Starting /dee2/code/volunteer_pipeline.sh SRR2962392 current disk space = 3058845999104 free memory = 1527640524 SRR2962392 SRAfilesize 00beadca2eb0e2674900824b13c9d6ae SRR2962392.sra SRR2962392.sra file validated SRR2962392 is single end SRR2962392 is conventional basespace SRR2962392 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR2962392_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 39 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.64425 31.0 31.0 34.0 30.0 34.0 2 32.24775 34.0 31.0 34.0 30.0 34.0 3 32.4395 34.0 31.0 34.0 30.0 34.0 4 35.9945 37.0 35.0 37.0 35.0 37.0 5 35.89375 37.0 35.0 37.0 35.0 37.0 6 35.9405 37.0 35.0 37.0 35.0 37.0 7 35.8795 37.0 35.0 37.0 35.0 37.0 8 35.95675 37.0 35.0 37.0 35.0 37.0 9 37.619 39.0 37.0 39.0 35.0 39.0 10-11 37.541624999999996 39.0 37.0 39.0 35.0 39.0 12-13 37.56425 39.0 37.0 39.0 34.5 39.0 14-15 38.802875 40.0 38.0 41.0 35.0 41.0 16-17 38.708 40.0 38.0 41.0 34.5 41.0 18-19 38.598625 40.0 38.0 41.0 34.0 41.0 20-21 38.37287499999999 40.0 38.0 41.0 33.5 41.0 22-23 38.121125 39.5 37.5 40.5 33.5 41.0 24-25 37.23975 39.0 36.5 41.0 32.0 41.0 26-27 33.064750000000004 39.0 33.5 41.0 2.0 41.0 28-29 31.884875 38.5 31.5 41.0 2.0 41.0 30-31 28.1345 38.0 13.5 40.5 2.0 41.0 32-33 26.27525 37.0 2.0 40.0 2.0 41.0 34-35 28.588875 37.0 12.0 40.0 8.5 41.0 36-37 32.039 37.5 23.0 40.0 15.5 41.0 38-39 33.717875 37.5 33.0 40.0 13.5 41.0 40-41 31.152124999999998 38.0 30.5 40.0 2.0 41.0 42-43 33.0905 37.0 32.0 40.0 15.0 41.0 44-45 34.323499999999996 38.0 33.5 40.0 23.5 41.0 46-47 34.570875 38.0 34.5 40.0 24.5 41.0 48-49 34.287125 37.5 34.0 40.0 23.5 41.0 50-51 33.628375000000005 37.0 33.0 40.0 20.5 41.0 52-53 32.633125 37.0 32.5 40.0 5.0 41.0 54-55 31.136125 37.0 30.0 40.0 2.0 41.0 56-57 30.224375000000002 36.0 28.0 40.0 2.0 41.0 58-59 30.011625000000002 36.0 28.0 39.5 2.0 41.0 60-61 29.284125 35.0 26.5 39.0 2.0 41.0 62-63 27.419 34.5 15.0 38.5 2.0 40.0 64-65 23.6735 32.5 2.0 37.5 2.0 40.0 66-67 20.84675 28.0 2.0 36.0 2.0 40.0 68-69 21.124375 29.0 2.0 36.0 2.0 39.0 70-71 20.899625 29.0 2.0 35.0 2.0 39.0 72-73 20.3795 28.0 2.0 35.0 2.0 38.5 74-75 19.7245 26.5 2.0 35.0 2.0 37.5 76-77 19.049125 26.0 2.0 34.0 2.0 36.0 78-79 19.002249999999997 26.0 2.0 35.0 2.0 37.0 80-81 18.874875 24.5 2.0 34.5 2.0 36.0 82-83 18.99325 25.5 2.0 34.0 2.0 36.0 84-85 18.81575 26.0 2.0 34.0 2.0 35.0 86-87 18.494875 25.0 2.0 34.0 2.0 35.0 88-89 17.773875 21.5 2.0 34.0 2.0 35.0 90-91 16.828625000000002 10.0 2.0 34.0 2.0 35.0 92-93 14.63275 2.0 2.0 32.5 2.0 35.0 94-95 14.271125000000001 2.0 2.0 32.0 2.0 35.0 96-97 14.028875 2.0 2.0 32.0 2.0 35.0 98-99 13.7375 2.0 2.0 31.5 2.0 35.0 100-101 12.97475 2.0 2.0 31.0 2.0 34.5 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-11 0.0 1101 12-13 0.0 1101 14-15 0.0 1101 16-17 0.0 1101 18-19 0.0 1101 20-21 0.0 1101 22-23 0.0 1101 24-25 0.0 1101 26-27 0.0 1101 28-29 0.0 1101 30-31 0.0 1101 32-33 0.0 1101 34-35 0.0 1101 36-37 0.0 1101 38-39 0.0 1101 40-41 0.0 1101 42-43 0.0 1101 44-45 0.0 1101 46-47 0.0 1101 48-49 0.0 1101 50-51 0.0 1101 52-53 0.0 1101 54-55 0.0 1101 56-57 0.0 1101 58-59 0.0 1101 60-61 0.0 1101 62-63 0.0 1101 64-65 0.0 1101 66-67 0.0 1101 68-69 0.0 1101 70-71 0.0 1101 72-73 0.0 1101 74-75 0.0 1101 76-77 0.0 1101 78-79 0.0 1101 80-81 0.0 1101 82-83 0.0 1101 84-85 0.0 1101 86-87 0.0 1101 88-89 0.0 1101 90-91 0.0 1101 92-93 0.0 1101 94-95 0.0 1101 96-97 0.0 1101 98-99 0.0 1101 100-101 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 1.0 7 5.0 8 12.0 9 25.0 10 32.0 11 58.0 12 29.0 13 31.0 14 49.0 15 69.0 16 85.0 17 149.0 18 175.0 19 225.0 20 238.0 21 165.0 22 141.0 23 111.0 24 59.0 25 54.0 26 59.0 27 94.0 28 100.0 29 103.0 30 100.0 31 136.0 32 147.0 33 180.0 34 196.0 35 256.0 36 265.0 37 362.0 38 255.0 39 33.