Starting /dee2/code/volunteer_pipeline.sh SRR11445637 current disk space = 3051674750976 free memory = 1488432476 SRR11445637 SRAfilesize ba66b079062817dbdf8fc6a09c914a4d SRR11445637.sra SRR11445637.sra file validated SRR11445637 is paired end SRR11445637 is conventional basespace SRR11445637 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11445637_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 37 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 24.465 32.0 12.0 32.0 2.0 32.0 2 31.1425 32.0 32.0 32.0 32.0 32.0 3 34.58875 37.0 32.0 37.0 32.0 37.0 4 35.04875 37.0 32.0 37.0 32.0 37.0 5 36.23875 37.0 37.0 37.0 37.0 37.0 6 39.58075 41.0 41.0 41.0 37.0 41.0 7 39.8385 41.0 41.0 41.0 37.0 41.0 8 39.48225 41.0 41.0 41.0 37.0 41.0 9 40.02875 41.0 41.0 41.0 37.0 41.0 10-14 39.8746 41.0 41.0 41.0 37.0 41.0 15-19 38.89635 41.0 40.2 41.0 35.0 41.0 20-24 38.509499999999996 41.0 38.6 41.0 33.0 41.0 25-29 38.357749999999996 41.0 38.6 41.0 33.0 41.0 30-34 38.71625 41.0 39.4 41.0 33.0 41.0 35-39 39.236149999999995 41.0 41.0 41.0 37.0 41.0 40-44 38.65805 41.0 38.6 41.0 33.0 41.0 45-49 38.262950000000004 41.0 37.8 41.0 33.0 41.0 50-54 38.663700000000006 41.0 38.6 41.0 34.0 41.0 55-59 38.3717 41.0 38.6 41.0 31.0 41.0 60-64 38.35850000000001 41.0 38.6 41.0 32.0 41.0 65-69 37.963 41.0 37.0 41.0 30.0 41.0 70-74 37.11735 41.0 36.0 41.0 28.0 41.0 75-79 37.716449999999995 41.0 37.0 41.0 30.0 41.0 80-84 37.28125000000001 41.0 36.0 41.0 28.0 41.0 85-89 35.527649999999994 40.2 32.0 41.0 23.0 41.0 90-94 36.443799999999996 40.2 36.0 41.0 24.0 41.0 95-99 36.3487 41.0 35.0 41.0 23.0 41.0 100-104 34.713350000000005 39.4 32.0 41.0 18.0 41.0 105-109 36.58365 41.0 36.0 41.0 24.0 41.0 110-114 37.105650000000004 41.0 37.0 41.0 26.0 41.0 115-119 36.730399999999996 41.0 37.0 41.0 23.0 41.0 120-124 34.44315 39.4 32.0 41.0 18.0 41.0 125-129 34.66925 39.4 34.0 41.0 18.0 41.0 130-134 34.3172 37.8 31.0 41.0 14.0 41.0 135-139 34.4544 38.6 32.0 41.0 14.0 41.0 140-144 33.3339 37.0 30.0 41.0 12.0 41.0 145-149 30.324 34.0 22.0 40.2 12.0 41.0 150 32.106 37.0 27.0 41.0 12.0 41.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 1.0 19 2.0 20 4.0 21 3.0 22 10.0 23 10.0 24 28.0 25 25.0 26 35.0 27 56.0 28 63.0 29 69.0 30 75.0 31 118.0 32 132.0 33 160.0 34 201.0 35 209.0 36 324.0 37 468.0 38 604.0 39 848.0 40 555.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 24.29876060013046 25.11415525114155 26.190476190476193 24.396607958251792 2 24.85 25.5 25.8 23.849999999999998 3 25.124999999999996 27.525 24.25 23.1 4 24.75 26.375 23.974999999999998 24.9 5 26.55 27.6 23.599999999999998 22.25 6 26.8 27.05 25.4 20.75 7 26.325 26.174999999999997 26.5 21.0 8 25.674999999999997 28.15 31.6 14.575 9 27.075 28.775000000000002 29.849999999999998 14.299999999999999 10-14 27.384999999999998 29.69 27.445000000000004 15.479999999999999 15-19 23.919999999999998 29.975 30.37 15.735 20-24 22.33 30.28 31.314999999999998 16.075 25-29 23.44 28.95 30.895 16.715 30-34 22.585 30.075000000000003 31.405 15.934999999999999 35-39 21.85 30.035 31.324999999999996 16.79 40-44 21.92 30.39 31.455 16.235 45-49 21.78 30.755 30.7 16.765 50-54 