Starting /dee2/code/volunteer_pipeline.sh ERR3959283 current disk space = 1547644248064 free memory = 1600403060 ERR3959283 SRAfilesize 7592f8463917e5c1124440499759fc4b ERR3959283.sra ERR3959283.sra file validated ERR3959283 is paired end ERR3959283 is conventional basespace ERR3959283 read1 length is 20-140 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3959283_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 20-140 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5915 37.0 37.0 37.0 37.0 37.0 2 36.468 37.0 37.0 37.0 37.0 37.0 3 36.474 37.0 37.0 37.0 37.0 37.0 4 36.42 37.0 37.0 37.0 37.0 37.0 5 36.373 37.0 37.0 37.0 37.0 37.0 6 36.55 37.0 37.0 37.0 37.0 37.0 7 36.5455 37.0 37.0 37.0 37.0 37.0 8 36.458 37.0 37.0 37.0 37.0 37.0 9 36.5385 37.0 37.0 37.0 37.0 37.0 10-14 36.478500000000004 37.0 37.0 37.0 37.0 37.0 15-19 36.4719 37.0 37.0 37.0 37.0 37.0 20-24 36.42925675412177 37.0 37.0 37.0 37.0 37.0 25-29 36.46313897129714 37.0 37.0 37.0 37.0 37.0 30-34 36.405649284492746 37.0 37.0 37.0 37.0 37.0 35-39 36.44682583390355 37.0 37.0 37.0 37.0 37.0 40-44 36.428630851828835 37.0 37.0 37.0 37.0 37.0 45-49 36.420858427286575 37.0 37.0 37.0 37.0 37.0 50-54 36.39568171317989 37.0 37.0 37.0 37.0 37.0 55-59 36.46094217593216 37.0 37.0 37.0 37.0 37.0 60-64 36.443446046110616 37.0 37.0 37.0 37.0 37.0 65-69 36.428148633998696 37.0 37.0 37.0 37.0 37.0 70-74 36.39020903479707 37.0 37.0 37.0 37.0 37.0 75-79 36.37974211011469 37.0 37.0 37.0 37.0 37.0 80-84 36.348176713978134 37.0 37.0 37.0 37.0 37.0 85-89 36.344945460939726 37.0 37.0 37.0 37.0 37.0 90-94 36.39333733757238 37.0 37.0 37.0 37.0 37.0 95-99 36.37439254206213 37.0 37.0 37.0 37.0 37.0 100-104 36.34682221888104 37.0 37.0 37.0 37.0 37.0 105-109 36.30588708298588 37.0 37.0 37.0 37.0 37.0 110-114 36.31790615254202 37.0 37.0 37.0 37.0 37.0 115-119 36.357882101228185 37.0 37.0 37.0 37.0 37.0 120-124 36.366224436790816 37.0 37.0 37.0 37.0 37.0 125-129 36.261795848401086 37.0 37.0 37.0 37.0 37.0 130-134 36.21804661288995 37.0 37.0 37.0 37.0 37.0 135-139 36.17220673076908 37.0 37.0 37.0 37.0 37.0 140 36.52350364963504 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 27 2.0 28 5.0 29 10.0 30 28.0 31 22.0 32 56.0 33 88.0 34 146.0 35 290.0 36 2856.0 37 497.0 >>END_MODULE >>Per base sequence content pass #Base G A T C 1 27.85 22.650000000000002 19.900000000000002 29.599999999999998 2 25.474999999999998 22.0 23.9 28.625 3 24.05 22.625 26.174999999999997 27.150000000000002 4 25.15 23.775 25.124999999999996 25.95 5 24.95 22.875 25.424999999999997 26.75 6 24.925 23.025000000000002 24.175 27.875 7 25.85 22.225 24.474999999999998 27.450000000000003 8 23.599999999999998 23.400000000000002 23.275000000000002 29.725 9 25.05 23.575 23.425 27.950000000000003 10-14 25.445 23.43 23.9 27.224999999999998 15-19 25.490000000000002 23.715 23.98 26.815 20-24 24.511865425052566 24.106338239711626 23.891058375888655 27.49073795934715 25-29 25.5482511165755 23.716565463943393 23.520851106538867 27.21433231294224 30-34 25.416226547960363 23.912278054423822 23.31874654192445 27.35274885569136 35-39 25.60133124905451 