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 11.511511511511511 46.371371371371374 25.95095095095095 16.166166166166164 2 16.125 47.575 22.95 13.350000000000001 3 40.125 22.85 20.724999999999998 16.3 4 15.85 23.25 20.65 40.25 5 16.45 46.375 21.825 15.35 6 40.699999999999996 23.025000000000002 20.275000000000002 16.0 7 16.075 22.2 45.25 16.475 8 40.75 22.275 21.075 15.9 9 40.6 21.9 21.725 15.775 10-11 15.775 35.1625 33.5 15.562500000000002 12-13 15.8 22.125 33.5 28.575 14-15 15.125 47.475 21.575 15.825 16-17 28.175 22.6375 20.825 28.3625 18-19 15.7 34.9625 21.375 27.962500000000002 20-21 28.6125 34.0625 22.225 15.1 22-23 27.6625 22.7375 33.9625 15.6375 24-25 15.58325912733749 35.364457448161815 21.76567866683628 27.286604757664417 26-27 15.921389917402449 27.285673597265735 41.02819709484478 15.76473939048704 28-29 27.330539095244976 22.040757334874982 35.106229223876284 15.52247434600376 30-31 24.1886918701907 23.93777183004349 36.03211776513884 15.841418534626966 32-33 17.53982300884956 26.548672566371685 37.9646017699115 17.946902654867255 34-35 17.59484609878311 25.697924123120973 37.995705082319255 18.711524695776667 36-37 17.775 26.575 38.6125 17.0375 38-39 17.26321230133092 25.313347977774907 39.17818839643365 18.245251324460522 40-41 17.767494040106577 25.48029729350722 38.4938998737905 18.25830879259571 42-43 18.6625 25.1 38.4 17.837500000000002 44-45 17.075000000000003 25.8 38.6625 18.462500000000002 46-47 18.099999999999998 25.424999999999997 39.387499999999996 17.0875 48-49 18.387500000000003 25.825 38.224999999999994 17.5625 50-51 18.3125 25.337500000000002 37.775 18.575 52-53 18.2375 27.1125 36.7875 17.8625 54-55 19.6375 27.525 34.125 18.712500000000002 56-57 19.05 30.2625 30.7625 19.925 58-59 19.400000000000002 30.099999999999998 30.85 19.650000000000002 60-61 18.8875 31.3 29.9375 19.875 62-63 19.59601259181532 30.967995802728225 30.82371458551941 18.61227701993704 64-65 18.89835666463786 30.827754108338407 30.097382836275106 20.17650639074863 66-67 18.90734714848433 29.097448193183766 31.769138551121767 20.226066107210137 68-69 19.927808693036546 29.553316288163632 32.38080914423222 18.138065874567605 70-71 19.447496468372314 29.493015225239365 31.8945220530529 19.164966253335425 72-73 19.65605914496946 29.717132754741243 32.17614914818386 18.450658952105435 74-75 19.181802749957562 29.96095739263283 32.01493804107961 18.842301816329996 76-77 19.96210816396831 29.297278677230455 32.39751980709611 18.343093351705132 78-79 20.094936708860757 30.37974683544304 30.67862165963432 18.846694796061886 80-81 19.516728624535315 31.95596225336002 30.55476122390621 17.972547898198457 82-83 20.442887526585764 30.276491930439136 30.414112348304766 18.866508194670338 84-85 19.4375 30.325000000000003 30.6875 19.55 86-87 19.2375 30.887500000000003 29.625 20.25 88-89 18.1620654396728 31.99130879345603 30.22750511247444 19.619120654396728 90-91 19.16001953442943 30.994628031906235 30.603939443268764 19.241412990395574 92-93 18.547263681592042 