Starting /dee2/code/volunteer_pipeline.sh SRR11389844 current disk space = 1544532967424 free memory = 1602046380 SRR11389844 SRAfilesize fb4efb4522a8e239875df8d4a088aafe SRR11389844.sra SRR11389844.sra file validated SRR11389844 is paired end SRR11389844 is conventional basespace SRR11389844 read1 length is 44-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389844_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 44-76 %GC 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 30.81025 32.0 32.0 32.0 32.0 32.0 2 31.11275 32.0 32.0 32.0 32.0 32.0 3 31.049 32.0 32.0 32.0 32.0 32.0 4 31.16225 32.0 32.0 32.0 32.0 32.0 5 31.08975 32.0 32.0 32.0 32.0 32.0 6 34.0045 36.0 36.0 36.0 32.0 36.0 7 34.0495 36.0 36.0 36.0 32.0 36.0 8 34.0595 36.0 36.0 36.0 32.0 36.0 9 33.93325 36.0 36.0 36.0 32.0 36.0 10-11 33.916 36.0 36.0 36.0 32.0 36.0 12-13 34.060625 36.0 36.0 36.0 32.0 36.0 14-15 34.012874999999994 36.0 36.0 36.0 32.0 36.0 16-17 34.074625 36.0 36.0 36.0 32.0 36.0 18-19 34.054249999999996 36.0 36.0 36.0 32.0 36.0 20-21 34.0055 36.0 36.0 36.0 32.0 36.0 22-23 33.870000000000005 36.0 36.0 36.0 32.0 36.0 24-25 33.68962500000001 36.0 36.0 36.0 29.5 36.0 26-27 33.684625 36.0 36.0 36.0 29.5 36.0 28-29 33.512 36.0 36.0 36.0 24.0 36.0 30-31 33.533 36.0 36.0 36.0 27.0 36.0 32-33 33.368875 36.0 36.0 36.0 21.0 36.0 34-35 33.351 36.0 36.0 36.0 21.0 36.0 36-37 33.37712500000001 36.0 36.0 36.0 21.0 36.0 38-39 33.407624999999996 36.0 36.0 36.0 21.0 36.0 40-41 33.295125 36.0 36.0 36.0 17.5 36.0 42-43 33.181875000000005 36.0 36.0 36.0 21.0 36.0 44-45 33.06424190422605 36.0 36.0 36.0 17.5 36.0 46-47 32.94497351826701 36.0 36.0 36.0 14.0 36.0 48-49 32.98461730865432 36.0 36.0 36.0 14.0 36.0 50-51 32.766758379189596 36.0 34.0 36.0 14.0 36.0 52-53 32.6199649737303 36.0 34.0 36.0 14.0 36.0 54-55 32.29404404404404 36.0 32.0 36.0 14.0 36.0 56-57 32.4261931652801 36.0 32.0 36.0 14.0 36.0 58-59 32.1427498121713 36.0 32.0 36.0 14.0 36.0 60-61 32.0969196093163 36.0 32.0 36.0 14.0 36.0 62-63 32.13792516109914 36.0 32.0 36.0 14.0 36.0 64-65 32.15505574403763 36.0 32.0 36.0 14.0 36.0 66-67 32.09965417831759 36.0 32.0 36.0 14.0 36.0 68-69 32.00943807809634 36.0 32.0 36.0 14.0 36.0 70-71 31.974956599318297 36.0 32.0 36.0 14.0 36.0 72-73 31.835710428443267 36.0 32.0 36.0 14.0 36.0 74-75 31.7496974451633 36.0 32.0 36.0 14.0 36.0 76 30.495535714285715 36.0 27.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 5.0 22 5.0 23 19.0 24 28.0 25 43.0 26 57.0 27 115.0 28 128.0 29 185.0 30 232.0 31 319.0 32 394.0 33 571.0 34 904.0 35 993.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.725 11.3 15.725 38.25 2 22.925 13.15 32.324999999999996 31.6 3 22.95 19.1 23.5 34.449999999999996 4 28.9 25.025 20.0 26.075 5 25.974999999999998 31.125000000000004 22.6 20.3 6 22.45 31.95 25.825 19.775000000000002 7 18.099999999999998 26.85 34.925 20.125 8 18.775 26.200000000000003 31.900000000000002 23.125 9 19.900000000000002 21.975 34.4 23.724999999999998 10-11 21.8125 31.337500000000002 24.45 22.400000000000002 12-13 22.95 25.1 27.525 24.425 14-15 21.4375 26.8375 27.55 24.175 16-17 22.3625 27.500000000000004 25.4875 24.65 18-19 22.425 26.85 27.400000000000002 23.325000000000003 20-21 22.55 26.937499999999996 26.875 23.6375 22-23 22.912499999999998 25.5625 27.6375 23.8875 24-25 22.650000000000002 26.2875 26.700000000000003 24.3625 26-27 22.475 26.85 26.5 24.175 28-29 22.525000000000002 