23.17583581261661 23.478392415914477 27.744440522414404 40-44 25.71876105300389 23.637006720226367 23.24288818149664 27.401344045273103 45-49 26.21747494178394 23.169990887921436 23.210489014883063 27.402045155411564 50-54 24.897338403041825 23.721166032953107 23.38149556400507 28.000000000000004 55-59 25.302245250431778 23.219546886111956 23.879914660164584 27.59829320329168 60-64 25.693913929208044 23.127069009421948 23.376623376623375 27.802393684746622 65-69 25.958987961640485 23.286064068557437 23.740053050397876 27.014894919404203 70-74 25.688261181045952 23.620919046156995 23.191075631972165 27.499744140824887 75-79 25.985506501516163 23.08166726627949 23.025132343115587 27.90769388908876 80-84 25.993804852865253 23.05110996386164 23.56220960247806 27.392875580795046 85-89 26.144909496395414 22.94486800477154 23.058969970437218 27.851252528395833 90-94 25.66897918731417 22.727035626727872 23.676386208335508 27.927598977622452 95-99 26.07803954564577 22.360117795540596 23.822044594026085 27.739798064787546 100-104 25.802679140973844 23.65511375717627 23.04380182862003 27.498405273229853 105-109 25.71413172361755 23.525924328985663 23.17559555890913 27.584348388487655 110-114 25.802939575394667 23.244420250408275 23.140990745781163 27.811649428415897 115-119 26.54059699851575 22.522126326205267 23.231268209554177 27.706008465724807 120-124 26.395064473099154 22.89350822587817 22.915740329035128 27.79568697198755 125-129 26.647871440654075 23.591767691006485 22.565548350718917 27.194812517620527 130-134 26.751592356687897 23.06073703366697 23.3450864422202 26.84258416742493 135-139 27.16492788324497 23.008950458924804 22.71820306709994 27.10791859073029 140 25.343065693430656 24.116788321167885 22.16058394160584 28.37956204379562 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.0 2 0.5 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 1.5 24 2.5 25 2.0 26 2.5 27 3.0 28 3.5 29 5.0 30 6.5 31 8.5 32 13.5 33 16.5 34 17.0 35 27.0 36 39.5 37 45.5 38 59.5 39 82.5 40 104.0 41 116.0 42 128.0 43 142.5 44 168.5 45 177.0 46 168.5 47 171.5 48 169.0 49 148.5 50 139.0 51 129.5 52 107.0 53 108.5 54 108.0 55 102.0 56 99.0 57 89.5 58 85.5 59 83.5 60 79.5 61 75.0 62 73.5 63 81.5 64 81.5 65 67.0 66 71.0 67 92.5 68 86.0 69 64.5 70 64.5 71 65.0 72 63.5 73 67.0 74 57.5 75 37.0 76 26.5 77 27.0 78 20.5 79 17.0 80 15.0 81 9.5 82 8.0 83 9.0 84 7.0 85 3.5 86 1.0 87 0.5 88 0.5 89 1.0 90 1.0 91 1.0 92 1.0 93 0.5 94 0.5 95 1.0 96 1.0 97 1.0 98 0.5 99 0.0 100 0.0 >>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 0.0 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 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 20-24 12.0 25-29 7.0 30-34 13.0 35-39 6.0 40-44 8.0 45-49 8.0 50-54 3.0 55-59 13.0 60-64 5.0 65-69 10.0 70-74 14.0 75-79 20.0 80-84 16.0 85-89 22.0 90-94 28.0 95-99 32.0 100-104 57.0 105-109 41.0 110-114 33.0 115-119 41.0 120-124 41.0 125-129 49.0 130-134 8.0 135-139 88.0 140-141 3425.