31.8407960199005 30.447761194029848 19.164179104477615 94-95 18.840860631905407 31.96355882923047 30.95561155262648 18.239968986237642 96-97 19.182246542027663 31.02295181638547 29.578963368293053 20.215838273293812 98-99 18.662251655629138 32.11920529801324 29.311258278145697 19.90728476821192 100-101 19.160926737633062 31.559173450219163 29.981214777708203 19.298685034439576 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 38.0 1 22.0 2 5.5 3 3.5 4 1.5 5 1.0 6 3.5 7 4.5 8 2.0 9 0.5 10 2.5 11 9.5 12 51.5 13 60.5 14 32.0 15 28.0 16 38.5 17 46.0 18 43.5 19 49.5 20 52.5 21 64.0 22 71.0 23 73.5 24 75.5 25 74.5 26 79.5 27 80.0 28 88.0 29 94.5 30 88.5 31 91.5 32 98.5 33 92.5 34 87.0 35 96.5 36 103.0 37 106.5 38 112.0 39 108.5 40 117.0 41 134.0 42 138.0 43 145.5 44 143.0 45 131.5 46 128.0 47 128.5 48 118.5 49 108.5 50 105.5 51 83.5 52 75.5 53 76.5 54 58.0 55 40.0 56 33.0 57 23.5 58 15.0 59 12.5 60 9.5 61 5.5 62 2.5 63 2.5 64 0.5 65 1.0 66 1.0 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 0.1 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 1.7375000000000003 26-27 12.225 28-29 13.5125 30-31 25.275 32-33 29.375 34-35 12.687499999999998 36-37 0.0 38-39 3.2625 40-41 10.8625 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 4.7 64-65 17.849999999999998 66-67 27.0125 68-69 16.8875 70-71 20.3625 72-73 22.225 74-75 26.3625 76-77 27.425 78-79 28.9 80-81 12.575 82-83 0.08750000000000001 84-85 0.0 86-87 0.0 88-89 2.1999999999999997 90-91 23.2125 92-93 37.1875 94-95 35.5125 96-97 17.7625 98-99 5.625 100-101 0.1875 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 86.35000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 99.07353792704112 85.55 2 0.2895193977996526 0.5 3 0.08685581933989578 0.22499999999999998 4 0.08685581933989578 0.3 5 0.028951939779965255 0.125 6 0.05790387955993051 0.3 7 0.028951939779965255 0.17500000000000002 8 0.0 0.0 9 0.028951939779965255 0.22499999999999998 >10 0.2895193977996526 4.5 >50 0.0 0.0 >100 0.028951939779965255 8.1 >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 AAGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTT 324 8.1 No Hit AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA 32 0.8 No Hit AAGCAGTGGTATCAACGCAGAGTACTTTTTNNNTTTTTTTTTTTTTTTTT 30 0.75 No Hit AAGCAGTGGTATCAACGCAGAGTACNNNNNNNNNTTTTNNNTTTTTTTTT 20 0.5 No Hit AAGCAGTGGTATCAACGCAGAGTACTTTNNNNNNTTTTTTTTTTTTTTTT 18 0.44999999999999996 No Hit AAGCAGTGGTATCAACGCAGAGTANNNNNNNNNNNTTTNNNTTTTTTTTT 18 0.44999999999999996 No Hit AAGCAGTGGTATCAACGCAGAGTACTTTTTNNTTTTTTTTTTTTTTTTTT 15 0.375 No Hit AAGCAGTGGTATCAACGCAGAGTACTTTTNNNNNTTTTTTTTTTTTTTTT 14 0.35000000000000003 No Hit AAGCAGTGGTATCAACGCAGAGTACTTTTTNNNNTTTTTTTTTTTTTTTT 12 0.3 No Hit AAGCAGTGGTATCAACGCAGAGTACNNNNNNNNNTTTTTNNTTTTTTTTT 11 0.27499999999999997 No Hit AAGCAGTGGTATCAACGCAGAGTACNNTNNNNNNTTTTTNTTTTTTTTTT 10 0.25 No Hit AAGCAGTGGTATCAACGCAGAGTACNNNNNNNNNTTTTTNTTTTTTTTTT 9 0.22499999999999998 No Hit AAGCAGTGGTATCAACGCAGAGTACTTTNNNNNNTTTTTNTTTTTTTTTT 7 0.17500000000000002 No Hit AGCAGTGGTATCAACGCAGAGTACTTTTTTTTTTTTTTTTTTTTTTTTTT 6 0.15 No Hit AAGCAGTGGTATCAACGCAGAGTACNTTNNNNNNTTTTTNTTTTTTTTTT 6 0.15 No Hit AAGCAGTGGTATCAACGCAGAGTACATGGGGTATTAAATAAAAACTAACC 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 0.0125 0.0 0.0 0.0 0.0 82-83 0.025 0.0 0.0 0.0 0.0 84-85 0.025 0.0 0.0 0.0 0.0 86-87 0.025 0.0 0.0 0.0 0.0 88-89 