25.4625 26.9625 25.05 30-31 23.525 27.237499999999997 25.7 23.5375 32-33 22.112499999999997 26.924999999999997 27.187499999999996 23.775 34-35 23.1625 25.887500000000003 27.237499999999997 23.7125 36-37 22.912499999999998 26.5875 26.1125 24.3875 38-39 23.0375 26.275 26.3625 24.325 40-41 22.8 26.625 26.7625 23.8125 42-43 21.7875 26.387500000000003 27.962500000000002 23.8625 44-45 22.26528316039505 25.703212901612705 27.265908238529818 24.765595699462434 46-47 23.68388145554583 25.75965987245217 25.30949105914718 25.24696761285482 48-49 22.061030515257627 26.40070035017509 27.01350675337669 24.524762381190595 50-51 22.336168084042022 25.07503751875938 27.188594297148573 25.400200100050025 52-53 22.47935951963973 25.093820365273956 26.38228671503628 26.044533400050035 54-55 22.45995995995996 25.925925925925924 26.463963963963966 25.150150150150154 56-57 22.07336922499061 25.841993239013394 27.043946412920995 25.040691123075 58-59 22.58953168044077 26.270974204858504 26.984723265715 24.154770848985724 60-61 22.58953168044077 25.006260956674183 28.174305033809166 24.229902329075884 62-63 22.95164119268354 26.13380105236783 26.797795038837386 24.11676271611125 64-65 24.037134612972025 25.743319533308238 26.10713837661523 24.112407477104504 66-67 22.555918572505654 24.55390801708972 27.93415431012817 24.956019100276453 68-69 23.188223452440866 24.73578258681429 26.182687468545545 25.893306492199297 70-71 22.825812956894378 25.699521048651373 26.733047643055208 24.74161835139904 72-73 22.4977856510186 25.559913956725293 26.420346703783377 25.52195368847273 74-75 23.455469376838728 22.867076758491574 28.496924311313187 25.18052955335651 76 26.11607142857143 0.0 37.983630952380956 35.90029761904761 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 39.0 1 25.0 2 7.0 3 2.5 4 2.0 5 3.0 6 3.0 7 2.0 8 2.0 9 1.5 10 1.0 11 1.0 12 1.0 13 1.0 14 1.0 15 0.5 16 0.5 17 2.0 18 11.5 19 21.0 20 26.5 21 31.5 22 26.5 23 18.5 24 14.5 25 12.5 26 13.0 27 17.5 28 19.5 29 21.0 30 29.0 31 35.0 32 41.0 33 48.0 34 58.0 35 80.5 36 96.0 37 105.0 38 121.0 39 137.0 40 161.5 41 184.5 42 192.5 43 211.5 44 233.5 45 238.0 46 235.5 47 219.5 48 217.0 49 209.0 50 176.5 51 155.5 52 130.0 53 110.5 54 108.5 55 102.5 56 100.0 57 107.0 58 110.0 59 111.5 60 112.0 61 98.5 62 88.0 63 77.5 64 68.0 65 63.0 66 53.5 67 50.5 68 48.5 69 40.0 70 30.5 71 28.0 72 28.5 73 26.5 74 22.0 75 17.5 76 12.5 77 9.5 78 9.0 79 8.5 80 6.0 81 4.5 82 3.0 83 1.0 84 1.5 85 1.0 86 0.5 87 1.0 88 0.5 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 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 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 44 1.0 45 0.0 46 1.0 47 0.0 48 0.0 49 0.0 50 0.0 51 1.0 52 0.0 53 1.0 54 0.0 55 2.0 56 1.0 57 0.0 58 0.0 59 0.0 60 0.0 61 1.0 62 2.0 63 4.0 64 1.0 65 4.0 66 4.0 67 2.0 68 2.0 69 3.0 70 6.0 71 5.0 72 15.0 73 83.0 74 244.0 75 929.0 76 2688.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.0 #Duplication Level Percentage of deduplicated Percentage of total 1 97.18421052631578 92.325 2 2.0 3.8 3 0.5 1.425 4 0.13157894736842105 0.5 5 0.07894736842105263 0.375 6 0.02631578947368421 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.07894736842105263 1.425 >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 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 30 0.75 No Hit GTCAATTAGAAGAATAAAGAAGAATTACTGCATTTCGTAACTTATTTTTT 16 0.4 No Hit