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.375 #Duplication Level Percentage of deduplicated Percentage of total 1 94.25165562913908 88.94999999999999 2 5.5364238410596025 10.45 3 0.2119205298013245 0.6 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >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 pass >>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 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAACATC 15 0.002212866 69.40269 112-113 TGAGGAC 15 0.0026595048 66.28846 76-77 AACATCA 20 0.0069158417 52.052013 112-113 >>END_MODULE ERR3959283 read2 length is 20-140 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3959283_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 20-140 %GC 54 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.439 37.0 37.0 37.0 37.0 37.0 2 36.4225 37.0 37.0 37.0 37.0 37.0 3 36.442 37.0 37.0 37.0 37.0 37.0 4 36.414 37.0 37.0 37.0 37.0 37.0 5 36.362 37.0 37.0 37.0 37.0 37.0 6 36.444 37.0 37.0 37.0 37.0 37.0 7 36.399 37.0 37.0 37.0 37.0 37.0 8 36.521 37.0 37.0 37.0 37.0 37.0 9 36.4255 37.0 37.0 37.0 37.0 37.0 10-14 36.4459 37.0 37.0 37.0 37.0 37.0 15-19 36.352900000000005 37.0 37.0 37.0 37.0 37.0 20-24 36.29352569680033 37.0 37.0 37.0 37.0 37.0 25-29 36.319074044990906 37.0 37.0 37.0 37.0 37.0 30-34 36.331517805436825 37.0 37.0 37.0 37.0 37.0 35-39 36.315316205220675 37.0 37.0 37.0 37.0 37.0 40-44 36.33787912867969 37.0 37.0 37.0 37.0 37.0 45-49 36.27903930375122 37.0 37.0 37.0 37.0 37.0 50-54 36.21275206861388 37.0 37.0 37.0 37.0 37.0 55-59 36.26717756529302 37.0 37.0 37.0 37.0 37.0 60-64 36.31289376304798 37.0 37.0 37.0 37.0 37.0 65-69 36.218550063954375 37.0 37.0 37.0 37.0 37.0 70-74 36.29702392953748 37.0 37.0 37.0 37.0 37.0 75-79 36.319833249565995 37.0 37.0 37.0 37.0 37.0 80-84 36.26520418806247 37.0 37.0 37.0 37.0 37.0 85-89 36.232568591794305 37.0 37.0 37.0 37.0 37.0 90-94 36.17025101701806 37.0 37.0 37.0 37.0 37.0 95-99 36.207108600258735 37.0 37.0 37.0 37.0 37.0 100-104 36.18137870734775 37.0 37.0 37.0 37.0 37.0 105-109 36.18957450885236 37.0 37.0 37.0 37.0 37.0 110-114 36.118842398497506 37.0 37.0 37.0 37.0 37.0 115-119 36.0080861558472 37.0 37.0 37.0 37.0 37.0 120-124 36.065865461014425 37.0 37.0 37.0 37.0 37.0 125-129 35.96558224016705 37.0 37.0 37.0 37.0 37.0 130-134 35.98749019722787 37.0 37.0 37.0 37.0 37.0 135-139 35.86004543224028 37.0 37.0 37.0 37.0 37.0 140 36.499723909442295 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 26 1.0 27 0.0 28 3.0 29 12.0 30 13.0 31 40.0 32 54.0 33 99.0 34 201.0 35 543.0 36 2720.0 37 314.0 >>END_MODULE >>Per base sequence content pass #Base G A T C 1 28.849999999999998 22.3 18.224999999999998 30.625000000000004 2 28.9 20.1 22.175 28.825 3 26.775 22.1 22.625 28.499999999999996 4 26.85 22.575 23.175 27.400000000000002 5 26.700000000000003 23.625 22.975 26.700000000000003 6 27.975 21.825 24.099999999999998 26.1 7 28.675 22.675 21.125 27.525 8 26.325 24.025 22.425 27.224999999999998 9 28.925 22.650000000000002 21.7 26.724999999999998 10-14 27.075 23.875 22.085 26.965 15-19 27.52 23.9 21.87 26.71 20-24 28.14251401120897 23.448759007205762 21.742393915132105 26.666333066453163 25-29 27.066312465540577 23.186807678813093 22.665530549847126 27.081349305799208 