Starting /dee2/code/volunteer_pipeline.sh SRR6793146 current disk space = 3089573879808 free memory = 1482124176 SRR6793146 SRAfilesize cb1c5669a78c1a9fa6cd888134dde072 SRR6793146.sra SRR6793146.sra file validated SRR6793146 is single end SRR6793146 is conventional basespace SRR6793146 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6793146_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.527 32.0 32.0 32.0 32.0 32.0 2 31.6625 32.0 32.0 32.0 32.0 32.0 3 31.6845 32.0 32.0 32.0 32.0 32.0 4 31.7015 32.0 32.0 32.0 32.0 32.0 5 31.70925 32.0 32.0 32.0 32.0 32.0 6 35.13075 36.0 36.0 36.0 36.0 36.0 7 35.428 36.0 36.0 36.0 36.0 36.0 8 35.41875 36.0 36.0 36.0 36.0 36.0 9 35.33775 36.0 36.0 36.0 36.0 36.0 10-14 35.357749999999996 36.0 36.0 36.0 36.0 36.0 15-19 35.36775000000001 36.0 36.0 36.0 36.0 36.0 20-24 35.30025 36.0 36.0 36.0 36.0 36.0 25-29 35.24435 36.0 36.0 36.0 36.0 36.0 30-34 35.25279999999999 36.0 36.0 36.0 36.0 36.0 35-39 35.18320000000001 36.0 36.0 36.0 36.0 36.0 40-44 35.141450000000006 36.0 36.0 36.0 36.0 36.0 45-49 35.08555 36.0 36.0 36.0 36.0 36.0 50-54 35.1054 36.0 36.0 36.0 36.0 36.0 55-59 34.97935 36.0 36.0 36.0 36.0 36.0 60-64 34.9417 36.0 36.0 36.0 34.4 36.0 65-69 34.83579999999999 36.0 36.0 36.0 32.0 36.0 70-74 34.66805 36.0 36.0 36.0 32.0 36.0 75-79 34.72305 36.0 36.0 36.0 32.0 36.0 80-84 34.573899999999995 36.0 36.0 36.0 32.0 36.0 85-89 34.5787 36.0 36.0 36.0 32.0 36.0 90-94 34.40555 36.0 36.0 36.0 32.0 36.0 95-99 34.33705 36.0 36.0 36.0 32.0 36.0 100-104 34.4359 36.0 36.0 36.0 32.0 36.0 105-109 34.261900000000004 36.0 36.0 36.0 32.0 36.0 110-114 34.28484999999999 36.0 36.0 36.0 32.0 36.0 115-119 34.18495 36.0 36.0 36.0 32.0 36.0 120-124 34.10055 36.0 36.0 36.0 32.0 36.0 125-129 34.01565000000001 36.0 36.0 36.0 30.0 36.0 130-134 33.819849999999995 36.0 34.4 36.0 28.0 36.0 135-139 33.301750000000006 36.0 32.0 36.0 27.0 36.0 140-144 33.35125 36.0 32.0 36.0 27.0 36.0 145-149 32.67405 36.0 32.0 36.0 27.0 36.0 150-151 30.617874999999998 34.0 29.5 36.0 20.5 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 3.0 20 3.0 21 4.0 22 3.0 23 3.0 24 6.0 25 11.0 26 25.0 27 36.0 28 60.0 29 65.0 30 93.0 31 98.0 32 147.0 33 281.0 34 730.0 35 2432.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 25.45 11.05 15.075 48.425000000000004 2 22.5 17.5 31.55 28.449999999999996 3 22.55 22.25 22.725 32.475 4 26.8 27.725 17.5 27.975 5 26.75 30.075000000000003 19.15 24.025 6 22.56281407035176 33.618090452261306 21.934673366834172 21.884422110552766 7 19.05 17.5 40.5 22.95 8 22.975 20.4 28.675 27.950000000000003 9 22.025 20.45 32.324999999999996 25.2 10-14 22.900000000000002 26.775 25.69 24.635 15-19 23.176158807940396 26.526326316315817 27.87139356967848 22.4261213060653 20-24 23.73 26.795 26.625 22.85 25-29 24.060000000000002 26.529999999999998 25.31 24.099999999999998 30-34 23.235 25.86 25.650000000000002 25.255 35-39 23.78 25.865 25.324999999999996 25.03 40-44 23.57 25.655 26.375 24.4 45-49 22.751137556877843 25.876293814690737 26.70133506675334 24.671233561678083 50-54 23.582358235823584 27.182718271827184 26.712671267126716 22.522252225222523 55-59 22.884576915383075 26.7753550710142 26.955391078215644 23.384676935387077 60-64 22.869999999999997 25.295 27.944999999999997 23.89 65-69 23.775 25.705 26.6 23.919999999999998 70-74 23.18 26.75 26.135 23.935000000000002 75-79 23.503525528829325 26.49397409611442 25.463819572935943 24.538680802120318 80-84 23.199279711884753 25.570228091236498 25.880352140856345 25.350140056022408 85-89 24.082041020510257 26.278139069534767 26.353176588294147 23.28664332166083 90-94 24.415870315705206 26.63731425426527 25.681693100515336 23.265122329514185 95-99 22.930637573816433 27.05935341807627 26.27364628165349 