21.665 30.12 32.1 16.115 55-59 21.0 30.73 32.379999999999995 15.89 60-64 20.661033051652584 30.591529576478827 32.06660333016651 16.680834041702084 65-69 20.785 31.230000000000004 32.275 15.709999999999999 70-74 21.11 31.125000000000004 32.269999999999996 15.495000000000001 75-79 20.48 30.904999999999998 32.7 15.915000000000001 80-84 20.080000000000002 31.8 32.105 16.014999999999997 85-89 20.39 32.005 31.865 15.740000000000002 90-94 19.575 32.2 31.985000000000003 16.24 95-99 20.115 32.18 31.795 15.909999999999998 100-104 19.895 31.965 32.519999999999996 15.620000000000001 105-109 19.265 32.615 32.665 15.455 110-114 19.03 33.71 32.365 14.895 115-119 19.45 33.08 31.990000000000002 15.479999999999999 120-124 19.165 32.915 31.874999999999996 16.045 125-129 19.31 33.485 31.569999999999997 15.634999999999998 130-134 18.709999999999997 34.050000000000004 30.91 16.33 135-139 18.285 34.085 31.209999999999997 16.42 140-144 18.65 33.805 31.165 16.38 145-149 19.38 33.695 31.405 15.52 150 18.2 35.075 29.95 16.775000000000002 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 28.0 1 24.0 2 14.5 3 12.5 4 15.0 5 9.5 6 8.0 7 9.0 8 6.0 9 4.0 10 4.5 11 8.0 12 7.0 13 5.0 14 7.0 15 6.5 16 4.0 17 6.5 18 9.5 19 10.5 20 10.0 21 8.5 22 8.5 23 10.5 24 16.5 25 20.0 26 29.0 27 39.5 28 39.5 29 46.5 30 67.5 31 86.5 32 99.0 33 131.0 34 158.5 35 179.0 36 199.0 37 205.0 38 224.5 39 232.5 40 208.0 41 195.0 42 194.0 43 185.0 44 169.0 45 145.5 46 121.5 47 113.0 48 109.5 49 97.5 50 95.0 51 82.5 52 63.5 53 51.5 54 43.0 55 32.0 56 18.5 57 14.5 58 14.5 59 12.5 60 7.0 61 5.5 62 6.5 63 3.5 64 1.5 65 2.5 66 4.0 67 2.5 68 2.0 69 1.5 70 1.0 71 1.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content fail #Base N-Count 1 23.35 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 0.005 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 93.425 #Duplication Level Percentage of deduplicated Percentage of total 1 94.67487289269468 88.44999999999999 2 4.575862991704576 8.55 3 0.5351886540005352 1.5 4 0.05351886540005352 0.2 5 0.05351886540005352 0.25 6 0.02675943270002676 0.15 7 0.02675943270002676 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.05351886540005352 0.7250000000000001 >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 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 19 0.475 No Hit CAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 10 0.25 No Hit CGGCAACGGATATCTCGGCTCTCGCATCGATGAAGAACGTAGCGAAATGC 7 0.17500000000000002 No Hit GATGGTGGTAGCTGGAGGGACTAGGTTTGGGAGGCACGTGGTTGTTTTAT 6 0.15 No Hit CCAAAAAAAAAAAAAAAAAAAAGATCGGAAGAGCACACGTCTGAACTCCA 5 0.125 Illumina Multiplexing PCR Primer 2.01 (100% over 29bp) TAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 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 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.037500000000000006 0.0 0.0 0.0 0.0 14-15 0.0625 0.0 0.0 0.0 0.0 16-17 0.075 0.0 0.0 0.0 0.0 18-19 0.075 0.0 0.0 0.0 0.0 20-21 0.4 0.0 0.0 0.0 0.0 22-23 1.1 0.0 0.0 0.0 0.0 24-25 1.375 0.0 0.0 0.0 0.0 26-27 1.4625 0.0 0.0 0.0 0.0 28-29 1.5875 0.0 0.0 0.0 0.0 30-31 1.7374999999999998 0.0 0.0 0.0 0.0 32-33 1.9 0.0 0.0 0.0 0.0 