CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200122.C_bairdi.megan.Trinity.fasta.salmon.idx -l ISR -1 /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200131.C_bairdi.329774.D12.infected.megan_R1.fq -2 /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200131.C_bairdi.329774.D12.infected.megan_R2.fq -o D12_infected_01 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200122.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200131.C_bairdi.329774.D12.infected.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200131.C_bairdi.329774.D12.infected.megan_R2.fq } ### [ output ] => { D12_infected_01 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D12_infected_01/logs [2020-02-06 21:03:01.729] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-02-06 21:03:01.729] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-02-06 21:03:01.729] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-02-06 21:03:01.729] [jointLog] [info] parsing read library format [2020-02-06 21:03:01.729] [jointLog] [info] There is 1 library. [2020-02-06 21:03:01.815] [jointLog] [info] Loading pufferfish index [2020-02-06 21:03:01.816] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 124.23 ms ----------------------------------------- size = 38529 ----------------------------------------- | Loading contig offsets | Time = 37.288 ms ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 14.36 ms ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 75.988 ms ----------------------------------------- size = 13572252 Number of ones: 38528 Number of ones per inventory item: 512 Inventory entries filled: 76 ----------------------------------------- | Loading contig boundaries | Time = 119.96 ms ----------------------------------------- size = 13572252 ----------------------------------------- | Loading sequence | Time = 61.828 ms ----------------------------------------- size = 12416412 ----------------------------------------- | Loading positions | Time = 131.57 ms ----------------------------------------- size = 19804148 ----------------------------------------- | Loading reference sequence | Time = 43.961 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 19.294 ms ----------------------------------------- [2020-02-06 21:03:02.495] [jointLog] [info] done [2020-02-06 21:03:02.495] [jointLog] [info] Index contained 19,670 targets [2020-02-06 21:03:02.510] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,052,282, hits per frag: 2.43244 processed 1,000,001 fragments hits: 2,106,584, hits per frag: 2.30382 processed 1,500,000 fragments hits: 3,164,936, hits per frag: 2.29553 processed 2,000,000 fragments hits: 4,232,277, hits per frag: 2.40663 processed 2,500,001 fragments hits: 5,295,242, hits per frag: 2.33768 processed 3,000,000 fragments hits: 6,347,975, hits per frag: 2.16789 processed 3,500,000 fragments hits: 7,407,135, hits per frag: 2.27218 processed 4,000,000 fragments hits: 8,460,622, hits per frag: 2.23509 processed 4,500,000 fragments hits: 9,518,282, hits per frag: 2.14064 processed 5,000,000 fragments hits: 10,581,947, hits per frag: 2.14118 processed 5,500,001 fragments hits: 11,645,223, hits per frag: 2.12506 processed 6,000,000 fragments hits: 12,701,339, hits per frag: 2.14137 [2020-02-06 21:03:20.749] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-06 21:03:20.755] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-06 21:03:20.755] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:03:20.765] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:03:20.776] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-06 21:03:20.778] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:03:20.779] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:03:20.779] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-06 21:03:20.780] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-06 21:03:20.781] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-06 21:03:20.781] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:03:20.781] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-06 21:03:20.788] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-06 21:03:20.790] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:03:20.793] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-06 21:03:20.808] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments [2020-02-06 21:03:20.812] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-06 21:03:20.815] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-06 21:03:20.816] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:03:20.818] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-06 21:03:20.828] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-06 21:03:20.829] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:03:20.829] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:03:20.837] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:03:20.844] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:03:20.846] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-06 21:03:20.848] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:03:20.848] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-06 21:03:21.029] [jointLog] [info] Computed 65,558 rich equivalence classes for further processing [2020-02-06 21:03:21.029] [jointLog] [info] Counted 6,338,387 total reads in the equivalence classes [2020-02-06 21:03:21.044] [jointLog] [info] Number of mappings discarded because of alignment score : 661,936 [2020-02-06 21:03:21.044] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 32,217 [2020-02-06 21:03:21.044] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-02-06 21:03:21.044] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,669 [2020-02-06 21:03:21.044] [jointLog] [info] Mapping rate = 99.3519% [2020-02-06 21:03:21.044] [jointLog] [info] finished quantifyLibrary() [2020-02-06 21:03:21.045] [jointLog] [info] Starting optimizer [2020-02-06 21:03:21.062] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-02-06 21:03:21.065] [jointLog] [info] iteration = 0 | max rel diff. = 23262.4 [2020-02-06 21:03:21.266] [jointLog] [info] iteration = 100 | max rel diff. = 4.47073 [2020-02-06 21:03:21.434] [jointLog] [info] iteration = 200 | max rel diff. = 9.41736 [2020-02-06 21:03:21.603] [jointLog] [info] iteration = 300 | max rel diff. = 2.37717 [2020-02-06 21:03:21.772] [jointLog] [info] iteration = 400 | max rel diff. = 0.428437 [2020-02-06 21:03:21.940] [jointLog] [info] iteration = 500 | max rel diff. = 0.0680179 [2020-02-06 21:03:22.108] [jointLog] [info] iteration = 600 | max rel diff. = 0.125135 [2020-02-06 21:03:22.276] [jointLog] [info] iteration = 700 | max rel diff. = 0.662162 [2020-02-06 21:03:22.281] [jointLog] [info] iteration = 704 | max rel diff. = 0.00650071 [2020-02-06 21:03:22.282] [jointLog] [info] Finished optimizer [2020-02-06 21:03:22.282] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D12_infected_01/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200122.C_bairdi.megan.Trinity.fasta.gene_trans_map > D12_infected_01/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200122.C_bairdi.megan.Trinity.fasta.salmon.idx -l ISR -1 /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200131.C_bairdi.329775.D12.uninfected.megan_R1.fq -2 /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200131.C_bairdi.329775.D12.uninfected.megan_R2.fq -o D12_uninfected_01 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200122.