23.73636272645381 100-104 23.650912728182043 26.451612903225808 26.641660415103775 23.25581395348837 105-109 23.504380475594495 25.70212765957447 27.133917396745932 23.659574468085108 110-114 23.85146631968772 26.448803923531177 25.482934641177057 24.216795115604043 115-119 23.63891112890312 26.24099279423539 26.46617293835068 23.65392313851081 120-124 24.82996599319864 25.870174034806958 26.150230046009206 23.149629925985195 125-129 24.50553302288318 27.68514345801412 24.310249862300335 23.499073656802363 130-134 24.88744372186093 26.853426713356676 25.20760380190095 23.051525762881443 135-139 25.01252128618652 26.990884503656215 23.96574176099369 24.03085244916358 140-144 25.728446981075397 27.110243316311205 23.14008210673876 24.021227595874635 145-149 25.27263631815908 27.378689344672335 23.371685842921462 23.976988494247124 150-151 23.995493803980473 29.64075603955439 21.992740017524095 24.371010138941042 >>END_MODULE >>Per sequence GC content warn #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 0.0 22 0.0 23 0.5 24 1.5 25 3.0 26 2.5 27 1.5 28 2.5 29 3.0 30 5.5 31 10.5 32 11.0 33 12.0 34 27.5 35 50.5 36 79.5 37 107.5 38 98.5 39 98.5 40 116.0 41 124.0 42 145.0 43 161.0 44 183.0 45 208.5 46 219.5 47 236.0 48 219.5 49 194.5 50 184.5 51 169.5 52 165.5 53 175.0 54 162.5 55 125.0 56 110.5 57 121.0 58 111.5 59 74.0 60 66.0 61 49.5 62 34.0 63 31.5 64 13.5 65 7.0 66 11.5 67 13.5 68 10.0 69 10.5 70 9.5 71 5.5 72 4.5 73 4.5 74 3.5 75 1.5 76 0.5 77 0.0 78 0.5 79 0.5 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 0.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.5 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.005 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.005 50-54 0.01 55-59 0.02 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.015 80-84 0.04 85-89 0.05 90-94 0.065 95-99 0.09 100-104 0.025 105-109 0.125 110-114 0.09 115-119 0.08 120-124 0.02 125-129 0.145 130-134 0.05 135-139 0.16999999999999998 140-144 0.13 145-149 0.05 150-151 0.13749999999999998 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.3 #Duplication Level Percentage of deduplicated Percentage of total 1 89.0485312899106 69.72500000000001 2 5.842911877394636 9.15 3 2.075351213282248 4.875 4 1.0217113665389528 3.2 5 0.5108556832694764 2.0 6 0.4789272030651341 2.25 7 0.2554278416347382 1.4000000000000001 8 0.19157088122605362 1.2 9 0.19157088122605362 1.35 >10 0.38314176245210724 4.8500000000000005 >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 CCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATA 41 1.0250000000000001 No Hit CGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCT 25 0.625 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 20 0.5 No Hit CGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAGGGAT 16 0.4 No Hit CAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCT 14 0.35000000000000003 No Hit CTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGA 13 0.325 No Hit CGCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCT 13 0.325 No Hit CGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCC 11 0.27499999999999997 No Hit CAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGG 11 0.27499999999999997 No Hit CCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCG 10 0.25 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 10 0.25 No Hit CCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCA 10 0.25 No Hit TCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGC 9 0.22499999999999998 No Hit CCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAAT 9 0.22499999999999998 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGA 9 0.22499999999999998 No Hit CGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCA 9 0.22499999999999998 No Hit CTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTATTCAACGAGTC 9 0.22499999999999998 No Hit CCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAA 9 0.22499999999999998 No Hit CTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTT 8 0.2 No Hit GTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCT 8 0.2 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAA 8 0.2 No Hit CTCAAAGCAAGCCTACGCTCTGGATACATTAGCATGGGATAACATCATAG 8 0.2 No Hit CTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAG 8 0.2 No Hit GCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTC 8 0.2 No Hit CCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAG 7 0.17500000000000002 No Hit CCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCT 7 0.17500000000000002 No Hit CAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAG 7 0.17500000000000002 No Hit TTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTG 7 0.17500000000000002 No Hit CGCGGGCTCTGCCCGTTGCTCTGATGATTCATGATAACTCGACGGATCGC 7 0.17500000000000002 No Hit CAGAAATTTGAATGATGCGTCGCCAGCACGAAGGCCGTGCGATCCGTCGA 7 0.17500000000000002 No Hit CCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTA 7 0.17500000000000002 No Hit GCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTA 7 0.17500000000000002 No Hit TCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAA 6 0.15 No Hit CAAACCCCGACTTCTGGAAGGGACGCATTTATTAGATAAAAGGTCGACGC 6 0.15 No Hit CCCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAAT 6 0.15 No Hit GCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTC 6 0.15 No Hit CCCCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAA 6 0.15 No Hit TGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGT 6 0.15 No Hit TGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTT 6 0.15 No Hit ATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAG 6 0.15 No Hit CCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAA 6 0.15 No Hit CAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTC 6 0.15 No Hit CCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAG 6 0.15 No Hit CGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCC 6 0.15 No Hit GTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCT 6 0.15 No Hit GGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCC 6 0.15 No Hit CCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATT 6 0.15 No Hit CTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTCCGGAATC 5 0.125 No Hit CCGCGGCTGCTGGCACCAGACTTGCCCTCCAATGGATCCTCGTTAAGGGA 5 0.125 No Hit CTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGATGTAT 5 0.125 No Hit GTCGACGCGGGCTCTGCCCGTTGCTCTGATGATTCATGATAACTCGACGG 5 0.125 No Hit GTCGCCAGCACGAAGGCCGTGCGATCCGTCGAGTTATCATGAATCATCAG 5 0.125 No Hit CGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACT 5 0.125 No Hit CCCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAA 5 0.125 No Hit CTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCTCTATCCTACCATC 5 0.125 No Hit CCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGC 5 0.125 No Hit CTCCAATGGATCCTCGTTAAGGGATTTAGATTGTACTCATTCCAATTACC 5 0.125 No Hit GCTTCTTAGAGGGACTATGGCCTTCCAGGCCAAGGAAGTTTGAGGCAATA 5 0.125 No Hit GCGCTCCTGGCCTTAACTGGCCGGGTCGTGCCTCCGGTGCTGTTACTTTG 5 0.125 No Hit CTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACAGCACCGGAGGCACGA 5 0.125 No Hit CTTTGGGTTGGGTCGGCCGGTCCGCCTCAGGTGTGCACCGGTCGCCTCGT 5 0.125 No Hit CTCAGGTGTGCACCGGTCGCCTCGTCCCTTCTACCGGCGATGCGCTCCTG 5 0.125 No Hit CCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTGTAAGTAT 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 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.037500000000000006 