34-35 1.9625 0.0 0.0 0.0 0.0 36-37 2.025 0.0 0.0 0.0 0.0 38-39 2.025 0.0 0.0 0.0 0.0 40-41 2.1 0.0 0.0 0.0 0.0 42-43 2.175 0.0 0.0 0.0 0.0 44-45 2.2625 0.0 0.0 0.0 0.0 46-47 2.375 0.0 0.0 0.0 0.0 48-49 2.5 0.0 0.0 0.0 0.0 50-51 2.575 0.0 0.0 0.0 0.0 52-53 2.6 0.0 0.0 0.0 0.0 54-55 2.7125000000000004 0.0 0.0 0.0 0.0 56-57 2.875 0.0 0.0 0.0 0.0 58-59 3.025 0.0 0.0 0.0 0.0 60-61 3.1125 0.0 0.0 0.0 0.0 62-63 3.175 0.0 0.0 0.0 0.0 64-65 3.2625 0.0 0.0 0.0 0.0 66-67 3.4375 0.0 0.0 0.0 0.0 68-69 3.575 0.0 0.0 0.0 0.0 70-71 3.7375 0.0 0.0 0.0 0.0 72-73 3.8625 0.0 0.0 0.0 0.0 74-75 3.9625000000000004 0.0 0.0 0.0 0.0 76-77 4.0375 0.0 0.0 0.0 0.0 78-79 4.1 0.0 0.0 0.0 0.0 80-81 4.25 0.0 0.0 0.0 0.0 82-83 4.3 0.0 0.0 0.0 0.0 84-85 4.487500000000001 0.0 0.0 0.0 0.0 86-87 4.6 0.0 0.0 0.0 0.0 88-89 4.825 0.0 0.0 0.0 0.0 90-91 5.0 0.0 0.0 0.0 0.0 92-93 5.2125 0.0 0.0 0.0 0.0 94-95 5.4625 0.0 0.0 0.0 0.0 96-97 5.6125 0.0 0.0 0.0 0.0 98-99 5.862500000000001 0.0 0.0 0.0 0.0 100-101 5.9375 0.0 0.0 0.0 0.0 102-103 6.2125 0.0 0.0 0.0 0.0 104-105 6.4 0.0 0.0 0.0 0.0 106-107 6.550000000000001 0.0 0.0 0.0 0.0 108-109 6.7 0.0 0.0 0.0 0.0 110-111 6.8875 0.0 0.0 0.0 0.0 112-113 7.0625 0.0 0.0 0.0 0.0 114-115 7.324999999999999 0.0 0.0 0.0 0.0 116-117 7.637499999999999 0.0 0.0 0.0 0.0 118-119 8.0125 0.0 0.0 0.0 0.0 120-121 8.15 0.0 0.0 0.0 0.0 122-123 8.4375 0.0 0.0 0.0 0.0 124-125 8.7375 0.0 0.0 0.0 0.0 126-127 9.125 0.0 0.0 0.0 0.0 128-129 9.3375 0.0 0.0 0.0 0.0 130-131 9.4875 0.0 0.0 0.0 0.0 132-133 9.7125 0.0 0.0 0.0 0.0 134-135 9.975000000000001 0.0 0.0 0.0 0.0 136-137 10.2 0.0 0.0 0.0 0.0 138 10.3 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGCACTT 10 0.0070063258 143.775 5 AGGCACT 10 0.0070063258 143.775 4 GCACTTT 10 0.0070063258 143.775 6 CTATGGA 10 0.0070063258 143.775 8 TGGCCAT 10 0.0070063258 143.775 2 >>END_MODULE SRR11445637 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11445637_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 27 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 19.81625 27.0 2.0 32.0 2.0 32.0 2 31.09 32.0 32.0 32.0 32.0 32.0 3 33.24 32.0 32.0 37.0 32.0 37.0 4 34.3575 37.0 32.0 37.0 32.0 37.0 5 35.8075 37.0 37.0 37.0 32.0 37.0 6 38.62625 41.0 41.0 41.0 32.0 41.0 7 39.451 41.0 41.0 41.0 37.0 41.0 8 38.937 41.0 41.0 41.0 37.0 41.0 9 36.58325 41.0 37.0 41.0 22.0 41.0 10-14 39.1943 41.0 41.0 41.0 35.0 41.0 15-19 36.910900000000005 40.2 36.6 41.0 28.0 41.0 20-24 27.659749999999995 31.0 16.0 38.6 12.0 41.0 25-29 30.970000000000006 36.0 23.0 41.0 12.0 41.0 30-34 30.408500000000004 36.0 22.0 41.0 12.0 41.0 35-39 29.10715 34.0 18.0 40.2 12.0 41.0 40-44 28.7651 32.0 14.0 41.0 12.0 41.0 45-49 28.216250000000002 31.0 16.0 40.2 12.0 41.0 50-54 26.925100000000004 29.0 14.0 37.8 12.0 41.0 55-59 26.656200000000002 27.0 14.0 38.6 12.0 41.0 60-64 28.406150000000004 31.0 18.0 40.2 12.0 41.0 65-69 28.055950000000003 32.0 12.0 39.4 12.0 41.0 70-74 26.3327 27.0 12.0 37.8 12.0 41.0 75-79 25.040750000000003 24.0 12.0 36.0 12.0 40.2 80-84 26.12025 26.0 12.0 37.0 12.0 41.0 85-89 25.35465 23.0 12.0 37.0 12.0 41.0 90-94 24.6505 22.0 12.0 37.0 12.0 41.0 95-99 24.75965 23.0 