjdb) | 16593457 Number of splices: GT/AG | 16720103 Number of splices: GC/AG | 219056 Number of splices: AT/AC | 10562 Number of splices: Non-canonical | 61704 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.02% Deletion average length | 2.39 Insertion rate per base | 0.01% Insertion average length | 1.84 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1092757 % of reads mapped to multiple loci | 2.47% Number of reads mapped to too many loci | 3745735 % of reads mapped to too many loci | 8.46% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 5.58% % of reads unmapped: other | 0.12% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6269382 6269382 6269382 N_multimapping 1092757 1092757 1092757 N_noFeature 2051342 2749600 35515163 N_ambiguous 843148 148518 745 UnstrandedReadsAssigned:34013700 PositiveStrandReadsAssigned:34010072 NegativeStrandReadsAssigned:1392282 Dataset is classified positive stranded MeadianReadLen=151 20thPercentileLength=144 echo kmer=139 SRR11462735 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: SRR11462735-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 44,270,329 reads, 35,259,965 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,361 rounds 52401 SRR11462735.ke.tsv 34699 SRR11462735.se.tsv 87100 total ==> SRR11462735.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 3991 54.8231 Potri.005G024800.1.v4.1 1035 936 1166 32.8382 Potri.004G059700.1.v4.1 961 862 0 0 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 3490.47 32.3527 Potri.016G087400.1.v4.1 270 171 2338 360.417 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 2412.98 37.9976 Potri.012G127500.1.v4.1 977 878 91 2.73215 ==> SRR11462735.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 13 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 160 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 7 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 91 SRR11462735 completed mapping pipeline successfully