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.075 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.0875 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.1 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.1 0.0 0.0 0.0 0.0 70-71 0.1 0.0 0.0 0.0 0.0 72-73 0.125 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.15 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 82-83 0.16249999999999998 0.0 0.0 0.0 0.0 84-85 0.21250000000000002 0.0 0.0 0.0 0.0 86-87 0.225 0.0 0.0 0.0 0.0 88-89 0.275 0.0 0.0 0.0 0.0 90-91 0.3375 0.0 0.0 0.0 0.0 92-93 0.4125 0.0 0.0 0.0 0.0 94-95 0.44999999999999996 0.0 0.0 0.0 0.0 96-97 0.525 0.0 0.0 0.0 0.0 98-99 0.6 0.0 0.0 0.0 0.0 100-101 0.7 0.0 0.0 0.0 0.0 102-103 0.8500000000000001 0.0 0.0 0.0 0.0 104-105 1.0875 0.0 0.0 0.0 0.0 106-107 1.4125 0.0 0.0 0.0 0.0 108-109 1.65 0.0 0.0 0.0 0.0 110-111 1.9625 0.0 0.0 0.0 0.0 112-113 2.5125 0.0 0.0 0.0 0.0 114-115 2.9375 0.0 0.0 0.0 0.0 116-117 3.3625 0.0 0.0 0.0 0.0 118-119 4.0375 0.0 0.0 0.0 0.0 120-121 4.4875 0.0 0.0 0.0 0.0 122-123 5.275 0.0 0.0 0.0 0.0 124-125 5.7625 0.0 0.0 0.0 0.0 126-127 6.5625 0.0 0.0 0.0 0.0 128-129 7.4125 0.0 0.0 0.0 0.0 130-131 8.125 0.0 0.0 0.0 0.0 132-133 9.0 0.0 0.0 0.0 0.0 134-135 10.05 0.0 0.0 0.0 0.0 136-137 11.162500000000001 0.0 0.0 0.0 0.0 138-139 12.475 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGTCTGC 10 0.006830828 145.0 9 ACGTAGT 10 0.006830828 145.0 4 CGTAGTC 10 0.006830828 145.0 5 GACGTAG 10 0.006830828 145.0 3 GGGACGT 10 0.006830828 145.0 1 >>END_MODULE Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017883 READS because READLEN < 1 Read 2017883 spots for SRR6793146.sra Written 2017883 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra Rejected 2017864 READS because READLEN < 1 Read 2017864 spots for SRR6793146.sra Written 2017864 spots for SRR6793146.sra SRR ids: ['SRR6793146.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_1zec9vi0 SRR6793146.sra spots: 40357299 blocks: [[1, 2017864], [2017865, 4035728], [4035729, 6053592], [6053593, 8071456], [8071457, 10089320], [10089321, 12107184], [12107185, 14125048], [14125049, 16142912], [16142913, 18160776], [18160777, 20178640], [20178641, 22196504], [22196505, 24214368], [24214369, 26232232], [26232233, 28250096], [28250097, 30267960], [30267961, 32285824], [32285825, 34303688], [34303689, 36321552], [36321553, 38339416], [38339417, 40357299]] SRR6793146 file size 13654064 SRR6793146 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 SRR6793146 SRR6793146_1.fastq Input file: SRR6793146_1.fastq trimmed: SRR6793146-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 Thu Feb 13 14:38:07 2025 >> started Thu Feb 13 14:38:32 2025 >> done (24.448s) 40357299 reads processed; of these: 3128 ( 0.01%) short reads filtered out after trimming by size control 776 ( 0.00%) empty reads filtered out after trimming by size control 40353395 (99.99%) reads available; of these: 1788152 ( 4.43%) trimmed reads available after processing 38565243 (95.57%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 199 0.00% 19 162 0.00% 20 171 0.00% 21 205 0.00% 22 204 0.00% 23 229 0.00% 24 267 0.00% 25 356 0.00% 26 380 0.00% 27 401 0.00% 28 437 0.00% 29 444 0.00% 30 534 0.00% 31 511 0.00% 32 589 0.00% 33 610 0.00% 34 670 0.00% 35 745 0.00% 36 794 0.00% 37 744 0.00% 38 937 0.00% 39 785 0.00% 40 880 0.00% 41 1041 0.00% 42 934 0.00% 43 965 0.00% 44 987 0.00% 45 972 0.00% 46 1053 0.00% 47 1061 0.00% 48 1071 0.00% 49 1110 0.00% 50 1088 0.00% 51 1172 0.00% 52 1151 0.00% 53 1201 0.00% 54 1217 0.00% 55 1315 0.00% 56 1421 0.00% 57 1412 0.00% 58 1550 0.00% 59 2067 0.01% 60 1775 0.00% 61 1927 0.00% 62 1910 0.00% 63 1824 0.00% 64 1723 0.00% 65 1681 0.00% 66 1671 0.00% 67 1713 0.00% 68 1820 0.00% 