Starting /dee2/code/volunteer_pipeline.sh SRR12682229 current disk space = 1547231027200 free memory = 1597706340 SRR12682229 SRAfilesize a7209fda2edba702dfc76918d319858b SRR12682229.sra SRR12682229.sra file validated SRR12682229 is single end SRR12682229 is conventional basespace SRR12682229 read1 length is 35-150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12682229_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 35-150 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.505 32.0 32.0 32.0 32.0 32.0 2 31.5375 32.0 32.0 32.0 32.0 32.0 3 31.62275 32.0 32.0 32.0 32.0 32.0 4 31.61675 32.0 32.0 32.0 32.0 32.0 5 31.63125 32.0 32.0 32.0 32.0 32.0 6 34.882 36.0 36.0 36.0 36.0 36.0 7 35.25525 36.0 36.0 36.0 36.0 36.0 8 35.1755 36.0 36.0 36.0 36.0 36.0 9 35.2335 36.0 36.0 36.0 36.0 36.0 10-14 35.142900000000004 36.0 36.0 36.0 36.0 36.0 15-19 35.10745 36.0 36.0 36.0 36.0 36.0 20-24 35.0251 36.0 36.0 36.0 36.0 36.0 25-29 34.8833 36.0 36.0 36.0 34.4 36.0 30-34 34.8365 36.0 36.0 36.0 32.8 36.0 35-39 34.80630798949737 36.0 36.0 36.0 32.0 36.0 40-44 34.76654163540885 36.0 36.0 36.0 33.6 36.0 45-49 34.56920000385289 36.0 36.0 36.0 32.0 36.0 50-54 34.568084042021006 36.0 36.0 36.0 32.0 36.0 55-59 34.48084910028868 36.0 36.0 36.0 32.8 36.0 60-64 34.327970661272246 36.0 36.0 36.0 32.0 36.0 65-69 34.18330231546317 36.0 36.0 36.0 32.0 36.0 70-74 34.144815499249574 36.0 36.0 36.0 32.0 36.0 75-79 34.08482731778512 36.0 36.0 36.0 32.0 36.0 80-84 33.993490319037065 36.0 36.0 36.0 30.0 36.0 85-89 33.865535918273466 36.0 36.0 36.0 29.0 36.0 90-94 33.87422501941076 36.0 36.0 36.0 30.0 36.0 95-99 33.86120129563808 36.0 36.0 36.0 28.0 36.0 100-104 33.667487836364785 36.0 36.0 36.0 27.0 36.0 105-109 33.437691077625274 36.0 33.6 36.0 27.0 36.0 110-114 33.378187302545726 36.0 33.6 36.0 27.0 36.0 115-119 32.94185099120455 36.0 32.0 36.0 27.0 36.0 120-124 32.203940649820325 34.4 32.0 36.0 24.6 36.0 125-129 32.22891011641885 33.6 32.0 36.0 25.8 36.0 130-134 31.715961685150717 32.0 32.0 36.0 22.2 36.0 135-139 31.758900783449526 33.6 32.0 36.0 24.6 36.0 140-144 31.806482620357258 35.2 32.0 36.0 21.0 36.0 145-149 31.69698825472502 32.0 32.0 36.0 22.2 36.0 150 26.17478152309613 27.0 14.0 32.0 14.0 36.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 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 1.0 19 1.0 20 2.0 21 0.0 22 3.0 23 9.0 24 19.0 25 32.0 26 43.0 27 75.0 28 67.0 29 93.0 30 132.0 31 191.0 32 225.0 33 366.0 34 937.0 35 1803.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 28.707176794198553 9.227306826706677 7.151787946986747 54.91372843210802 2 22.73068267066767 13.028257064266066 35.38384596149037 28.857214303575894 3 20.80520130032508 15.428857214303576 22.1055263815954 41.66041510377595 4 28.507126781695426 22.50562640660165 18.254563640910227 30.732683170792697 5 25.156289072268066 29.35733933483371 22.005501375343837 23.48087021755439 6 22.923504165614744 30.37111840444332 24.539257763191113 22.16611966675082 7 17.97949487371843 20.455113778444613 39.40985246311578 22.155538884721178 8 20.955238809702426 20.980245061265315 31.257814453613403 26.806701675418854 9 21.05526381595399 20.4801200300075 32.53313328332083 25.93148287071768 10-14 