GCCGAGTTTAATTGCAGTCAATTAGAAGAATAAAGAAGAATTACTGCATT 11 0.27499999999999997 No Hit CGTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTC 6 0.15 No Hit GTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTTCT 5 0.125 No Hit TCGTAACTTATTTTTTCTCTTTTTATTTTGTTTCTTTTTATTTAGACCTT 5 0.125 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 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 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.0 0.0 0.0 0.0 0.0 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 59 0.0 0.0 0.0 0.0 0.0 60 0.0 0.0 0.0 0.0 0.0 61 0.0 0.0 0.0 0.0 0.0 62 0.0 0.0 0.0 0.0 0.0 63 0.0 0.0 0.0 0.0 0.0 64 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR11389844 read2 length is 44-76 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR11389844_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 44-76 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.532 32.0 32.0 32.0 21.0 32.0 2 28.64525 32.0 32.0 32.0 14.0 32.0 3 28.94875 32.0 32.0 32.0 14.0 32.0 4 28.71025 32.0 32.0 32.0 14.0 32.0 5 28.76775 32.0 32.0 32.0 14.0 32.0 6 30.82575 36.0 32.0 36.0 14.0 36.0 7 31.2925 36.0 32.0 36.0 14.0 36.0 8 30.61125 36.0 32.0 36.0 14.0 36.0 9 30.75175 36.0 32.0 36.0 14.0 36.0 10-11 30.853875000000002 36.0 32.0 36.0 14.0 36.0 12-13 31.128999999999998 36.0 32.0 36.0 14.0 36.0 14-15 31.0095 36.0 32.0 36.0 14.0 36.0 16-17 30.93775 36.0 32.0 36.0 14.0 36.0 18-19 30.853375 36.0 32.0 36.0 14.0 36.0 20-21 30.533625 36.0 32.0 36.0 14.0 36.0 22-23 30.680374999999998 36.0 32.0 36.0 14.0 36.0 24-25 30.54675 36.0 32.0 36.0 14.0 36.0 26-27 30.578 36.0 32.0 36.0 14.0 36.0 28-29 30.460124999999998 36.0 32.0 36.0 14.0 36.0 30-31 30.4685 36.0 29.5 36.0 14.0 36.0 32-33 30.429125 36.0 32.0 36.0 14.0 36.0 34-35 30.205875 36.0 24.0 36.0 14.0 36.0 36-37 30.192375 36.0 24.0 36.0 14.0 36.0 38-39 30.212875 36.0 27.0 36.0 14.0 36.0 40-41 30.025875 36.0 24.0 36.0 14.0 36.0 42-43 29.898 36.0 24.0 36.0 14.0 36.0 44-45 30.131282039259816 36.0 24.0 36.0 14.0 36.0 46-47 29.809056253558136 36.0 21.0 36.0 14.0 36.0 48-49 29.63831915957979 36.0 17.5 36.0 14.0 36.0 50-51 29.714607303651825 36.0 21.0 36.0 14.0 36.0 52-53 29.533525143857894 36.0 21.0 36.0 14.0 36.0 54-55 29.536411411411414 36.0 17.5 36.0 14.0 36.0 56-57 29.174659591440754 36.0 21.0 36.0 14.0 36.0 58-59 29.24755822689707 36.0 17.5 36.0 14.0 36.0 60-61 29.155647382920108 36.0 17.5 36.0 14.0 36.0 62-63 29.177648205833524 36.0 17.5 36.0 14.0 36.0 64-65 29.362893829469346 36.0 21.0 36.0 14.0 36.0 66-67 28.8191538719124 36.0 14.0 36.0 14.0 36.0 68-69 28.805163058627834 36.0 14.0 36.0 14.0 36.0 70-71 28.943652009229346 36.0 14.0 36.0 14.0 36.0 72-73 28.630698203408127 36.0 14.0 36.0 14.0 36.0 74-75 28.73339389138792 36.0 14.0 36.0 14.0 36.0 76 27.54865269461078 32.0 14.0 36.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 14 4.0 15 16.0 16 24.0 17 18.0 18 18.0 19 15.0 20 17.0 21 28.0 22 44.0 23 78.0 24 129.0 25 160.0 26 219.0 27 252.0 28 337.0 29 380.0 30 444.0 31 494.0 32 504.0 33 459.0 34 281.0 35 79.