30-34 27.48202885437088 22.922636103151863 22.284220580103554 27.3111144623737 35-39 27.600785142684586 23.01575318335095 22.452060999547033 26.931400674417432 40-44 28.335854765506806 22.980332829046898 21.49773071104387 27.186081694402418 45-49 27.412092081963067 22.914242347584114 22.17050341512775 27.503162155325068 50-54 27.55174512987013 23.097605519480517 22.49391233766234 26.856737012987015 55-59 28.19508721965112 22.809337334079235 22.270253776127753 26.725321670141888 60-64 27.684076433121017 22.771974522292993 22.394904458598727 27.14904458598726 65-69 28.065339458907605 22.76671771311894 22.28177641653905 26.886166411434402 70-74 27.731479114474155 22.848816401656528 22.061455084615776 27.35824939925354 75-79 27.8605436952849 22.863871397122818 22.38775405723647 26.887830850355808 80-84 28.214597117505257 23.25998871621275 22.054675078217162 26.470739088064832 85-89 28.178411948878505 22.927680542010982 22.306626289585793 26.587281219524716 90-94 27.99732771468215 23.094711958476797 22.462613700601263 26.445346626239786 95-99 28.177279044628612 23.297472589694753 22.3812220106038 26.144026355072835 100-104 28.34081180050544 23.699004590231574 21.85259683325597 26.107586776007015 105-109 28.887167570358898 22.912470952749807 21.869351923573458 26.33100955331784 110-114 28.552951523617367 23.08448445341197 22.27223343163123 26.090330591339438 115-119 28.47438290811035 23.470234391205143 22.054552997303464 26.00082970338104 120-124 29.37659231529143 23.340092549264284 22.28461498466178 24.99870015078251 125-129 28.678474114441414 23.7109620624607 21.903164954936074 25.707398868161814 130-134 28.92312579415502 24.147606946209233 21.80220245658619 25.127064803049553 135-139 28.940637322817864 23.521261856549078 22.103804753277203 25.434296067355856 140 30.756488128106017 22.280508006626174 21.479845389287686 25.483158475980122 >>END_MODULE >>Per sequence GC content fail #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 0.0 25 0.0 26 0.5 27 0.5 28 2.0 29 4.0 30 4.0 31 7.5 32 10.5 33 14.0 34 18.0 35 21.5 36 29.0 37 40.0 38 52.0 39 66.5 40 75.5 41 100.5 42 122.5 43 128.0 44 142.0 45 146.0 46 150.0 47 160.5 48 154.0 49 145.5 50 147.5 51 132.0 52 109.0 53 109.5 54 107.5 55 83.0 56 73.0 57 84.0 58 84.0 59 80.5 60 84.0 61 87.5 62 88.0 63 87.0 64 93.5 65 106.0 66 97.0 67 83.0 68 86.5 69 84.5 70 81.5 71 70.5 72 68.0 73 66.5 74 60.5 75 55.5 76 48.0 77 43.0 78 32.5 79 23.5 80 16.5 81 14.5 82 14.5 83 10.5 84 6.0 85 4.0 86 3.5 87 2.5 88 2.5 89 2.0 90 1.0 91 1.0 92 1.5 93 1.5 94 1.0 95 0.5 96 0.0 97 0.0 98 0.0 99 1.0 100 3.5 >>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 0.0 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 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 20-24 6.0 25-29 10.0 30-34 10.0 35-39 4.0 40-44 9.0 45-49 15.0 50-54 11.0 55-59 7.0 60-64 8.0 65-69 6.0 70-74 5.0 75-79 6.0 80-84 5.0 85-89 5.0 90-94 4.0 95-99 9.0 100-104 5.0 105-109 6.0 110-114 9.0 115-119 7.0 120-124 16.0 125-129 50.0 130-134 22.0 135-139 143.0 140-141 3622.