23.270817704426104 24.651162790697676 24.72118029507377 27.35683920980245 15-19 23.26081520380095 23.29082270567642 26.16654163540885 27.28182045511378 20-24 23.925981495373843 24.671167791947987 24.781195298824706 26.62165541385346 25-29 23.475868967241812 24.046011502875718 24.711177794448613 27.76694173543386 30-34 23.63590897724431 23.305826456614152 24.991247811952988 28.067016754188543 35-39 24.10102525631408 23.695923980995246 23.95598899724931 28.247061765441362 40-44 24.2110527631908 23.44586146536634 24.861215303825958 27.481870467616904 45-49 23.74831190916821 23.738308407942778 24.753663782323812 27.759715900565197 50-54 23.34167083541771 23.986993496748372 25.092546273136566 27.57878939469735 55-59 23.77758870927381 23.82763625444172 24.328111706120815 28.066663330163657 60-64 23.251503006012026 23.08617234468938 25.796593186372746 27.86573146292585 65-69 23.372974057905566 23.50845501530433 25.620954388077678 27.49761653871243 70-74 24.061321940185977 23.840160844433274 24.87057049509927 27.227946720281476 75-79 24.61515242982191 23.443002314116107 24.59502968105443 27.346815575007543 80-84 24.57841058265172 22.78602443703928 24.38654953044532 28.24901544986368 85-89 24.32048681541582 23.240365111561868 24.84787018255578 27.591277890466532 90-94 24.839006439742413 23.382398037411836 24.103035878564857 27.675559644280895 95-99 23.257622899813317 23.682845882596972 24.839244969923254 28.220286247666458 100-104 24.378372658977888 23.574224949740767 24.2461115225902 27.80129086869114 105-109 24.52260222246197 23.325062034739457 24.905599309526377 27.246736433272194 110-114 24.968089239136468 23.541816970975084 24.624007991564458 26.86608579832399 115-119 24.523066250433576 23.17030870620881 24.69071568967511 27.615909353682504 120-124 24.0710531085735 24.18584979759531 24.33689807262401 27.40619902120718 125-129 24.707973590655154 24.073133570340275 23.438293550025392 27.78059928897918 130-134 24.70167868940875 22.584777186004178 24.391559360884514 28.321984763702556 135-139 24.59839357429719 23.1425702811245 24.010327022375215 28.248709122203095 140-144 25.2572569497773 23.137766856089694 23.544770388573184 28.060205805559825 145-149 25.701562762560915 22.197949924382456 23.15577213913628 28.94471517392035 150 27.153558052434455 0.0 32.70911360799001 40.13732833957553 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 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 0.5 24 1.0 25 1.0 26 0.5 27 0.0 28 0.5 29 2.5 30 5.5 31 6.5 32 8.5 33 11.5 34 14.5 35 24.0 36 38.0 37 40.0 38 43.5 39 75.0 40 86.5 41 88.5 42 102.5 43 110.0 44 130.5 45 140.0 46 160.5 47 176.5 48 188.5 49 211.5 50 196.5 51 175.5 52 180.5 53 172.5 54 153.5 55 169.5 56 166.0 57 125.5 58 113.0 59 107.0 60 92.5 61 84.5 62 70.0 63 67.5 64 65.0 65 53.0 66 45.0 67 48.0 68 50.5 69 41.0 70 33.0 71 29.0 72 30.5 73 24.5 74 15.0 75 16.0 76 15.5 77 8.0 78 5.0 79 4.0 80 2.0 81 1.0 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 pass #Base N-Count 1 0.025 2 0.025 3 0.025 4 0.025 5 0.025 6 0.975 7 0.025 8 0.025 9 0.025 10-14 0.025 15-19 0.025 20-24 0.025 25-29 0.025 30-34 0.025 35-39 0.005001000200040008 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.010008507231146475 60-64 