12.0 36.0 12.0 41.0 100-104 23.228550000000002 22.0 12.0 34.0 12.0 40.2 105-109 23.828000000000003 22.0 12.0 35.0 12.0 40.2 110-114 22.091749999999998 20.0 12.0 31.0 12.0 38.6 115-119 22.5943 22.0 12.0 32.0 12.0 39.4 120-124 22.9073 22.0 12.0 32.0 12.0 38.6 125-129 20.625799999999998 18.0 12.0 29.0 12.0 37.0 130-134 20.614 18.0 12.0 28.0 12.0 37.0 135-139 20.5195 18.0 12.0 28.0 12.0 37.0 140-144 19.7793 14.0 12.0 27.0 12.0 37.0 145-149 19.69655 16.0 12.0 26.0 12.0 36.0 150 20.128 12.0 12.0 27.0 12.0 37.0 >>END_MODULE >>Per sequence quality scores warn #Quality Count 15 3.0 16 10.0 17 46.0 18 88.0 19 182.0 20 204.0 21 278.0 22 317.0 23 328.0 24 297.0 25 293.0 26 267.0 27 240.0 28 226.0 29 211.0 30 205.0 31 173.0 32 153.0 33 112.0 34 95.0 35 90.0 36 69.0 37 64.0 38 28.0 39 18.0 40 3.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 5.534014804370814 0.14099400775467041 90.34191046880508 3.9830807190694393 2 0.7250000000000001 0.05 98.97500000000001 0.25 3 0.25 0.05 99.52499999999999 0.17500000000000002 4 0.75 0.1 98.875 0.27499999999999997 5 0.15 0.1 99.575 0.17500000000000002 6 0.27499999999999997 0.22499999999999998 99.425 0.075 7 0.125 0.22499999999999998 99.45 0.2 8 0.35000000000000003 0.05 99.4 0.2 9 2.0 0.15 97.275 0.575 10-14 0.280014000700035 0.24001200060003 99.25496274813742 0.2250112505625281 15-19 3.58 2.03 92.545 1.8450000000000002 20-24 19.73 28.235 37.3 14.735000000000001 25-29 12.534999999999998 41.71 34.25 11.505 30-34 12.754999999999999 34.18 38.67 14.395 35-39 12.370618530926546 28.471423571178562 44.382219110955546 14.775738786939346 40-44 11.875 27.865000000000002 47.12 13.139999999999999 45-49 12.020601030051504 31.481574078703932 43.77718885944297 12.720636031801591 50-54 13.114999999999998 33.129999999999995 40.495 13.26 55-59 13.975000000000001 33.019999999999996 38.47 14.535 60-64 14.865 32.635 36.605 15.895000000000001 65-69 15.09 32.125 36.325 16.46 70-74 15.015 31.445 36.36 17.18 75-79 14.895 32.235 36.15 16.72 80-84 14.210710535526777 32.916645832291614 35.68178408920446 17.19085954297715 85-89 14.59 34.195 34.96 16.255 90-94 15.22 32.800000000000004 35.72 16.259999999999998 95-99 15.5 33.339999999999996 34.875 16.285 100-104 15.58 33.335 33.879999999999995 17.205000000000002 105-109 15.8 34.415 33.615 16.17 110-114 15.370000000000001 34.975 32.945 16.71 115-119 15.865000000000002 34.64 32.074999999999996 17.419999999999998 120-124 15.476547654765477 34.478447844784476 32.26322632263226 17.78177817781778 125-129 16.215 34.07 32.885 16.830000000000002 130-134 16.425 33.625 33.495000000000005 16.455000000000002 135-139 16.045 33.515 32.495000000000005 17.945 140-144 16.805 32.865 32.45 17.88 145-149 17.119999999999997 34.04 31.305 17.535 150 15.375 33.775 33.6 17.25 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 111.0 1 117.0 2 101.5 3 58.0 4 30.5 5 24.5 6 19.5 7 17.5 8 22.5 9 23.0 10 26.5 11 32.5 12 33.5 13 29.5 14 30.5 15 39.5 16 47.0 17 62.0 18 74.0 19 91.0 20 101.5 21 109.0 22 144.0 23 171.5 24 195.0 25 213.0 26 219.0 27 225.0 28 213.5 29 197.0 30 203.0 31 190.5 32 142.5 33 110.0 34 91.0 35 77.5 36 64.5 37 52.5 38 52.0 39 47.0 40 