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200131.C_bairdi.329775.D12.uninfected.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200131.C_bairdi.329775.D12.uninfected.megan_R2.fq } ### [ output ] => { D12_uninfected_01 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D12_uninfected_01/logs [2020-02-06 21:11:52.517] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-02-06 21:11:52.517] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-02-06 21:11:52.517] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-02-06 21:11:52.517] [jointLog] [info] parsing read library format [2020-02-06 21:11:52.517] [jointLog] [info] There is 1 library. [2020-02-06 21:11:52.588] [jointLog] [info] Loading pufferfish index [2020-02-06 21:11:52.588] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 340.08 ms ----------------------------------------- size = 38529 ----------------------------------------- | Loading contig offsets | Time = 277.51 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 173.77 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 144.15 ms ----------------------------------------- size = 13572252 Number of ones: 38528 Number of ones per inventory item: 512 Inventory entries filled: 76 ----------------------------------------- | Loading contig boundaries | Time = 95.164 ms ----------------------------------------- size = 13572252 ----------------------------------------- | Loading sequence | Time = 59.64 ms ----------------------------------------- size = 12416412 ----------------------------------------- | Loading positions | Time = 382.9 ms ----------------------------------------- size = 19804148 ----------------------------------------- | Loading reference sequence | Time = 187.59 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 346.09 us ----------------------------------------- [2020-02-06 21:11:53.799] [jointLog] [info] done [2020-02-06 21:11:53.799] [jointLog] [info] Index contained 19,670 targets [2020-02-06 21:11:53.815] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,151,279, hits per frag: 3.18593 processed 1,000,000 fragments hits: 2,302,971, hits per frag: 2.62074 processed 1,500,000 fragments hits: 3,459,644, hits per frag: 2.49863 processed 2,000,000 fragments hits: 4,625,014, hits per frag: 2.40629 processed 2,500,000 fragments hits: 5,786,773, hits per frag: 2.46627 processed 3,000,001 fragments hits: 6,931,044, hits per frag: 2.38576 processed 3,500,000 fragments hits: 8,086,821, hits per frag: 2.39137 processed 4,000,000 fragments hits: 9,236,972, hits per frag: 2.35641 processed 4,500,000 fragments hits: 10,389,955, hits per frag: 2.35982 processed 5,000,000 fragments hits: 11,551,147, hits per frag: 2.38419 processed 5,500,000 fragments hits: 12,713,511, hits per frag: 2.33539 processed 6,000,000 fragments hits: 13,858,647, hits per frag: 2.34553[2020-02-06 21:12:09.990] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:12:09.994] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-06 21:12:10.003] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:12:10.008] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-06 21:12:10.011] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-06 21:12:10.013] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-06 21:12:10.020] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-06 21:12:10.037] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:12:10.042] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-06 21:12:10.047] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-06 21:12:10.049] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-06 21:12:10.055] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:12:10.072] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments [2020-02-06 21:12:10.096] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments [2020-02-06 21:12:10.104] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:12:10.107] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-06 21:12:10.109] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-06 21:12:10.109] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-06 21:12:10.112] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:12:10.115] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-06 21:12:10.115] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-06 21:12:10.116] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-06 21:12:10.117] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-06 21:12:10.117] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-06 21:12:10.119] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-06 21:12:10.120] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-06 21:12:10.120] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-06 21:12:10.123] [jointLog] [info] Thread saw mini-batch with a maximum of 0.22% zero probability fragments [2020-02-06 21:12:10.269] [jointLog] [info] Computed 46,334 rich equivalence classes for further processing [2020-02-06 21:12:10.269] [jointLog] [info] Counted 6,295,903 total reads in the equivalence classes [2020-02-06 21:12:10.284] [jointLog] [info] Number of mappings discarded because of alignment score : 724,619 [2020-02-06 21:12:10.284] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 20,735 [2020-02-06 21:12:10.284] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-02-06 21:12:10.284] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,420 [2020-02-06 21:12:10.284] [jointLog] [info] Mapping rate = 99.5522% [2020-02-06 21:12:10.284] [jointLog] [info] finished quantifyLibrary() [2020-02-06 21:12:10.285] [jointLog] [info] Starting optimizer [2020-02-06 21:12:10.301] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-02-06 21:12:10.304] [jointLog] [info] iteration = 0 | max rel diff. = 26951.6 [2020-02-06 21:12:10.494] [jointLog] [info] iteration = 100 | max rel diff. = 5.50074 [2020-02-06 21:12:10.651] [jointLog] [info] iteration = 200 | max rel diff. = 2.0893 [2020-02-06 21:12:10.808] [jointLog] [info] iteration = 300 | max rel diff. = 0.164198 [2020-02-06 21:12:10.966] [jointLog] [info] iteration = 400 | max rel diff. = 0.0470168 [2020-02-06 21:12:11.124] [jointLog] [info] iteration = 500 | max rel diff. = 0.0494535 [2020-02-06 21:12:11.281] [jointLog] [info] iteration = 600 | max rel diff. = 0.0402461 [2020-02-06 21:12:11.395] [jointLog] [info] iteration = 674 | max rel diff. = 0.00996907 [2020-02-06 21:12:11.396] [jointLog] [info] Finished optimizer [2020-02-06 21:12:11.396] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D12_uninfected_01/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200122.C_bairdi.megan.Trinity.fasta.gene_trans_map > D12_uninfected_01/quant.sf.genes