0.02003606491685033 65-69 0.01003461943705785 70-74 0.03014923873172202 75-79 0.0 80-84 0.010096930533117932 85-89 0.010140959334753067 90-94 0.020439448134900357 95-99 0.020738282870178346 100-104 0.04230565838180857 105-109 0.010787486515641856 110-114 0.0 115-119 0.011560693641618497 120-124 0.006041565973900435 125-129 0.012695188523549577 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 35-39 1.0 40-44 0.0 45-49 1.0 50-54 1.0 55-59 2.0 60-64 6.0 65-69 8.0 70-74 2.0 75-79 8.0 80-84 17.0 85-89 26.0 90-94 42.0 95-99 71.0 100-104 71.0 105-109 99.0 110-114 121.0 115-119 146.0 120-124 171.0 125-129 160.0 130-134 184.0 135-139 192.0 140-144 179.0 145-149 890.0 150-151 1602.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 80.27499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 89.03768296480847 71.475 2 5.543444409841171 8.9 3 2.584864528184366 6.225 4 1.183431952662722 3.8 5 0.4360012457178449 1.7500000000000002 6 0.49828713796325136 2.4 7 0.2802865151043289 1.575 8 0.09342883836810963 0.6 9 0.03114294612270321 0.22499999999999998 >10 0.3114294612270321 3.05 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source CCCGACTGTCCCTATTAATCATTACTCCGATCCCGAAGGCCAACACAATA 19 0.475 No Hit CTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATT 16 0.4 No Hit CCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCCTGTATTTAGCCTTGGA 12 0.3 No Hit ATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATA 12 0.3 No Hit CCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCAT 11 0.27499999999999997 No Hit CCGACATCGAAGGATCAAAAAGCAACGTCGCTATGAACGCTTGGCTGCCA 11 0.27499999999999997 No Hit CGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGAACCC 11 0.27499999999999997 No Hit CTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGTTTTGCCGACTTCC 10 0.25 No Hit CTCCAATGGATCCTCGTTAAGGGATTTAGATTGTACTCATTCCAATTACC 10 0.25 No Hit CACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCTT 10 0.25 No Hit CTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGG 9 0.22499999999999998 No Hit CCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGC 8 0.2 No Hit CGCTATTGGAGCTGGAATTACCGCGGCTGCTGGCACCAGACTTGCCCTCC 8 0.2 No Hit CTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTG 8 0.2 No Hit CTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCGGA 7 0.17500000000000002 No Hit CTTGTTACGACTTCTCCTTCCTCTAAATGATAAGGTTCAATGGACTTCTC 7 0.17500000000000002 No Hit CATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACC 7 0.17500000000000002 No Hit CTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGTTTGTTGCACGT 7 0.17500000000000002 No Hit GTCCTTTTCATCTTTCCCTCGCGGTACTTGTTCGCTATCGGTCTCTCGCC 7 0.17500000000000002 No Hit CTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTT 7 0.17500000000000002 No Hit CATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCTTTTATCTAAT 7 0.17500000000000002 No Hit GTCGAGTTATCATGAATCATCGGATCAGCGAGCAAAGCCCGCGTCAGCCT 7 0.17500000000000002 No Hit CTGGAAATCAGAATCAAACGAGCTTTTACCCTTTTGTTCCACACGAGATT 7 0.17500000000000002 No Hit CCCGCGTCAGCCTTTTATCTAATAAATGCGCCCCTCCCAGAAGTCGGGGT 6 0.15 No Hit ATCGCTTCGAGCCTCCACCAGAGTTTCCTCTGGCTTCGCCCCGCTCAGGC 6 0.15 No Hit GTTCGATTAGTCTTTCGCCCCTATACCCAAGTCAGACGAACGATTTGCAC 6 0.15 No Hit CCCCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTA 6 0.15 No Hit CTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAG 6 0.15 No Hit CCGGTATTGTTATTTATTGTCACTACCTCCCCGTGTCAGGATTGGGTAAT 6 0.15 No Hit GGCAGAAATTTGAATGATGCGTCGCCGGCACGAGGGCCGTGCGATCCGTC 6 0.15 No Hit CGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACT 6 0.15 No Hit CCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAGCT 6 0.15 No Hit CCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAG 6 0.15 No Hit CCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACGATG 6 0.15 No Hit CCCTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCA 6 0.15 No Hit CTTGTCCGTACCAGTTCTGAGTCGACTGTTCAGCGCTCGGGGAAAGCCCC 6 0.15 No Hit CCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCA 6 0.15 No Hit CGTCAGTATCGCTTCGAGCCTCCACCAGAGTTTCCTCTGGCTTCGCCCCG 6 0.15 No Hit GCCGCAGGCTCCACGCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTT 6 0.15 No Hit GTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAG 5 0.125 No Hit CTCCTACTCATCGGGGCATGGCGCTCGCCCAGATGGCCGGGTGTGGGTCG 5 0.125 No Hit CCCGAGCCCAGTCCTCAGAGCCAATCCTTTTCCCGAAGTTACGGATCCGT 5 0.125 No Hit CCGGAACCCAAAGACTTTGATTTCTCATAAGGTGCCGGCGGAGTCCTATA 5 0.125 No Hit ATCCGTGCGACGTGGGGCTGGATCTCAGTGGATCGTGGCAGCAAGGCCAC 5 0.125 No Hit GGCCACGCTTTCACGGTTCGTATTCGTACTGGAAATCAGAATCAAACGAG 5 0.125 No Hit CCCGAAGTTACGGATCCGTTTTGCCGACTTCCCTTGCCTACATTGTTCCA 5 0.125 No Hit AGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGC 5 0.125 No Hit CCCATGCTAATGTATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTC 5 0.125 No Hit CCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGG 5 0.125 No Hit CAACAACTTAAATATACGCTATTGGAGCTGGAATTACCGCGGCTGCTGGC 5 0.125 No Hit CTAATTCTCCGTCACCCGTCACCACCATGGTAGGCCCCTATCCTACCATC 5 0.125 No Hit TGCTAATGTATCCAGAGCGATGGCTTGCTTTGAGCACTCTAATTTCTTCA 5 0.125 No Hit CGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCAT 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 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.025 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 90-91 0.025 0.0 0.0 0.0 0.0 92-93 0.025 0.0 0.0 0.0 0.0 94-95 0.025 0.0 0.0 0.0 0.0 96-97 0.025 0.0 0.0 0.0 0.0 98-99 0.025 0.0 0.0 0.0 0.0 100-101 0.025 0.0 0.0 0.0 0.0 102-103 0.025 0.0 0.0 0.0 0.0 104-105 0.025 0.0 0.0 0.0 0.0 106-107 0.025 0.0 0.0 0.0 0.0 108-109 0.025 0.0 0.0 0.0 0.0 110-111 0.025 0.0 0.0 0.0 0.0 112-113 0.025 0.0 0.0 0.0 0.0 114-115 0.025 0.0 0.0 0.0 0.0 116-117 0.025 0.0 0.0 0.0 0.0 118-119 0.025 0.0 0.0 0.0 0.0 120-121 0.025 0.0 0.0 0.0 0.0 122-123 0.025 0.0 0.0 0.0 0.0 124-125 0.025 0.0 0.0 0.0 0.0 126-127 0.025 0.0 0.0 0.0 0.0 128-129 0.025 0.0 0.0 0.0 0.0 130-131 0.05 0.0 0.0 0.0 0.0 132-133 0.05 0.0 0.0 0.0 0.0 134-135 0.05 0.0 0.0 0.0 0.0 136-137 0.05 0.0 0.0 0.0 0.0 138 0.05 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAAATCA 10 0.009148636 131.5 3 >>END_MODULE Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627105 READS because READLEN < 1 Read 1627105 spots for SRR12682229.sra Written 1627105 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra Rejected 1627094 READS because READLEN < 1 Read 1627094 spots for SRR12682229.sra Written 1627094 spots for SRR12682229.sra SRR ids: ['SRR12682229.