35.0 41 27.0 42 25.0 43 20.5 44 15.5 45 14.0 46 12.0 47 13.5 48 15.5 49 12.5 50 10.5 51 9.0 52 8.0 53 8.5 54 5.5 55 3.0 56 2.5 57 2.0 58 1.5 59 0.5 60 0.0 61 0.0 62 1.0 63 1.0 64 0.5 65 1.0 66 0.5 67 0.0 68 0.0 69 0.0 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content fail #Base N-Count 1 29.075 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 0.005 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.005 40-44 0.0 45-49 0.005 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 0.005 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 0.01 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 90.8 #Duplication Level Percentage of deduplicated Percentage of total 1 97.96255506607929 88.94999999999999 2 1.183920704845815 2.15 3 0.22026431718061676 0.6 4 0.08259911894273128 0.3 5 0.08259911894273128 0.375 6 0.16519823788546256 0.8999999999999999 7 0.027533039647577095 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.22026431718061676 2.9499999999999997 >50 0.05506607929515419 3.5999999999999996 >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 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 83 2.075 No Hit NTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 61 1.525 No Hit TTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 31 0.775 No Hit TTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 16 0.4 No Hit TTTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 15 0.375 No Hit TTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 15 0.375 No Hit TTTTTTTTTTTTTTTTTTTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 11 0.27499999999999997 No Hit TTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 10 0.25 No Hit NTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 10 0.25 No Hit TTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 10 0.25 No Hit NTTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 7 0.17500000000000002 No Hit NTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit NTTTTTTTTTTTTTTTTTTCCTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit TTTTTTTTTTTTTTTTTTATTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit TTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit TTTTTTTTTTTTTTTTTTTTCTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit NTTTTTTTTTTTTTTTTTTGTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit GTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 5 0.125 No Hit TTTTTTTTTTTTTTTTTTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 5 0.125 No Hit NTTTTTTTTTTTTTTTTTTACTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 5 0.125 No Hit >>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 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.037500000000000006 0.0 0.0 0.0 0.0 14-15 0.0625 0.0 0.0 0.0 0.0 16-17 0.075 0.0 0.0 0.0 0.0 18-19 0.075 0.0 0.0 0.0 0.0 20-21 0.3125 0.0 0.0 0.0 0.0 22-23 0.8625 0.0 0.0 0.0 0.0 24-25 1.0875 0.0 0.0 0.0 0.0 26-27 1.1375000000000002 0.0 0.0 0.0 0.0 28-29 1.1875 0.0 0.0 0.0 0.0 30-31 1.3375 0.0 0.0 0.0 0.0 32-33 1.4625 0.0 0.0 0.0 0.0 34-35 1.525 0.0 0.0 0.0 0.0 36-37 1.575 0.0 0.0 0.0 0.0 38-39 1.575 0.0 0.0 0.0 0.0 40-41 