Starting /dee2/code/volunteer_pipeline.sh SRR12682219 current disk space = 1547691880448 free memory = 1603013896 SRR12682219 SRAfilesize 5204b0a9809abc985c1ed7abffcd7078 SRR12682219.sra SRR12682219.sra file validated SRR12682219 is single end SRR12682219 is conventional basespace SRR12682219 read1 length is 45-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12682219_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 45-150 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.46825 32.0 32.0 32.0 32.0 32.0 2 31.502 32.0 32.0 32.0 32.0 32.0 3 31.61075 32.0 32.0 32.0 32.0 32.0 4 31.60125 32.0 32.0 32.0 32.0 32.0 5 31.658 32.0 32.0 32.0 32.0 32.0 6 34.832 36.0 36.0 36.0 36.0 36.0 7 35.141 36.0 36.0 36.0 36.0 36.0 8 35.04775 36.0 36.0 36.0 36.0 36.0 9 35.1575 36.0 36.0 36.0 36.0 36.0 10-14 35.13265 36.0 36.0 36.0 36.0 36.0 15-19 35.06275000000001 36.0 36.0 36.0 36.0 36.0 20-24 34.95395 36.0 36.0 36.0 35.2 36.0 25-29 34.858799999999995 36.0 36.0 36.0 33.6 36.0 30-34 34.8215 36.0 36.0 36.0 33.6 36.0 35-39 34.7528 36.0 36.0 36.0 32.8 36.0 40-44 34.74400000000001 36.0 36.0 36.0 32.8 36.0 45-49 34.56856829900808 36.0 36.0 36.0 32.0 36.0 50-54 34.5256773160451 36.0 36.0 36.0 32.0 36.0 55-59 34.39868904701199 36.0 36.0 36.0 32.0 36.0 60-64 34.25097571405409 36.0 36.0 36.0 32.0 36.0 65-69 34.130144953760684 36.0 36.0 36.0 32.0 36.0 70-74 34.0880253669587 36.0 36.0 36.0 32.0 36.0 75-79 34.01395297234653 36.0 36.0 36.0 32.0 36.0 80-84 33.916448041635576 36.0 36.0 36.0 30.0 36.0 85-89 33.826614441204 36.0 36.0 36.0 28.0 36.0 90-94 33.86715161317067 36.0 36.0 36.0 29.0 36.0 95-99 33.73082311770831 36.0 36.0 36.0 27.0 36.0 100-104 33.672038797043726 36.0 36.0 36.0 27.0 36.0 105-109 33.39448970736796 36.0 33.6 36.0 27.0 36.0 110-114 33.178063256770415 36.0 32.0 36.0 27.0 36.0 115-119 32.85708969552374 36.0 32.0 36.0 27.0 36.0 120-124 32.219893741511626 34.4 32.0 36.0 24.6 36.0 125-129 32.084079191718736 34.4 32.0 36.0 23.4 36.0 130-134 31.659070592636976 32.8 32.0 36.0 21.0 36.0 135-139 31.791006152143513 32.8 32.0 36.0 23.4 36.0 140-144 31.891636321726793 35.2 32.0 36.0 23.4 36.0 145-149 31.62319984118716 32.0 32.0 36.0 21.0 36.0 150 26.350197109067018 27.0 14.0 32.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 3.0 20 2.0 21 4.0 22 5.0 23 16.0 24 19.0 25 29.0 26 42.0 27 72.0 28 87.0 29 95.0 30 135.0 31 176.0 32 219.0 33 356.0 34 927.0 35 1813.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 29.45 9.950000000000001 8.774999999999999 51.824999999999996 2 21.525 13.600000000000001 32.85 32.025 3 21.425 15.225 21.224999999999998 42.125 4 27.725 22.675 19.625 29.975 5 25.775 28.050000000000004 22.475 23.7 6 22.47983870967742 31.37600806451613 24.243951612903224 21.900201612903224 7 18.075 23.9 36.625 21.4 8 20.175 21.0 31.175000000000004 27.650000000000002 9 20.45 20.724999999999998 32.35 26.474999999999998 10-14 22.855 26.135 24.425 26.584999999999997 15-19 23.655 23.96 25.619999999999997 26.765 20-24 23.535 24.735 24.995 26.735 25-29 24.095 23.68 24.645 27.58 30-34 23.935000000000002 23.294999999999998 25.055 27.715 35-39 23.925 24.815 23.98 27.279999999999998 40-44 23.811190559527976 24.25621281064053 24.671233561678083 27.26136306815341 45-49 23.524409763905563 24.2547018807523 24.92997198879552 27.290916366546618 50-54 23.577398528602174 24.813572894249535 24.698463540363345 26.910565036784945 55-59 23.446341829836246 24.783414292152838 24.97871701136762 26.791526866643295 60-64 23.1520922074668 23.031821598596842 