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_o0r7o8s_ SRR12682229.sra spots: 32541891 blocks: [[1, 1627094], [1627095, 3254188], [3254189, 4881282], [4881283, 6508376], [6508377, 8135470], [8135471, 9762564], [9762565, 11389658], [11389659, 13016752], [13016753, 14643846], [14643847, 16270940], [16270941, 17898034], [17898035, 19525128], [19525129, 21152222], [21152223, 22779316], [22779317, 24406410], [24406411, 26033504], [26033505, 27660598], [27660599, 29287692], [29287693, 30914786], [30914787, 32541891]] SRR12682229 file size 10268327 SRR12682229 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 SRR12682229 SRR12682229_1.fastq Input file: SRR12682229_1.fastq trimmed: SRR12682229-trimmed.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- minimum overlap length for adapter detection (-k): inf -- number of concurrent threads (-t): 20 Sat Dec 7 03:54:05 2024 >> started Sat Dec 7 03:54:24 2024 >> done (19.578s) 32541891 reads processed; of these: 0 ( 0.00%) short reads filtered out after trimming by size control 1512 ( 0.00%) empty reads filtered out after trimming by size control 32540379 (100.00%) reads available; of these: 12797 ( 0.04%) trimmed reads available after processing 32527582 (99.96%) untrimmed reads available after processing Length distribution of reads after trimming: length count percentage 21 1 0.00% 22 19 0.00% 23 23 0.00% 24 26 0.00% 25 30 0.00% 26 42 0.00% 27 43 0.00% 28 75 0.00% 29 75 0.00% 30 112 0.00% 31 107 0.00% 32 133 0.00% 33 150 0.00% 34 150 0.00% 35 238 0.00% 36 252 0.00% 37 268 0.00% 38 352 0.00% 39 453 0.00% 40 488 0.00% 41 562 0.00% 42 575 0.00% 43 587 0.00% 44 626 0.00% 45 685 0.00% 46 837 0.00% 47 949 0.00% 48 1236 0.00% 49 1395 0.00% 50 1581 0.00% 51 1712 0.01% 52 1949 0.01% 53 1933 0.01% 54 2015 0.01% 55 2290 0.01% 56 2423 0.01% 57 2768 0.01% 58 3246 0.01% 59 3614 0.01% 60 4115 0.01% 61 4508 0.01% 62 4959 0.02% 63 5161 0.02% 64 5451 0.02% 65 5658 0.02% 66 6278 0.02% 67 7014 0.02% 68 7465 0.02% 69 8150 0.03% 70 8849 0.03% 71 10323 0.03% 72 11541 0.04% 73 12453 0.04% 74 13415 0.04% 75 14296 0.04% 76 16214 0.05% 77 16648 0.05% 78 18253 0.06% 79 20655 0.06% 80 22623 0.07% 81 23972 0.07% 82 26686 0.08% 83 28271 0.09% 84 31464 0.10% 85 36377 0.11% 86 40450 0.12% 87 42603 0.13% 88 45128 0.14% 89 47952 0.15% 90 52269 0.16% 91 54396 0.17% 92 62806 0.19% 93 67943 0.21% 94 70261 0.22% 95 78954 0.24% 96 85505 0.26% 97 90511 0.28% 98 101244 0.31% 99 102191 0.31% 100 105810 0.33% 101 110098 0.34% 102 119652 0.37% 103 131128 0.40% 104 136161 0.42% 105 138837 0.43% 106 146977 0.45% 107 158717 0.49% 108 154452 0.47% 109 170829 0.52% 110 173913 0.53% 111 187126 0.58% 112 204547 0.63% 113 200635 0.62% 114 216279 0.66% 115 228902 0.70% 116 238242 0.73% 117 228510 0.70% 118 230036 0.71% 119 245074 0.75% 120 262251 0.81% 121 253887 0.78% 122 275342 0.85% 123 280930 0.86% 124 270697 0.83% 125 275176 0.85% 126 286672 0.88% 127 277413 0.85% 128 286529 0.88% 129 303048 0.93% 130 291732 0.90% 131 291589 0.90% 132 292112 0.90% 133 299362 0.92% 134 291211 0.89% 135 296079 0.91% 136 304721 0.94% 137 304555 0.94% 138 290919 0.89% 139 299780 0.92% 140 294117 0.90% 141 286469 0.88% 142 286144 0.88% 143 282698 0.87% 144 298814 