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.35 #Duplication Level Percentage of deduplicated Percentage of total 1 94.35612082670907 89.025 2 5.325914149443562 10.05 3 0.29146793852676206 0.8250000000000001 4 0.026497085320614733 0.1 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >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 pass >>END_MODULE >>Adapter Content warn #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 0.0125 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 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 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.0875 0.0 0.0 0.0 0.0 64-65 0.1125 0.0 0.0 0.0 0.0 66-67 0.1875 0.0 0.0 0.0 0.0 68-69 0.21250000000000002 0.0 0.0 0.0 0.0 70-71 0.2375 0.0 0.0 0.0 0.0 72-73 0.3125 0.0 0.0 0.0 0.0 74-75 0.4125 0.0 0.0 0.0 0.0 76-77 0.55 0.0 0.0 0.0 0.0 78-79 0.65 0.0 0.0 0.0 0.0 80-81 0.7375 0.0 0.0 0.0 0.0 82-83 0.8875 0.0 0.0 0.0 0.0 84-85 0.9874999999999999 0.0 0.0 0.0 0.0 86-87 1.175 0.0 0.0 0.0 0.0 88-89 1.2875 0.0 0.0 0.0 0.0 90-91 1.4249999999999998 0.0 0.0 0.0 0.0 92-93 1.6625 0.0 0.0 0.0 0.0 94-95 1.9375 0.0 0.0 0.0 0.0 96-97 2.2249999999999996 0.0 0.0 0.0 0.0 98-99 2.5625 0.0 0.0 0.0 0.0 100-101 2.8875 0.0 0.0 0.0 0.0 102-103 3.3875 0.0 0.0 0.0 0.0 104-105 3.825 0.0 0.0 0.0 0.0 106-107 4.1375 0.0 0.0 0.0 0.0 108-109 4.45 0.0 0.0 0.0 0.0 110-111 4.6625 0.0 0.0 0.0 0.0 112-113 4.9125 0.0 0.0 0.0 0.0 114-115 5.2625 0.0 0.0 0.0 0.0 116-117 5.55 0.0 0.0 0.0 0.0 118-119 5.925000000000001 0.0 0.0 0.0 0.0 120-121 6.2 0.0 0.0 0.0 0.0 122-123 6.5625 0.0 0.0 0.0 0.0 124-125 7.012499999999999 0.0 0.0 0.0 0.0 126-127 7.175 0.0 0.0 0.0 0.0 128 7.175 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATCGTCA 10 0.009200822 131.25 2 >>END_MODULE Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347485 spots for ERR3959283.sra Written 2347485 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra Read 2347482 spots for ERR3959283.sra Written 2347482 spots for ERR3959283.sra SRR ids: ['ERR3959283.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ac12g1i6 ERR3959283.sra spots: 46949643 blocks: [[1, 2347482], [2347483, 4694964], [4694965, 7042446], [7042447, 9389928], [9389929, 11737410], [11737411, 14084892], [14084893, 16432374], [16432375, 18779856], [18779857, 21127338], [21127339, 23474820], [23474821, 25822302], [25822303, 28169784], [28169785, 30517266], [30517267, 32864748], [32864749, 35212230], [35212231, 37559712], [37559713, 39907194], [39907195, 42254676], [42254677, 44602158], [44602159, 46949643]] ERR3959283 file size 14445781 ERR3959283 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 ERR3959283 ERR3959283_1.fastq ERR3959283_2.fastq Input file: ERR3959283_1.fastq Paired file: ERR3959283_2.fastq trimmed: ERR3959283-trimmed-pair1.fastq, ERR3959283-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- 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 -- number of concurrent threads (-t): 20 Sat Dec 7 02:24:49 2024 >> started Sat Dec 7 02:25:34 2024 >> done (45.104s) 46949643 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 0 ( 0.00%) empty read pairs filtered out after trimming by size control 