1.625 0.0 0.0 0.0 0.0 42-43 1.6749999999999998 0.0 0.0 0.0 0.0 44-45 1.7625 0.0 0.0 0.0 0.0 46-47 1.8375 0.0 0.0 0.0 0.0 48-49 1.9 0.0 0.0 0.0 0.0 50-51 1.9874999999999998 0.0 0.0 0.0 0.0 52-53 2.025 0.0 0.0 0.0 0.0 54-55 2.075 0.0 0.0 0.0 0.0 56-57 2.175 0.0 0.0 0.0 0.0 58-59 2.2874999999999996 0.0 0.0 0.0 0.0 60-61 2.35 0.0 0.0 0.0 0.0 62-63 2.4 0.0 0.0 0.0 0.0 64-65 2.5 0.0 0.0 0.0 0.0 66-67 2.675 0.0 0.0 0.0 0.0 68-69 2.775 0.0 0.0 0.0 0.0 70-71 2.9375 0.0 0.0 0.0 0.0 72-73 3.05 0.0 0.0 0.0 0.0 74-75 3.1375 0.0 0.0 0.0 0.0 76-77 3.1875 0.0 0.0 0.0 0.0 78-79 3.225 0.0 0.0 0.0 0.0 80-81 3.35 0.0 0.0 0.0 0.0 82-83 3.4375 0.0 0.0 0.0 0.0 84-85 3.6375 0.0 0.0 0.0 0.0 86-87 3.7375 0.0 0.0 0.0 0.0 88-89 3.975 0.0 0.0 0.0 0.0 90-91 4.1375 0.0 0.0 0.0 0.0 92-93 4.2875 0.0 0.0 0.0 0.0 94-95 4.475 0.0 0.0 0.0 0.0 96-97 4.575 0.0 0.0 0.0 0.0 98-99 4.8125 0.0 0.0 0.0 0.0 100-101 4.887499999999999 0.0 0.0 0.0 0.0 102-103 5.15 0.0 0.0 0.0 0.0 104-105 5.275 0.0 0.0 0.0 0.0 106-107 5.35 0.0 0.0 0.0 0.0 108-109 5.45 0.0 0.0 0.0 0.0 110-111 5.6625 0.0 0.0 0.0 0.0 112-113 5.825 0.0 0.0 0.0 0.0 114-115 6.112500000000001 0.0 0.0 0.0 0.0 116-117 6.325 0.0 0.0 0.0 0.0 118-119 6.6375 0.0 0.0 0.0 0.0 120-121 6.8 0.0 0.0 0.0 0.0 122-123 6.9875 0.0 0.0 0.0 0.0 124-125 7.199999999999999 0.0 0.0 0.0 0.0 126-127 7.487500000000001 0.0 0.0 0.0 0.0 128-129 7.699999999999999 0.0 0.0 0.0 0.0 130-131 7.7875 0.0 0.0 0.0 0.0 132-133 7.9125 0.0 0.0 0.0 0.0 134-135 8.0625 0.0 0.0 0.0 0.0 136-137 8.1875 0.0 0.0 0.0 0.0 138 8.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTTTTTT 120 4.9973787E-5 41.30029 1 GTTTTTT 125 0.0033142685 31.718618 1 TTTTTGC 40 3.1406342E-4 21.558752 15-19 TTTTGGA 40 0.008055038 17.965626 15-19 TTTTTGG 80 3.45859E-7 17.965626 10-14 TTTTTTC 160 3.6379788E-12 15.270782 10-14 TTTTTCT 60 0.00476338 14.3725 15-19 TTTTTAG 60 0.00476338 14.3725 15-19 TTTTTTG 285 0.0 13.616053 10-14 TTTTTTA 205 5.9705962E-6 9.114267 10-14 TTTTTTT 9560 0.0 5.8632584 2 >>END_MODULE Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917254 spots for SRR11445637.sra Written 917254 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra Read 917243 spots for SRR11445637.sra Written 917243 spots for SRR11445637.sra SRR ids: ['SRR11445637.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_0r5iwg9h SRR11445637.sra spots: 18344871 blocks: [[1, 917243], [917244, 1834486], [1834487, 2751729], [2751730, 3668972], [3668973, 4586215], [4586216, 5503458], [5503459, 6420701], [6420702, 7337944], [7337945, 8255187], [8255188, 9172430], [9172431, 10089673], [10089674, 11006916], [11006917, 11924159], [11924160, 12841402], [12841403, 13758645], [13758646, 14675888], [14675889, 15593131], [15593132, 16510374], [16510375, 17427617], [17427618, 18344871]] SRR11445637 file size 6176859 SRR11445637 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 SRR11445637 SRR11445637_1.fastq SRR11445637_2.fastq Input file: SRR11445637_1.fastq Paired file: SRR11445637_2.fastq trimmed: SRR11445637-trimmed-pair1.fastq, SRR11445637-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 Wed Feb 12 14:31:11 2025 >> started Wed Feb 12 