25.597594587822602 28.218491606113755 65-69 23.101995787784578 24.636445692508275 25.193059873633537 27.068498646073614 70-74 23.87287880309268 23.968269906617127 25.233457174415104 26.92539411587509 75-79 24.413924942147098 23.895764161384445 24.061776838716167 27.62853405775229 80-84 24.002222895827018 23.64858037789229 24.886329190663837 27.46286753561685 85-89 23.98821916417001 23.86634844868735 24.917483369725282 27.22794901741736 90-94 24.571750948815264 24.00759052210483 24.66919684070161 26.7514616883783 95-99 23.08092095005457 24.447793773712384 24.796008523465517 27.67527675276753 100-104 23.310023310023308 23.91926255562619 24.819877092604365 27.950837041746134 105-109 24.745965331739388 23.865674074879095 24.452534912785957 26.935825680595553 110-114 24.399798533773577 23.97448094465275 24.243102579886955 27.38261794168672 115-119 24.670861004310847 23.272748456250728 24.787370383315857 27.26902015612257 120-124 24.453268173488087 23.530849114233355 24.886988393402564 27.12889431887599 125-129 24.349068242321927 23.888059216933964 23.686773586130773 28.076098954613336 130-134 24.53193832599119 23.816079295154186 24.37362334801762 27.278359030837002 135-139 25.09303174024079 23.889091572418824 24.531192995257207 26.48668369208318 140-144 24.614782948768088 24.0281579976535 23.94211967149003 27.41493938208838 145-149 25.271317829457363 23.092161929371233 22.859603789836346 28.776916451335055 150 27.92378449408673 0.0 34.03416557161629 38.042049934296976 >>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 0.0 24 0.5 25 1.0 26 1.5 27 2.0 28 1.5 29 2.5 30 7.0 31 7.5 32 6.5 33 11.5 34 17.0 35 24.5 36 47.0 37 57.5 38 55.0 39 61.0 40 79.5 41 101.0 42 105.5 43 116.0 44 126.0 45 142.5 46 173.5 47 193.5 48 194.0 49 191.5 50 191.5 51 189.0 52 193.0 53 187.0 54 162.0 55 160.5 56 157.0 57 122.5 58 111.0 59 102.5 60 90.5 61 76.5 62 66.0 63 66.5 64 63.0 65 56.0 66 44.5 67 48.0 68 47.0 69 30.0 70 20.0 71 22.0 72 23.5 73 17.0 74 14.5 75 15.0 76 9.5 77 4.0 78 2.5 79 2.0 80 1.0 81 1.0 82 1.0 83 1.0 84 1.0 85 0.5 86 0.0 87 0.0 88 0.5 89 0.5 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 0.5 100 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 0.8 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 0.005 45-49 0.01000300090027008 50-54 0.005004504053648284 55-59 0.030037546933667083 60-64 0.03506662659052199 65-69 0.020054146194725758 70-74 0.03011443485243927 75-79 0.005030434126465114 80-84 0.015153811183512653 85-89 0.015231519090170594 90-94 0.025637081474644927 95-99 0.046753246753246755 100-104 0.042363905952128786 105-109 0.03259275354446195 110-114 0.011191315539141626 115-119 0.029118863199580687 120-124 0.012215978499877841 125-129 0.038943337444018955 130-134 0.006882786151834262 135-139 0.0072960747118050485 140-144 0.015640885274106515 145-149 0.01722356183258698 150 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 45-49 3.0 50-54 1.0 55-59 2.0 60-64 4.0 65-69 1.0 70-74 9.0 75-79 14.0 80-84 16.0 85-89 33.0 90-94 45.0 95-99 63.0 100-104 86.0 105-109 105.0 110-114 122.0 115-119 160.0 120-124 175.0 125-129 192.0 130-134 160.0 135-139 173.0 140-144 181.0 145-149 933.0 150-151 1522.