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.099999999999994 17.05 14.05 33.800000000000004 2 31.125000000000004 24.05 25.25 19.575 3 28.349999999999998 29.15 19.275000000000002 23.225 4 29.775000000000002 31.4 18.65 20.175 5 29.15 31.474999999999998 20.5 18.875 6 22.475 34.425 22.925 20.175 7 23.25 18.375 34.375 24.0 8 25.624999999999996 23.65 25.55 25.174999999999997 9 23.599999999999998 23.625 27.650000000000002 25.124999999999996 10-11 27.85 28.712500000000002 20.2625 23.175 12-13 26.924999999999997 23.4875 24.075 25.5125 14-15 25.15 26.137500000000003 24.7875 23.925 16-17 26.687499999999996 25.275 23.775 24.2625 18-19 25.7125 24.4 25.825 24.0625 20-21 26.875 26.0625 24.3 22.7625 22-23 27.8125 26.075 23.549999999999997 22.5625 24-25 25.2 26.25 24.837500000000002 23.7125 26-27 26.6125 26.25 24.1625 22.975 28-29 27.450000000000003 25.2375 23.7625 23.549999999999997 30-31 26.05 25.7875 23.2875 24.875 32-33 26.325 25.85 23.9875 23.8375 34-35 26.375 25.95 24.4 23.275000000000002 36-37 26.187500000000004 25.7 24.3875 23.724999999999998 38-39 25.8 26.474999999999998 24.775 22.95 40-41 25.674999999999997 25.224999999999998 24.349999999999998 24.75 42-43 27.4125 24.425 24.962500000000002 23.200000000000003 44-45 25.50318789848731 26.728341042630326 24.065508188523566 23.702962870358796 46-47 26.885081905714642 25.847192697261473 24.39664874327873 22.871076653745153 48-49 25.737868934467233 25.22511255627814 25.15007503751876 23.88694347173587 50-51 25.912956478239117 25.15007503751876 25.362681340670335 23.574287143571787 52-53 25.881911433575183 25.93194896172129 24.130597948461347 24.055541656242184 54-55 25.725725725725724 25.525525525525527 24.86236236236236 23.886386386386384 56-57 26.054839113559535 26.355327407036434 24.602479028421183 22.987354450982846 58-59 25.6198347107438 25.63235662409216 24.355121462559477 24.392687202604556 60-61 26.070623591284747 26.646631605309288 24.63060355622339 22.65214124718257 62-63 26.866232464929862 25.951903807615228 24.010521042084168 23.171342685370742 64-65 26.11912225705329 26.08150470219436 23.786833855799372 24.012539184952978 66-67 25.081637779452397 25.948254207485554 25.307711630243656 23.662396382818386 68-69 25.845380263984914 25.7950974230044 24.70144563167819 23.658076681332496 70-71 27.04608410979602 25.33366910098212 23.621254092168222 23.99899269705364 72-73 26.425855513307983 25.627376425855513 24.575411913814957 23.371356147021547 74-75 26.814814814814813 23.313131313131315 25.76430976430976 24.107744107744107 76 30.164670658682635 0.0 34.955089820359284 34.880239520958085 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 42.0 1 21.5 2 1.0 3 1.0 4 1.0 5 1.0 6 2.0 7 2.0 8 1.0 9 0.5 10 1.0 11 1.0 12 0.0 13 0.5 14 1.0 15 0.5 16 0.5 17 1.5 18 8.5 19 13.5 20 11.5 21 9.5 22 9.0 23 8.5 24 12.0 25 14.5 26 11.5 27 12.5 28 13.5 29 15.0 30 18.5 31 24.5 32 32.0 33 35.5 34 50.5 35 76.0 36 96.0 37 110.5 38 119.0 39 138.5 40 154.5 41 158.0 42 166.5 43 192.5 44 213.5 45 196.5 46 187.0 47 184.0 48 164.5 49 167.0 50 172.0 51 153.0 52 143.5 53 136.0 54 131.0 55 122.0 56 110.0 57 110.0 58 110.5 59 115.0 60 118.0 61 114.5 62 110.0 63 100.5 64 83.5 65 77.5 66 77.5 67 71.5 68 63.0 69 50.5 70 42.0 71 46.5 72 52.5 73 44.0 74 31.0 75 26.0 76 20.5 77 16.5 78 12.0 79 8.5 80 14.0 81 14.5 82 7.0 83 4.0 84 4.0 85 3.5 86 2.5 87 2.0 88 1.0 89 1.0 90 2.0 91 3.0 92 4.0 93 2.0 94 2.5 95 4.5 96 4.0 97 4.0 98 4.5 99 5.0 100 5.0 >>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 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 44 1.0 45 0.0 46 1.0 47 0.0 48 0.0 49 0.0 50 0.0 51 1.0 52 0.0 53 1.0 54 0.0 55 2.0 56 1.0 57 0.0 58 0.0 59 0.0 60 0.0 61 0.0 62 2.0 63 3.0 64 1.0 65 4.0 66 4.0 67 1.0 68 1.0 69 3.0 70 6.0 71 8.0 72 30.0 73 70.0 74 295.0 75 893.0 76 2672.