0.92% 145 284793 0.88% 146 360111 1.11% 147 594510 1.83% 148 1355458 4.17% 149 4619598 14.20% 150 13270705 40.78% 32540379 reads passed initial QC criterion=sequence-density sequence-density=0.67 sequence-density-rank=1 fanout-score=2.67 fanout-score-rank=30 prefix-density=1.77 prefix-fanout=1.0 sequence=CTTGGATGTGGCAGCCGTTTCTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=40 fanout-score=89.48 fanout-score-rank=1 prefix-density=1.67 prefix-fanout=1.1 sequence=CAAACTCCCCAGTGCAGAGAGCTTGATCAAATGTACCAATTACACACACAGACACACAGATACATACATACTCACAAGGAAGGATACACCAATTAAGAGCAAGTAAACAACAACACAATCACACCACACGCTCTGACTCGGCGCTTATTTACTAACCACAAGTTCATCATGATTAATGGACTAACAGTTACAAGGGTTGCACTTGCAGTTGTCGCCGCAGCTGCA Started job on | Dec 07 03:54:44 Started mapping on | Dec 07 03:54:44 Finished on | Dec 07 03:56:31 Mapping speed, Million of reads per hour | 1094.82 Number of input reads | 32540379 Average input read length | 138 UNIQUE READS: Uniquely mapped reads number | 14687893 Uniquely mapped reads % | 45.14% Average mapped length | 138.84 Number of splices: Total | 6168742 Number of splices: Annotated (sjdb) | 5814752 Number of splices: GT/AG | 6084271 Number of splices: GC/AG | 75112 Number of splices: AT/AC | 4543 Number of splices: Non-canonical | 4816 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 1.63 Insertion rate per base | 0.00% Insertion average length | 1.12 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1236306 % of reads mapped to multiple loci | 3.80% Number of reads mapped to too many loci | 14046644 % of reads mapped to too many loci | 43.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.05% % of reads unmapped: other | 5.85% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 16616180 16616180 16616180 N_multimapping 1236306 1236306 1236306 N_noFeature 923953 14334172 1045523 N_ambiguous 280652 1585 49031 UnstrandedReadsAssigned:13483288 PositiveStrandReadsAssigned:352136 NegativeStrandReadsAssigned:13593339 Dataset is classified negative stranded MeadianReadLen=149 20thPercentileLength=126 echo kmer=121 SRR12682229 Starting Kallisto single end mapping to ensembl reference transcriptome. kmer=31 [quant] fragment length distribution is truncated gaussian with mean = 100, sd = 20 [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in single-end mode [quant] will process file 1: SRR12682229-trimmed.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 32,540,379 reads, 13,918,831 reads pseudoaligned [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,143 rounds 52973 SRR12682229.ke.tsv 35125 SRR12682229.se.tsv 88098 total ==> SRR12682229.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 837 0.0332192 0.0045642 PNS24247 1044 945 59.1048 7.19269 PNS24249 1928 1829 122.703 7.71508 PNS24246 1044 945 59.1048 7.19269 PNS24248 1044 945 59.1048 7.19269 PNS24244 1471 1372 137.95 11.5629 PNS24243 293 194 2 1.18557 KQK14069 1603 1504 8420.4 643.851 KQK14071 474 375 607.733 186.373 ==> SRR12682229.se.tsv <== BRADI_1g14170v3 9668 BRADI_1g53295v3 101 BRADI_1g59795v3 331 BRADI_1g07683v3 0 BRADI_1g00485v3 5 BRADI_1g20270v3 773 BRADI_1g74790v3 397 BRADI_1g09890v3 0 BRADI_1g77505v3 146 BRADI_1g48960v3 0 SRR12682229 completed mapping pipeline successfully