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 83.5 #Duplication Level Percentage of deduplicated Percentage of total 1 90.59880239520957 75.64999999999999 2 4.790419161676647 8.0 3 2.095808383233533 5.25 4 1.2574850299401197 4.2 5 0.5089820359281437 2.125 6 0.32934131736526945 1.6500000000000001 7 0.11976047904191617 0.7000000000000001 8 0.08982035928143713 0.6 9 0.059880239520958084 0.44999999999999996 >10 0.14970059880239522 1.375 >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 CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 14 0.35000000000000003 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 11 0.27499999999999997 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 10 0.25 No Hit CTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGG 10 0.25 No Hit CGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCC 10 0.25 No Hit CTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTC 9 0.22499999999999998 No Hit CCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAG 9 0.22499999999999998 No Hit CTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGCACGT 8 0.2 No Hit CCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCT 8 0.2 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 8 0.2 No Hit CGGCAATTTCAAGCACTCTTTGACTCTCTTTTCAAAGTCCTTTTCATCTT 7 0.17500000000000002 No Hit CAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGC 7 0.17500000000000002 No Hit CTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTG 7 0.17500000000000002 No Hit CGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCAT 7 0.17500000000000002 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGA 6 0.15 No Hit GTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAG 6 0.15 No Hit CCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTAT 6 0.15 No Hit GTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTCGCG 6 0.15 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 6 0.15 No Hit CTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCAAAGACTTT 6 0.15 No Hit GTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACT 6 0.15 No Hit GTCGGGGCAGGCGGCGGGCGCAGGCGCCGCTTGCTAGCTTGGATTCTGAC 6 0.15 No Hit GTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCCA 6 0.15 No Hit CGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCC 6 0.15 No Hit CATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCTTTTATCTAAT 6 0.15 No Hit ATCGCTTCGAGCCTCCACCAGAGTTTCCTCTGGCTTCGCCCCGCTCAGGC 5 0.125 No Hit AGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTCGAG 5 0.125 No Hit CTGACTATGAAATACGAATGCCCCCGACTGTCCCTATTAATCATTACTCC 5 0.125 No Hit GGCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTC 5 0.125 No Hit GCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGATGCCGGAGGCACG 5 0.125 No Hit CCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGAC 5 0.125 No Hit CGGAAACCTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGG 5 0.125 No Hit CCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTC 5 0.125 No Hit CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 5 0.125 No Hit GCAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGG 5 0.125 No Hit ATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAAC 5 0.125 No Hit CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 5 0.125 No Hit CTCTAGAATTACTACGGTTATCCGAGTAGCACGTACCATCAAACAAACTA 5 0.125 No Hit CCGACTCGTTGACGGCGCCTCGTGGGGCGACAGGGTCCGGGCCGGACGGG 5 0.125 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 5 0.125 No Hit CCCACTTATCCTACACCTCTCAAGTCATTTCACAAAGTCGGACTAGAGTC 5 0.125 No Hit GTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGA 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 10-11 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 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0 0.0 0.0 0.0 0.0 126-127 0.0 0.0 0.0 0.0 0.0 128-129 