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.3 #Duplication Level Percentage of deduplicated Percentage of total 1 97.9491173416407 94.325 2 1.505711318795431 2.9000000000000004 3 0.25960539979231567 0.75 4 0.0778816199376947 0.3 5 0.10384215991692627 0.5 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.05192107995846314 0.44999999999999996 >10 0.05192107995846314 0.775 >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 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 21 0.525 No Hit TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 10 0.25 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 9 0.22499999999999998 No Hit GGAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGAGTGGCTTTAGAAGCCTGTGTACA 9 0.22499999999999998 No Hit CTGTATTACAATTTGGTGGAGGAACTTTAGGACATCCTTGGGGAAATGCA 5 0.125 No Hit GAACTTTAGGACATCCTTGGGGAAATGCACCTGGTGCAGCAGCTAATCGA 5 0.125 No Hit AAATTATCCGAGCAGCTTGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCG 5 0.125 No Hit ATCGATTAATAGATAAAACTAAATATGAAGAAGGTCTAAATAAAAAGAAA 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 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.0 0.0 0.0 0.0 0.0 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 59 0.0 0.0 0.0 0.0 0.0 60 0.0 0.0 0.0 0.0 0.0 61 0.0 0.0 0.0 0.0 0.0 62 0.025 0.0 0.0 0.0 0.0 63 0.025 0.0 0.0 0.0 0.0 64 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505684 spots for SRR11389844.sra Written 505684 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra Read 505677 spots for SRR11389844.sra Written 505677 spots for SRR11389844.sra SRR ids: ['SRR11389844.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jdyli76r SRR11389844.sra spots: 10113547 blocks: [[1, 505677], [505678, 1011354], [1011355, 1517031], [1517032, 2022708], [2022709, 2528385], [2528386, 3034062], [3034063, 3539739], [3539740, 4045416], [4045417, 4551093], [4551094, 5056770], [5056771, 5562447], [5562448, 6068124], [6068125, 6573801], [6573802, 7079478], [7079479, 7585155], [7585156, 8090832], [8090833, 8596509], [8596510, 9102186], [9102187, 9607863], [9607864, 10113547]] SRR11389844 file size 1911402 SRR11389844 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 SRR11389844 SRR11389844_1.fastq SRR11389844_2.fastq Input file: SRR11389844_1.fastq Paired file: SRR11389844_2.fastq trimmed: SRR11389844-trimmed-pair1.fastq, SRR11389844-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 08:00:32 2024 >> started Sat Dec 7 08:00:40 2024 >> done (8.545s) 10113547 read pairs processed; of these: 2 ( 0.00%) short read pairs filtered out after trimming by size control 41316 ( 0.41%) empty read pairs filtered out after trimming by size control 10072229 (99.59%) read pairs available; of these: 95601 ( 0.95%) trimmed read pairs available after processing 9976628 (99.05%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 28 2 0.00% 29 0 0.00% 30 2 0.00% 31 1 0.00% 32 2 0.00% 33 2 0.00% 34 4 0.00% 35 172 0.00% 36 205 0.00% 37 236 0.00% 38 316 0.00% 39 380 0.00% 40 436 0.00% 41 543 0.01% 42 589 0.01% 43 769 0.01% 44 826 0.01% 45 926 0.01% 46 976 0.01% 47 1089 0.01% 48 1270 0.01% 49 1433 0.01% 50 1615 0.02% 51 1859 0.02% 52 2173 0.02% 53 2510 0.02% 54 2552 0.03% 55 2813 0.03% 56 3404 0.03% 57 3892 0.04% 58 4351 0.04% 59 4910 0.05% 60 5267 0.05% 61 5464 0.05% 62 6351 0.06% 63 6755 0.07% 64 7749 0.08% 65 8691 0.09% 66 9335 0.09% 67 10153 0.10% 68 10353 0.10% 69 11764 0.12% 70 12457 0.12% 71 14554 