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content fail #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAGCAGT 70 0.0 80.4375 1 AGCAGTG 75 0.0 75.075 2 TGGTATC 70 0.0 74.69196 7 AGTGGTA 70 0.0 74.69196 5 GGTATCA 70 0.0 74.69196 8 GTATCAA 75 0.0 69.712494 9 GCAGTGG 75 0.0 69.712494 3 GTGGTAT 75 0.0 69.712494 6 CAGTGGT 75 0.0 69.712494 4 ATGGGGA 15 0.004956994 56.44737 26-27 CATGGGG 20 2.8464064E-4 53.18182 24-25 GTACTTT 35 6.679875E-8 47.316177 22-23 TACATGG 25 2.5984278E-5 47.316177 22-23 AGTACTT 35 8.442112E-8 45.964287 20-21 AGTACAT 25 3.093829E-5 45.964287 20-21 GAGTACT 35 8.442112E-8 45.964287 20-21 ACATGGG 25 8.557204E-4 42.545452 24-25 AGAGTAC 75 0.0 40.987263 18-19 ACGCAGA 75 0.0 40.21875 14-15 GCAGAGT 75 0.0 40.21875 16-17 >>END_MODULE Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra Read 5001238 spots for SRR2962392.sra Written 5001238 spots for SRR2962392.sra SRR ids: ['SRR2962392.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_r6d9razi SRR2962392.sra spots: 100024760 blocks: [[1, 5001238], [5001239, 10002476], [10002477, 15003714], [15003715, 20004952], [20004953, 25006190], [25006191, 30007428], [30007429, 35008666], [35008667, 40009904], [40009905, 45011142], [45011143, 50012380], [50012381, 55013618], [55013619, 60014856], [60014857, 65016094], [65016095, 70017332], [70017333, 75018570], [75018571, 80019808], [80019809, 85021046], [85021047, 90022284], [90022285, 95023522], [95023523, 100024760]] SRR2962392 file size 26560803 SRR2962392 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 SRR2962392 SRR2962392_1.fastq Input file: SRR2962392_1.fastq trimmed: SRR2962392-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 Mon Feb 10 12:17:57 2025 >> started Mon Feb 10 12:18:48 2025 >> done (51.531s) 100024760 reads processed; of these: 23548 ( 0.02%) short reads filtered out after trimming by size control 177821 ( 0.18%) empty reads filtered out after trimming by size control 99823391 (99.80%) reads available; of these: 40928888 (41.00%) trimmed reads available after processing 58894503 (59.00%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 18 6901 0.01% 19 8399 0.01% 20 10433 0.01% 21 15345 0.02% 22 27081 0.03% 23 27612 0.03% 24 46415 0.05% 25 112531 0.11% 26 47072 0.05% 27 898556 0.90% 28 136471 0.14% 29 90601 0.09% 30 180745 0.18% 31 192898 0.19% 32 171275 0.17% 33 176239 0.18% 34 144912 0.15% 35 155799 0.16% 36 170354 0.17% 37 149227 0.15% 38 133276 0.13% 39 147993 0.15% 40 173191 0.17% 41 232078 0.23% 42 158321 0.16% 43 161183 0.16% 44 174817 0.18% 45 206128 0.21% 46 264735 0.27% 47 303900 0.30% 48 382916 0.38% 49 524635 0.53% 50 768561 0.77% 51 1073411 1.08% 52 1416946 1.42% 53 1570858 1.57% 54 1619979 1.62% 55 1009608 1.01% 56 623039 0.62% 57 432785 0.43% 58 378665 0.38% 59 362608 0.36% 60 378872 0.38% 61 404740 0.41% 62 387928 0.39% 63 388638 0.39% 64 385880 0.39% 65 343459 0.34% 66 336478 0.34% 67 336401 0.34% 68 335287 0.34% 69 342458 0.34% 70 334577 0.34% 71 335081 0.34% 72 344651 0.35% 73 343938 0.34% 74 347134 0.35% 75 334182 0.33% 76 235219 0.24% 77 274363 0.27% 78 328363 0.33% 79 379981 0.38% 80 395522 0.40% 81 425778 0.43% 82 457976 0.46% 83 495862 0.50% 84 524019 0.52% 85 568666 0.57% 86 636423 0.64% 87 732525 0.73% 88 812819 0.81% 89 767941 0.77% 90 809420 0.81% 91 864250 0.87% 92 916682 0.92% 93 1060122 1.06% 94 1069382 1.07% 95 1141313 1.14% 96 1337814 1.34% 97 1510119 