14:31:34 2025 >> done (22.820s) 18344871 read pairs processed; of these: 10092 ( 0.06%) short read pairs filtered out after trimming by size control 1296 ( 0.01%) empty read pairs filtered out after trimming by size control 18333483 (99.94%) read pairs available; of these: 3711581 (20.24%) trimmed read pairs available after processing 14621902 (79.76%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 14419 0.08% 19 38339 0.21% 20 47102 0.26% 21 72666 0.40% 22 53542 0.29% 23 30249 0.16% 24 21171 0.12% 25 16974 0.09% 26 14834 0.08% 27 13327 0.07% 28 12297 0.07% 29 11483 0.06% 30 9880 0.05% 31 8964 0.05% 32 8672 0.05% 33 8511 0.05% 34 8639 0.05% 35 7951 0.04% 36 8075 0.04% 37 7953 0.04% 38 8331 0.05% 39 8120 0.04% 40 7769 0.04% 41 7923 0.04% 42 7539 0.04% 43 7357 0.04% 44 7240 0.04% 45 7188 0.04% 46 7030 0.04% 47 6997 0.04% 48 7081 0.04% 49 7155 0.04% 50 7024 0.04% 51 7207 0.04% 52 7034 0.04% 53 7178 0.04% 54 7286 0.04% 55 7654 0.04% 56 7630 0.04% 57 7861 0.04% 58 8216 0.04% 59 8342 0.05% 60 8721 0.05% 61 8991 0.05% 62 9230 0.05% 63 9145 0.05% 64 9440 0.05% 65 9792 0.05% 66 10159 0.06% 67 10611 0.06% 68 10516 0.06% 69 10503 0.06% 70 10872 0.06% 71 10898 0.06% 72 10947 0.06% 73 11314 0.06% 74 11550 0.06% 75 11941 0.07% 76 12001 0.07% 77 12319 0.07% 78 12440 0.07% 79 12709 0.07% 80 13079 0.07% 81 13331 0.07% 82 13361 0.07% 83 13534 0.07% 84 13607 0.07% 85 14191 0.08% 86 13881 0.08% 87 14153 0.08% 88 14529 0.08% 89 14533 0.08% 90 14358 0.08% 91 14500 0.08% 92 14824 0.08% 93 14428 0.08% 94 14332 0.08% 95 14677 0.08% 96 14720 0.08% 97 15320 0.08% 98 15371 0.08% 99 15499 0.08% 100 15755 0.09% 101 16124 0.09% 102 16126 0.09% 103 16337 0.09% 104 16390 0.09% 105 16629 0.09% 106 16889 0.09% 107 16684 0.09% 108 17035 0.09% 109 17647 0.10% 110 17416 0.09% 111 17608 0.10% 112 18245 0.10% 113 17456 0.10% 114 18098 0.10% 115 18786 0.10% 116 18402 0.10% 117 18962 0.10% 118 19185 0.10% 119 19789 0.11% 120 20381 0.11% 121 20411 0.11% 122 20610 0.11% 123 20922 0.11% 124 20840 0.11% 125 21492 0.12% 126 20671 0.11% 127 20896 0.11% 128 20745 0.11% 129 20968 0.11% 130 21031 0.11% 131 21941 0.12% 132 22614 0.12% 133 22707 0.12% 134 21786 0.12% 135 21234 0.12% 136 21190 0.12% 137 21230 0.12% 138 21616 0.12% 139 22179 0.12% 140 22849 0.12% 141 23579 0.13% 142 24460 0.13% 143 25729 0.14% 144 27204 0.15% 145 32519 0.18% 146 46737 0.25% 147 91419 0.50% 148 246277 1.34% 149 1315244 7.17% 150 14621902 79.76% 18333483 reads passed initial QC criterion=sequence-density sequence-density=1.66 sequence-density-rank=1 fanout-score=3.61 fanout-score-rank=16 prefix-density=2.00 prefix-fanout=3.0 sequence=CCTAAGATTGAGGA criterion=fanout-score sequence-density=0.02 sequence-density-rank=37 fanout-score=27.03 fanout-score-rank=1 prefix-density=0.24 prefix-fanout=2.1 sequence=GAGAATGCTAACACTGACGCTATTTCTGCTGTTTGTCAAGATGGGGTTCTGACTGTTACTGTTGAGAAATTACCACCTCCAGAGCCTAAGAAGCCTAAGACTATCGAGGTCAAGATTGCTTGAAGAAGAATGCTTGATTACATATATAATGTAGCTTGTTCTGTGTGCTAAGGTGATGATAAATAATGAGGGTTTTGCTGGGTGCTTTGCTTGGGGGTGCGGGATGATTTTGGGCGTGTTTGCGTTTGAATGAGTTCATTATTAGTTTTCTCTTTAGGAAACTGGTGATTGTTGTTCAAAACGTGGTATGAAATATATGAATGTAGTGGTGGCGTTATATATTACTTTTTCTTTCTACTTGGTTGCTTTACTCTAATTCATATGTATTTTTAGGTTTCTGCCAATTTTCTTCCCCTGAAC