0.0 0.0 0.0 0.0 0.0 130-131 0.0 0.0 0.0 0.0 0.0 132-133 0.0125 0.0 0.0 0.0 0.0 134-135 0.037500000000000006 0.0 0.0 0.0 0.0 136-137 0.05 0.0 0.0 0.0 0.0 138 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGCAGG 10 0.009117515 131.65 5 GGGGCAG 10 0.009117515 131.65 4 CAGGCGG 10 0.009117515 131.65 8 CCCTAAT 10 0.009117515 131.65 1 >>END_MODULE Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402074 READS because READLEN < 1 Read 1402074 spots for SRR12682219.sra Written 1402074 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra Rejected 1402070 READS because READLEN < 1 Read 1402070 spots for SRR12682219.sra Written 1402070 spots for SRR12682219.sra SRR ids: ['SRR12682219.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_td_0n96q SRR12682219.sra spots: 28041404 blocks: [[1, 1402070], [1402071, 2804140], [2804141, 4206210], [4206211, 5608280], [5608281, 7010350], [7010351, 8412420], [8412421, 9814490], [9814491, 11216560], [11216561, 12618630], [12618631, 14020700], [14020701, 15422770], [15422771, 16824840], [16824841, 18226910], [18226911, 19628980], [19628981, 21031050], [21031051, 22433120], [22433121, 23835190], [23835191, 25237260], [25237261, 26639330], [26639331, 28041404]] SRR12682219 file size 8795107 SRR12682219 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 SRR12682219 SRR12682219_1.fastq Input file: SRR12682219_1.fastq trimmed: SRR12682219-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sat Dec 7 03:12:25 2024 >> started Sat Dec 7 03:12:42 2024 >> done (17.457s) 28041404 reads processed; of these: 0 ( 0.00%) short reads filtered out after trimming by size control 1371 ( 0.00%) empty reads filtered out after trimming by size control 28040033 (100.00%) reads available; of these: 12205 ( 0.04%) trimmed reads available after processing 28027828 (99.96%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 22 18 0.00% 23 24 0.00% 24 17 0.00% 25 27 0.00% 26 37 0.00% 27 51 0.00% 28 68 0.00% 29 78 0.00% 30 98 0.00% 31 107 0.00% 32 131 0.00% 33 146 0.00% 34 140 0.00% 35 206 0.00% 36 211 0.00% 37 255 0.00% 38 346 0.00% 39 372 0.00% 40 463 0.00% 41 519 0.00% 42 555 0.00% 43 554 0.00% 44 578 0.00% 45 628 0.00% 46 739 0.00% 47 924 0.00% 48 1144 0.00% 49 1379 0.00% 50 1467 0.01% 51 1632 0.01% 52 1859 0.01% 53 1945 0.01% 54 1865 0.01% 55 2166 0.01% 56 2438 0.01% 57 2772 0.01% 58 3222 0.01% 59 3645 0.01% 60 4058 0.01% 61 4425 0.02% 62 4972 0.02% 63 4999 0.02% 64 5382 0.02% 65 5920 0.02% 66 6412 0.02% 67 7150 0.03% 68 7636 0.03% 69 8270 0.03% 70 8942 0.03% 71 10485 0.04% 72 11867 0.04% 73 13246 0.05% 74 13682 0.05% 75 14554 0.05% 76 16422 0.06% 77 17355 0.06% 78 18793 0.07% 79 21200 0.08% 80 22958 0.08% 81 24771 0.09% 82 27454 0.10% 83 29357 0.10% 84 32007 0.11% 85 36648 0.13% 86 41691 0.15% 87 43678 0.16% 88 47170 0.17% 89 49021 0.17% 90 53520 0.19% 91 55487 0.20% 92 62912 0.22% 93 67277 0.24% 94 70785 0.25% 95 78680 0.28% 96 84968 0.30% 97 90605 0.32% 98 99619 0.36% 99 101532 0.36% 100 104818 0.37% 101 109204 0.39% 102 116838 0.42% 103 125542 0.45% 104 132026 0.47% 105 134772 0.48% 106 140363 0.50% 107 151305 0.54% 108 149014 0.53% 109 160392 0.57% 110 163449 0.58% 111 172263 0.61% 112 185945 0.66% 113 185836 0.66% 114 198081 0.71% 115 211651 0.75% 116 215140 0.77% 117 208699 0.74% 118 211545 0.75% 119 220882 0.79% 120 237204 0.85% 121 228203 0.81% 122 247300 0.88% 123 257439 0.92% 124 245990 0.88% 125 244688 0.87% 126 251776 0.90% 127 246201 0.88% 128 249788 0.89% 129 263620 0.94% 130 256998 0.92% 