1.51% 98 1517013 1.52% 99 1482755 1.49% 100 1616358 1.62% 101 58894503 59.00% 99823391 reads passed initial QC criterion=sequence-density sequence-density=4.27 sequence-density-rank=1 fanout-score=2.54 fanout-score-rank=48 prefix-density=10.80 prefix-fanout=1.0 sequence=AGTACATGGGGA criterion=fanout-score sequence-density=0.16 sequence-density-rank=45 fanout-score=66.01 fanout-score-rank=1 prefix-density=10.80 prefix-fanout=1.0 sequence=AGTACATGGGCT Potential 3prime adapter identified. Now checking if in reference sequence Warning: gzbuffer added in zlib v1.2.3.5. Unable to change buffer size from default of 8192. 1 reads; of these: 1 (100.00%) were unpaired; of these: 0 (0.00%) aligned 0 times 0 (0.00%) aligned exactly 1 time 1 (100.00%) aligned >1 times 100.00% overall alignment rate Potential adapter found in reference sequence. Continuing without clipping. Started job on | Feb 10 12:20:59 Started mapping on | Feb 10 12:21:02 Finished on | Feb 10 12:28:22 Mapping speed, Million of reads per hour | 816.74 Number of input reads | 99823391 Average input read length | 81 UNIQUE READS: Uniquely mapped reads number | 57800664 Uniquely mapped reads % | 57.90% Average mapped length | 83.13 Number of splices: Total | 10051116 Number of splices: Annotated (sjdb) | 9222158 Number of splices: GT/AG | 9634260 Number of splices: GC/AG | 140003 Number of splices: AT/AC | 13915 Number of splices: Non-canonical | 262938 Mismatch rate per base, % | 0.65% Deletion rate per base | 0.03% Deletion average length | 2.06 Insertion rate per base | 0.02% Insertion average length | 1.83 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 12824546 % of reads mapped to multiple loci | 12.85% Number of reads mapped to too many loci | 2381035 % of reads mapped to too many loci | 2.39% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 26.73% % of reads unmapped: other | 0.14% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 29198181 29198181 29198181 N_multimapping 12824546 12824546 12824546 N_noFeature 6872547 29878216 34505516 N_ambiguous 476823 111164 78751 UnstrandedReadsAssigned:50451294 PositiveStrandReadsAssigned:27811284 NegativeStrandReadsAssigned:23216397 Dataset is classified unstranded MeadianReadLen=93 20thPercentileLength=60 echo kmer=55 SRR2962392 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in single-end mode [quant] will process file 1: SRR2962392-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 99,823,391 reads, 57,300,322 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,180 rounds 52401 SRR2962392.ke.tsv 34699 SRR2962392.se.tsv 87100 total ==> SRR2962392.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1919 6867.82 73.6719 Potri.005G024800.1.v4.1 1035 936 9985.39 219.607 Potri.004G059700.1.v4.1 961 862 381 9.09862 Potri.007G009000.2.v4.1 1416 1317 0 0 Potri.003G141000.2.v4.1 2943 2844 1171.51 8.47954 Potri.016G087400.1.v4.1 270 171 2212.85 266.387 Potri.015G069301.1.v4.1 564 465 0 0 Potri.010G195200.1.v4.1 1773 1674 146.871 1.80608 Potri.012G127500.1.v4.1 977 878 10719 251.314 ==> SRR2962392.se.tsv <== Potri.001G166300.v4.1 1 Potri.001G448400.v4.1 6 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 1138 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 1 Potri.001G040500.v4.1 11 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 641 SRR2962392 completed mapping pipeline successfully