69 1832 0.00% 70 1841 0.00% 71 2219 0.01% 72 2291 0.01% 73 2661 0.01% 74 2607 0.01% 75 3047 0.01% 76 2989 0.01% 77 2967 0.01% 78 3320 0.01% 79 3246 0.01% 80 3929 0.01% 81 4264 0.01% 82 4809 0.01% 83 5313 0.01% 84 5935 0.01% 85 6478 0.02% 86 6506 0.02% 87 6999 0.02% 88 7674 0.02% 89 8842 0.02% 90 9952 0.02% 91 11561 0.03% 92 13780 0.03% 93 15318 0.04% 94 16972 0.04% 95 19042 0.05% 96 20792 0.05% 97 22197 0.06% 98 24726 0.06% 99 28227 0.07% 100 29645 0.07% 101 33302 0.08% 102 38402 0.10% 103 43290 0.11% 104 46729 0.12% 105 47624 0.12% 106 50727 0.13% 107 57150 0.14% 108 60208 0.15% 109 67350 0.17% 110 71225 0.18% 111 85610 0.21% 112 90308 0.22% 113 90758 0.22% 114 100231 0.25% 115 104023 0.26% 116 107982 0.27% 117 105649 0.26% 118 109311 0.27% 119 119787 0.30% 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 62 0.00% 131 190 0.00% 132 79 0.00% 133 124 0.00% 134 163 0.00% 135 179 0.00% 136 111 0.00% 137 25 0.00% 138 56 0.00% 139 9 0.00% 140 0 0.00% 141 23 0.00% 142 5 0.00% 143 435 0.00% 144 277 0.00% 145 24 0.00% 146 31 0.00% 147 183 0.00% 148 1007 0.00% 149 653 0.00% 150 2783 0.01% 151 38565243 95.57% 40353395 reads passed initial QC criterion=sequence-density sequence-density=8.04 sequence-density-rank=1 fanout-score=45.89 fanout-score-rank=2 prefix-density=9.65 prefix-fanout=38.3 sequence=AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATC criterion=fanout-score sequence-density=0.03 sequence-density-rank=12 fanout-score=51.80 fanout-score-rank=1 prefix-density=0.94 prefix-fanout=1.5 sequence=CGCATCGCCGGCCCCCATCCACTTCCCTCCCGACAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTTTCCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGACGGAATTTACCGCCCGATTGGGGCTGCATTCCCAAACAACCCGACTCGCAGACAGCGCCTCGTGGTGCGGCAGGGTCCAGCCACGACGGGGCTCTCACCCTCTCCGGCGCCCCTTTCCAGGGGACTTGGGCCTGGTCCGCCGCTGAGGACGCTTCTCCAGACTACAATTCGGACGCCGCAGGCGCCAGATTCTCAAGCTGGGCATTTCCCGGTTCGCTCGCCGTTACTAGGGGAATCCTTGTAAGTTTCTTTTCCT 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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATC -o SRR6793146 - Input file: STDIN trimmed: SRR6793146-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACAGTGATC -- 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 Thu Feb 13 14:40:11 2025 >> started Thu Feb 13 14:40:46 2025 >> done (35.315s) 31385974 reads processed; of these: 29 ( 0.00%) short reads filtered out after trimming by size control 18 ( 0.00%) empty reads filtered out after trimming by size control 31385927 (100.00%) reads available; of these: 4974982 (15.85%) trimmed reads available after processing 26410945 (84.15%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 163 0.00% 19 120 0.00% 20 137 0.00% 21 161 0.00% 22 153 0.00% 23 182 0.00% 24 194 0.00% 25 273 0.00% 26 291 0.00% 27 307 0.00% 28 353 0.00% 29 340 0.00% 30 427 0.00% 31 398 0.00% 32 463 0.00% 33 454 0.00% 34 540 0.00% 35 585 0.00% 36 608 0.00% 37 601 0.00% 38 719 0.00% 39 615 0.00% 40 684 0.00% 41 806 0.00% 42 728 0.00% 43 769 0.00% 44 769 0.00% 45 778 0.00% 46 817 0.00% 47 825 0.00% 48 826 0.00% 49 856 0.00% 50 863 0.00% 51 905 0.00% 52 941 0.00% 53 942 0.00% 54 952 0.00% 55 998 0.00% 56 1095 0.00% 57 1083 0.00% 58 1265 0.00% 59 1618 0.01% 60 1410 0.00% 61 1470 0.00% 62 1474 0.00% 63 1433 0.00% 64 1341 0.00% 65 1338 0.00% 66 1324 0.00% 67 1315 0.00% 68 1408 0.00% 69 1425 0.00% 70 1447 0.00% 71 1715 0.01% 72 1796 0.01% 73 2080 0.01% 74 2084 0.01% 75 2370 0.01% 76 2299 0.01% 77 2317 0.01% 78 2574 0.01% 79 2543 0.01% 80 3074 0.01% 81 3336 0.01% 82 3805 0.01% 83 4172 0.01% 84 4649 0.01% 85 5023 0.02% 86 5127 0.02% 87 5469 0.02% 88 5941 0.02% 89 7038 0.02% 90 8053 0.03% 91 9194 0.03% 92 10831 0.03% 93 11661 0.04% 94 13160 0.04% 95 14876 0.05% 96 16217 