131 255627 0.91% 132 259224 0.92% 133 263646 0.94% 134 253621 0.90% 135 258872 0.92% 136 265450 0.95% 137 265151 0.95% 138 253243 0.90% 139 257845 0.92% 140 255445 0.91% 141 246261 0.88% 142 241998 0.86% 143 244626 0.87% 144 250876 0.89% 145 244291 0.87% 146 299811 1.07% 147 511587 1.82% 148 1148413 4.10% 149 3947196 14.08% 150 10931142 38.98% 28040033 reads passed initial QC criterion=sequence-density sequence-density=0.72 sequence-density-rank=1 fanout-score=2.77 fanout-score-rank=34 prefix-density=0.73 prefix-fanout=2.7 sequence=CCCAGCTCACGTTCCCTATTGGTGGGTGAACAATCCAACACTTGGTGAATTCTGCTTCACAATGATAGGAAGAGCCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCACAAGCCAGTTATCCCTGTGGTAACTTTTCTGACACCTCTAGCTTCAAACTCCGAAGATCTAAAGGATCGATAGGCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGATTTCTGTTCTCGTTGAGCTCATCTTAGGACACCTGCGTTATCTTTTAACAGATGTGCCGCCCCAGCCAAACTCCCCACCTGACAATGTCTTCCGCCCGGATCGGCCCGGTCAGACCGGGCCTTGGAGCCAAAAGGAGGGGACTTGCCCCGCTTCCGACCCACGGAATAAGTAAAATAACGTTAAAAGTAGTGGTATTTCACTTGCGCCCGTAAAGGCTCCCACTTATCCTACACCTCTC criterion=fanout-score sequence-density=0.04 sequence-density-rank=31 fanout-score=37.47 fanout-score-rank=1 prefix-density=1.57 prefix-fanout=1.0 sequence=TGGGTAATTTGTGCGCCTGCTGC Started job on | Dec 07 03:13:03 Started mapping on | Dec 07 03:13:03 Finished on | Dec 07 03:14:24 Mapping speed, Million of reads per hour | 1246.22 Number of input reads | 28040033 Average input read length | 137 UNIQUE READS: Uniquely mapped reads number | 14505448 Uniquely mapped reads % | 51.73% Average mapped length | 137.95 Number of splices: Total | 6077970 Number of splices: Annotated (sjdb) | 5752403 Number of splices: GT/AG | 5998366 Number of splices: GC/AG | 70518 Number of splices: AT/AC | 4389 Number of splices: Non-canonical | 4697 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 1.60 Insertion rate per base | 0.00% Insertion average length | 1.13 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 880058 % of reads mapped to multiple loci | 3.14% Number of reads mapped to too many loci | 10876374 % of reads mapped to too many loci | 38.79% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.41% % of reads unmapped: other | 4.93% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 12654527 12654527 12654527 N_multimapping 880058 880058 880058 N_noFeature 722426 14163203 841997 N_ambiguous 264902 1451 42954 UnstrandedReadsAssigned:13518120 PositiveStrandReadsAssigned:340794 NegativeStrandReadsAssigned:13620497 Dataset is classified negative stranded MeadianReadLen=149 20thPercentileLength=123 echo kmer=119 SRR12682219 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: SRR12682219-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,040,033 reads, 13,891,776 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,088 rounds 52973 SRR12682219.ke.tsv 35125 SRR12682219.se.tsv 88098 total ==> SRR12682219.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0.000271122 3.7133e-05 PNS24247 1044 945 50.6911 6.14923 PNS24249 1928 1829 131.197 8.22302 PNS24246 1044 945 50.6911 6.14923 PNS24248 1044 945 50.6911 6.14923 PNS24244 1471 1372 74.7296 6.24395 PNS24243 293 194 0 0 KQK14069 1603 1504 5423.51 413.385 KQK14071 474 375 376.739 115.168 ==> SRR12682219.se.tsv <== BRADI_1g14170v3 6271 BRADI_1g53295v3 64 BRADI_1g59795v3 226 BRADI_1g07683v3 0 BRADI_1g00485v3 6 BRADI_1g20270v3 871 BRADI_1g74790v3 295 BRADI_1g09890v3 0 BRADI_1g77505v3 115 BRADI_1g48960v3 1 SRR12682219 completed mapping pipeline successfully