46949643 (100.00%) read pairs available; of these: 81749 ( 0.17%) trimmed read pairs available after processing 46867894 (99.83%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 20 377 0.00% 21 899 0.00% 22 1336 0.00% 23 1729 0.00% 24 1944 0.00% 25 2364 0.01% 26 2593 0.01% 27 2857 0.01% 28 3051 0.01% 29 3288 0.01% 30 3551 0.01% 31 3776 0.01% 32 3816 0.01% 33 3972 0.01% 34 4129 0.01% 35 4301 0.01% 36 4358 0.01% 37 4484 0.01% 38 4500 0.01% 39 4681 0.01% 40 4803 0.01% 41 4902 0.01% 42 4816 0.01% 43 5039 0.01% 44 5089 0.01% 45 5195 0.01% 46 5301 0.01% 47 5362 0.01% 48 5472 0.01% 49 5468 0.01% 50 5545 0.01% 51 5570 0.01% 52 5865 0.01% 53 5915 0.01% 54 5926 0.01% 55 6101 0.01% 56 6088 0.01% 57 6052 0.01% 58 6174 0.01% 59 6450 0.01% 60 6617 0.01% 61 6649 0.01% 62 6685 0.01% 63 6758 0.01% 64 7228 0.02% 65 7299 0.02% 66 7314 0.02% 67 7343 0.02% 68 7572 0.02% 69 7952 0.02% 70 7903 0.02% 71 8184 0.02% 72 8402 0.02% 73 8891 0.02% 74 9137 0.02% 75 9340 0.02% 76 9856 0.02% 77 9838 0.02% 78 10447 0.02% 79 13200 0.03% 80 45660 0.10% 81 46035 0.10% 82 45912 0.10% 83 45091 0.10% 84 45213 0.10% 85 46469 0.10% 86 45915 0.10% 87 46800 0.10% 88 47510 0.10% 89 48584 0.10% 90 48081 0.10% 91 48717 0.10% 92 49618 0.11% 93 50954 0.11% 94 51791 0.11% 95 51840 0.11% 96 52404 0.11% 97 53943 0.11% 98 55758 0.12% 99 56628 0.12% 100 58152 0.12% 101 59724 0.13% 102 62924 0.13% 103 64719 0.14% 104 66411 0.14% 105 69174 0.15% 106 71096 0.15% 107 74047 0.16% 108 74640 0.16% 109 78789 0.17% 110 82902 0.18% 111 83783 0.18% 112 92129 0.20% 113 90582 0.19% 114 95906 0.20% 115 99397 0.21% 116 117268 0.25% 117 129665 0.28% 118 136017 0.29% 119 162981 0.35% 120 157987 0.34% 121 155931 0.33% 122 179155 0.38% 123 186034 0.40% 124 192445 0.41% 125 198116 0.42% 126 293370 0.62% 127 301757 0.64% 128 305010 0.65% 129 218621 0.47% 130 218440 0.47% 131 224841 0.48% 132 224381 0.48% 133 58010 0.12% 134 46748 0.10% 135 35349 0.08% 136 36434 0.08% 137 42544 0.09% 138 70658 0.15% 139 1517980 3.23% 140 39192849 83.48% 46949643 reads passed initial QC criterion=sequence-density sequence-density=0.16 sequence-density-rank=1 fanout-score=2.92 fanout-score-rank=30 prefix-density=0.19 prefix-fanout=2.5 sequence=TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG criterion=fanout-score sequence-density=0.04 sequence-density-rank=38 fanout-score=387.25 fanout-score-rank=1 prefix-density=0.91 prefix-fanout=18.8 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=6.48 sequence-density-rank=1 fanout-score=45.11 fanout-score-rank=2 prefix-density=7.29 prefix-fanout=40.1 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGTCGGTAAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA criterion=fanout-score sequence-density=0.17 sequence-density-rank=6 fanout-score=143.51 fanout-score-rank=1 prefix-density=1.18 prefix-fanout=20.3 sequence=CCGCCGCCGCCG Potential 3prime adapter identified. Now checking if in reference sequence /dee2/code/volunteer_pipeline.sh: line 905: -f: command not found /dee2/code/volunteer_pipeline.sh: line 906: -f: command not found 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 TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG -y AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGTCGGTAAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA -o ERR3959283 ERR3959283_1.fastq ERR3959283_2.fastq Input file: ERR3959283_1.fastq Paired file: ERR3959283_2.fastq trimmed: ERR3959283-trimmed-pair1.fastq, ERR3959283-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGTCGGTAAGTGTAGATCTCGGTGGTCGCCGT -- 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 -- number of concurrent threads (-t): 20 Sat Dec 7 02:28:37 2024 >> started Sat Dec 7 02:29:01 2024 >> done (24.515s) 23474822 read pairs processed; of these: 9 ( 0.00%) short read pairs filtered out after trimming by size control 521 ( 0.00%) empty read pairs filtered out after trimming by size control 23474292 (100.00%) read pairs available; of these: 22534 ( 0.10%) trimmed read pairs available after processing 23451758 (99.90%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 0 0.00% 20 189 0.00% 21 473 0.00% 22 713 0.00% 23 828 0.00% 24 962 0.00% 25 1214 0.01% 26 1312 0.01% 27 1424 0.01% 28 1518 0.01% 29 1615 0.01% 30 1741 0.01% 31 1854 0.01% 32 1917 0.01% 33 1989 0.01% 34 2078 0.01% 35 2193 0.01% 36 2236 0.01% 37 2240 0.01% 38 2277 0.01% 39 2383 0.01% 40 2459 0.01% 41 2428 0.01% 42 2473 0.01% 43 2520 0.01% 44 2602 0.01% 45 2512 0.01% 46 2656 0.01% 47 2733 0.01% 48 2799 0.01% 49 2727 0.01% 50 2750 0.01% 51 2776 0.01% 52 2952 0.01% 53 2954 0.01% 54 2943 0.01% 55 3066 0.01% 56 3048 0.01% 57 3039 0.01% 58 3032 0.01% 59 3229 0.01% 60 3373 0.01% 61 3390 0.01% 62 3408 0.01% 63 3403 0.01% 64 3559 0.02% 65 3584 0.02% 66 3661 0.02% 67 3568 0.02% 68 3746 0.02% 69 3887 0.02% 70 3954 0.02% 71 4078 0.02% 72 4208 0.02% 73 4471 0.02% 74 4624 0.02% 75 4624 0.02% 76 4804 0.02% 77 4933 0.02% 78 5240 0.02% 79 6667 0.03% 80 23044 0.10% 81 23048 0.10% 82 22775 0.10% 83 22512 0.10% 84 22661 0.10% 85 23193 0.10% 86 23046 0.10% 87 23369 0.10% 88 23911 0.10% 89 24290 0.10% 90 24152 0.10% 91 24461 0.10% 92 24822 0.11% 93 25508 0.11% 94 25791 0.11% 95 25796 0.11% 96 26105 0.11% 97 26881 0.11% 98 27956 0.12% 99 28335 0.12% 100 29225 0.12% 101 29862 0.13% 102 31578 0.13% 103 32402 0.14% 104 33407 0.14% 105 34541 0.15% 106 35324 0.15% 107 37035 0.16% 108 37212 0.16% 109 39515 0.17% 110 41133 0.18% 111 41953 0.18% 112 46247 0.20% 113 45266 0.19% 114 47947 0.20% 115 49619 0.21% 116 58562 0.25% 117 64810 0.28% 118 67796 0.29% 119 81285 0.35% 120 78942 0.34% 121 77658 0.33% 122 90004 0.38% 123 93151 0.40% 124 96255 0.41% 125 99043 0.42% 126 146477 0.62% 127 150897 0.64% 128 152808 0.65% 129 109154 0.46% 130 109060 0.46% 131 112000 0.48% 132 112170 0.48% 133 29050 0.12% 134 23474 0.10% 135 17883 0.08% 136 18347 0.08% 137 22281 0.09% 138 38822 0.17% 139 775588 3.30% 140 19574816 83.39% criterion=sequence-density sequence-density=0.16 sequence-density-rank=1 fanout-score=2.91 fanout-score-rank=32 prefix-density=0.19 prefix-fanout=2.5 sequence=TAGGCGTCCGGGTACTCCTTCTTGACCTCCTCCAGCTCCTTGAGCACCTG criterion=fanout-score sequence-density=0.05 sequence-density-rank=37 