criterion=sequence-density sequence-density=0.16 sequence-density-rank=1 fanout-score=2.08 fanout-score-rank=14 prefix-density=0.02 prefix-fanout=2.1 sequence=TTTTTTTTTTGG criterion=fanout-score sequence-density=0.04 sequence-density-rank=16 fanout-score=3.00 fanout-score-rank=1 prefix-density=0.03 prefix-fanout=3.0 sequence=GCGACGATGCGTGACACCCAGGCAGACGTGCCCTCGACCAAGAGGCCTCGGGCGCAACTTGCGTTCAAAGACTCGATGGTTCACGGGATTCTGCAATTCACACCAAGTATCGCATTTCGCTACGTTCTTCATCGAT SRR11445637 testing PE reads STAR mapping to Ensembl genome Unpaired reads removal Started job on | Feb 12 14:43:22 Started mapping on | Feb 12 14:43:25 Finished on | Feb 12 14:49:33 Mapping speed, Million of reads per hour | 175.29 Number of input reads | 17918435 Average input read length | 259 UNIQUE READS: Uniquely mapped reads number | 7051095 Uniquely mapped reads % | 39.35% Average mapped length | 245.15 Number of splices: Total | 391766 Number of splices: Annotated (sjdb) | 338428 Number of splices: GT/AG | 361209 Number of splices: GC/AG | 4713 Number of splices: AT/AC | 686 Number of splices: Non-canonical | 25158 Mismatch rate per base, % | 2.92% Deletion rate per base | 0.03% Deletion average length | 2.12 Insertion rate per base | 0.02% Insertion average length | 1.92 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 854608 % of reads mapped to multiple loci | 4.77% Number of reads mapped to too many loci | 59259 % of reads mapped to too many loci | 0.33% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 54.63% % of reads unmapped: other | 0.92% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 10012732 10012732 10012732 N_multimapping 854608 854608 854608 N_noFeature 665445 749745 6862350 N_ambiguous 187037 77857 5480 UnstrandedReadsAssigned:6198613 PositiveStrandReadsAssigned:6223493 NegativeStrandReadsAssigned:183265 Dataset is classified positive stranded MeadianReadLen=138 20thPercentileLength=138 echo kmer=133 SRR11445637 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR11445637-trimmed-pair1.fastq SRR11445637-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,918,435 reads, 12,812,549 reads pseudoaligned [quant] estimated average fragment length: 175.702 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,090 rounds 52401 SRR11445637.ke.tsv 34699 SRR11445637.se.tsv 87100 total ==> SRR11445637.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1843.3 1002 37.7272 Potri.005G024800.1.v4.1 1035 860.298 561 45.2581 Potri.004G059700.1.v4.1 961 786.303 20 1.76531 Potri.007G009000.2.v4.1 1416 1241.3 0 0 Potri.003G141000.2.v4.1 2943 2768.3 464 11.6329 Potri.016G087400.1.v4.1 270 107.654 70 45.1285 Potri.015G069301.1.v4.1 564 389.487 0 0 Potri.010G195200.1.v4.1 1773 1598.3 27 1.17243 Potri.012G127500.1.v4.1 977 802.303 2304 199.309 ==> SRR11445637.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 69 Potri.001G233950.v4.1 3 Potri.001G122700.v4.1 70 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 4 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 20 SRR11445637 completed mapping pipeline successfully