0.05% 97 17339 0.06% 98 19320 0.06% 99 22091 0.07% 100 23125 0.07% 101 26077 0.08% 102 30053 0.10% 103 33783 0.11% 104 36388 0.12% 105 37321 0.12% 106 39484 0.13% 107 44845 0.14% 108 46834 0.15% 109 52651 0.17% 110 55431 0.18% 111 67108 0.21% 112 70428 0.22% 113 70803 0.23% 114 78054 0.25% 115 81057 0.26% 116 83598 0.27% 117 81286 0.26% 118 84941 0.27% 119 95332 0.30% 120 103970 0.33% 121 116530 0.37% 122 109773 0.35% 123 116072 0.37% 124 115838 0.37% 125 124853 0.40% 126 134680 0.43% 127 132613 0.42% 128 142718 0.45% 129 134529 0.43% 130 142575 0.45% 131 140262 0.45% 132 156536 0.50% 133 157295 0.50% 134 173727 0.55% 135 169233 0.54% 136 165689 0.53% 137 168112 0.54% 138 156549 0.50% 139 166513 0.53% 140 158443 0.50% 141 164931 0.53% 142 172324 0.55% 143 186351 0.59% 144 189594 0.60% 145 194014 0.62% 146 206367 0.66% 147 274884 0.88% 148 581369 1.85% 149 437 0.00% 150 1856 0.01% 151 25036548 79.77% criterion=sequence-density sequence-density=0.37 sequence-density-rank=1 fanout-score=11.66 fanout-score-rank=7 prefix-density=1.81 prefix-fanout=2.4 sequence=CTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTC criterion=fanout-score sequence-density=0.08 sequence-density-rank=19 fanout-score=106.29 fanout-score-rank=1 prefix-density=5.72 prefix-fanout=1.6 sequence=CAAAGATTACCTGGGCCTGTCGG Started job on | Feb 13 14:41:22 Started mapping on | Feb 13 14:41:22 Finished on | Feb 13 14:43:34 Mapping speed, Million of reads per hour | 1100.55 Number of input reads | 40353348 Average input read length | 147 UNIQUE READS: Uniquely mapped reads number | 19044279 Uniquely mapped reads % | 47.19% Average mapped length | 146.45 Number of splices: Total | 7755938 Number of splices: Annotated (sjdb) | 7561138 Number of splices: GT/AG | 7595197 Number of splices: GC/AG | 113356 Number of splices: AT/AC | 11517 Number of splices: Non-canonical | 35868 Mismatch rate per base, % | 0.51% Deletion rate per base | 0.03% Deletion average length | 2.76 Insertion rate per base | 0.03% Insertion average length | 2.79 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2141488 % of reads mapped to multiple loci | 5.31% Number of reads mapped to too many loci | 18377268 % of reads mapped to too many loci | 45.54% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.53% % of reads unmapped: other | 0.43% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 19167581 19167581 19167581 N_multimapping 2141488 2141488 2141488 N_noFeature 1766170 10174962 10378163 N_ambiguous 350180 46763 46494 UnstrandedReadsAssigned:16927929 PositiveStrandReadsAssigned:8822554 NegativeStrandReadsAssigned:8619622 Dataset is classified unstranded MeadianReadLen=151 20thPercentileLength=148 echo kmer=143 SRR6793146 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: SRR6793146-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 40,353,348 reads, 31,376,170 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,155 rounds 52401 SRR6793146.ke.tsv 34699 SRR6793146.se.tsv 87100 total ==> SRR6793146.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 1240.63 24.06 Potri.005G024800.1.v4.1 1035 936 317 12.6041 Potri.004G059700.1.v4.1 961 862 4 0.172695 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 1292.23 16.9098 Potri.016G087400.1.v4.1 270 171 985.768 214.538 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 872.854 19.405 Potri.012G127500.1.v4.1 977 878 530 22.4651 ==> SRR6793146.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 179 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 228 Potri.001G212900.v4.1 28 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 6 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 18 SRR6793146 completed mapping pipeline successfully