fanout-score=367.09 fanout-score-rank=1 prefix-density=0.92 prefix-fanout=18.4 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=6.68 sequence-density-rank=1 fanout-score=45.23 fanout-score-rank=3 prefix-density=7.51 prefix-fanout=40.2 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGTCGGTAAGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA criterion=fanout-score sequence-density=0.17 sequence-density-rank=5 fanout-score=142.91 fanout-score-rank=1 prefix-density=1.16 prefix-fanout=20.4 sequence=CCGCCGCCGCCG ERR3959283 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 02:29:57 Started mapping on | Dec 07 02:29:57 Finished on | Dec 07 02:32:11 Mapping speed, Million of reads per hour | 1261.32 Number of input reads | 46949113 Average input read length | 272 UNIQUE READS: Uniquely mapped reads number | 39686792 Uniquely mapped reads % | 84.53% Average mapped length | 274.66 Number of splices: Total | 37593199 Number of splices: Annotated (sjdb) | 35621528 Number of splices: GT/AG | 36975940 Number of splices: GC/AG | 565738 Number of splices: AT/AC | 20678 Number of splices: Non-canonical | 30843 Mismatch rate per base, % | 0.07% Deletion rate per base | 0.00% Deletion average length | 1.48 Insertion rate per base | 0.00% Insertion average length | 1.16 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 473644 % of reads mapped to multiple loci | 1.01% Number of reads mapped to too many loci | 166445 % of reads mapped to too many loci | 0.35% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 12.89% % of reads unmapped: other | 1.21% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6876491 6876491 6876491 N_multimapping 473644 473644 473644 N_noFeature 1104094 38654806 1450744 N_ambiguous 916060 6570 237745 UnstrandedReadsAssigned:37666638 PositiveStrandReadsAssigned:1025416 NegativeStrandReadsAssigned:37998303 Dataset is classified negative stranded MeadianReadLen=140 20thPercentileLength=140 echo kmer=135 ERR3959283 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [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 paired-end mode [quant] will process pair 1: ERR3959283-trimmed-pair1.fastq ERR3959283-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 46,949,113 reads, 43,901,618 reads pseudoaligned [quant] estimated average fragment length: 240.408 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,210 rounds 52973 ERR3959283.ke.tsv 35125 ERR3959283.se.tsv 88098 total ==> ERR3959283.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 696.97 0 0 PNS24247 1044 804.592 66.4047 2.65956 PNS24249 1928 1688.59 795.451 15.1801 PNS24246 1044 804.592 66.4047 2.65956 PNS24248 1044 804.592 66.4047 2.65956 PNS24244 1471 1231.59 87.3349 2.28511 PNS24243 293 103.997 1 0.309859 KQK14069 1603 1363.59 57963.1 1369.79 KQK14071 474 247.307 1682.63 219.249 ==> ERR3959283.se.tsv <== BRADI_1g14170v3 53528 BRADI_1g53295v3 209 BRADI_1g59795v3 472 BRADI_1g07683v3 0 BRADI_1g00485v3 32 BRADI_1g20270v3 1611 BRADI_1g74790v3 1644 BRADI_1g09890v3 9 BRADI_1g77505v3 591 BRADI_1g48960v3 0 ERR3959283 completed mapping pipeline successfully