0.14% 72 23674 0.24% 73 95166 0.94% 74 763691 7.58% 75 4363953 43.33% 76 4676594 46.43% 10072229 reads passed initial QC criterion=sequence-density sequence-density=0.94 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=22 prefix-density=0.92 prefix-fanout=2.0 sequence=TTCAAATGTACA criterion=fanout-score sequence-density=0.11 sequence-density-rank=25 fanout-score=8.95 fanout-score-rank=1 prefix-density=0.66 prefix-fanout=1.4 sequence=CCGAACATGGAGAACATGGCGAGGCGGCCGTTCTTGATCTCCTT criterion=sequence-density sequence-density=0.62 sequence-density-rank=1 fanout-score=2.00 fanout-score-rank=30 prefix-density=0.61 prefix-fanout=2.0 sequence=GACGCCTATGTCCGCATCATCGGCTTCGACAACACCCGGCAGGTGCAGTGCATCAGCTTCATCGCCTTCAAGCC criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=9.08 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=2.8 sequence=CCTCAAGCCAAAGCCTCTTGCTAAGCGTACCACACTATACAGACGTGCGCGCGCAGCCATGGCACCCACCGTGATGGCTTCCTCCGCCACCTCCGTGGC SRR11389844 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 08:01:17 Started mapping on | Dec 07 08:01:17 Finished on | Dec 07 08:02:21 Mapping speed, Million of reads per hour | 566.56 Number of input reads | 10072229 Average input read length | 150 UNIQUE READS: Uniquely mapped reads number | 8010776 Uniquely mapped reads % | 79.53% Average mapped length | 149.73 Number of splices: Total | 3089536 Number of splices: Annotated (sjdb) | 2936755 Number of splices: GT/AG | 3050340 Number of splices: GC/AG | 35379 Number of splices: AT/AC | 854 Number of splices: Non-canonical | 2963 Mismatch rate per base, % | 1.03% Deletion rate per base | 0.01% Deletion average length | 1.34 Insertion rate per base | 0.00% Insertion average length | 1.24 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1195032 % of reads mapped to multiple loci | 11.86% Number of reads mapped to too many loci | 19754 % of reads mapped to too many loci | 0.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.11% % of reads unmapped: other | 1.29% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 866421 866421 866421 N_multimapping 1195032 1195032 1195032 N_noFeature 274755 7736988 399414 N_ambiguous 217481 1599 74863 UnstrandedReadsAssigned:7518540 PositiveStrandReadsAssigned:272189 NegativeStrandReadsAssigned:7536499 Dataset is classified negative stranded MeadianReadLen=76 20thPercentileLength=75 echo kmer=71 SRR11389844 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: SRR11389844-trimmed-pair1.fastq SRR11389844-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,072,229 reads, 8,894,082 reads pseudoaligned [quant] estimated average fragment length: 171.67 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,109 rounds 52973 SRR11389844.ke.tsv 35125 SRR11389844.se.tsv 88098 total ==> SRR11389844.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 765.419 8.11128 1.66357 PNS24247 1044 873.33 6.52778 1.17338 PNS24249 1928 1757.33 34.6083 3.09156 PNS24246 1044 873.33 6.52778 1.17338 PNS24248 1044 873.33 6.52778 1.17338 PNS24244 1471 1300.33 14.6971 1.77432 PNS24243 293 138.3 0 0 KQK14069 1603 1432.33 276.091 30.2595 KQK14071 474 305.547 15.6877 8.05996 ==> SRR11389844.se.tsv <== BRADI_1g14170v3 320 BRADI_1g53295v3 19 BRADI_1g59795v3 166 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 70 BRADI_1g74790v3 121 BRADI_1g09890v3 0 BRADI_1g77505v3 93 BRADI_1g48960v3 0 SRR11389844 completed mapping pipeline successfully