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 [2020-02-07 11:04:27.811] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-02-07 11:04:27.811] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-02-07 11:04:27.811] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-02-07 11:04:27.811] [jointLog] [info] parsing read library format [2020-02-07 11:04:27.811] [jointLog] [info] There is 1 library. [2020-02-07 11:04:27.886] [jointLog] [info] Loading pufferfish index [2020-02-07 11:04:27.886] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 12.644 ms ----------------------------------------- size = 38529 ----------------------------------------- | Loading contig offsets | Time = 236.27 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 158.02 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 59.425 ms ----------------------------------------- size = 13572252 Number of ones: 38528 Number of ones per inventory item: 512 Inventory entries filled: 76 ----------------------------------------- | Loading contig boundaries | Time = 104.36 ms ----------------------------------------- size = 13572252 ----------------------------------------- | Loading sequence | Time = 37.894 ms ----------------------------------------- size = 12416412 ----------------------------------------- | Loading positions | Time = 211.6 ms ----------------------------------------- size = 19804148 ----------------------------------------- | Loading reference sequence | Time = 62.673 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 18.293 ms ----------------------------------------- [2020-02-07 11:04:28.394] [jointLog] [info] done [2020-02-07 11:04:28.394] [jointLog] [info] Index contained 19,670 targets [2020-02-07 11:04:28.411] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,052,548, hits per frag: 3.67098 processed 1,000,000 fragments hits: 2,107,052, hits per frag: 2.29187 processed 1,500,000 fragments hits: 3,165,428, hits per frag: 2.45824 processed 2,000,000 fragments hits: 4,232,442, hits per frag: 2.20608 processed 2,500,000 fragments hits: 5,295,282, hits per frag: 2.19458 processed 3,000,000 fragments hits: 6,348,093, hits per frag: 2.16628 processed 3,500,000 fragments hits: 7,407,446, hits per frag: 2.17954 processed 4,000,000 fragments hits: 8,461,253, hits per frag: 2.25649 processed 4,500,000 fragments hits: 9,518,669, hits per frag: 2.14617 processed 5,000,000 fragments hits: 10,582,658, hits per frag: 2.15264 processed 5,500,001 fragments hits: 11,645,840, hits per frag: 2.19018 processed 6,000,001 fragments hits: 12,701,855, hits per frag: 2.14554[2020-02-07 11:04:47.192] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:04:47.196] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:04:47.211] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 11:04:47.212] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 11:04:47.212] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:04:47.227] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:04:47.235] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:04:47.239] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:04:47.240] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:04:47.240] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:04:47.241] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 11:04:47.241] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments [2020-02-07 11:04:47.246] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:04:47.252] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:04:47.256] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:04:47.260] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:04:47.260] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:04:47.261] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:04:47.264] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:04:47.272] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:04:47.272] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:04:47.273] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:04:47.283] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:04:47.285] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:04:47.287] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:04:47.287] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:04:47.288] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:04:47.291] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:04:47.422] [jointLog] [info] Computed 65,587 rich equivalence classes for further processing [2020-02-07 11:04:47.422] [jointLog] [info] Counted 6,338,368 total reads in the equivalence classes [2020-02-07 11:04:47.437] [jointLog] [info] Number of mappings discarded because of alignment score : 662,619 [2020-02-07 11:04:47.437] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 32,232 [2020-02-07 11:04:47.437] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-02-07 11:04:47.437] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,659 [2020-02-07 11:04:47.437] [jointLog] [info] Mapping rate = 99.3516% [2020-02-07 11:04:47.437] [jointLog] [info] finished quantifyLibrary() [2020-02-07 11:04:47.437] [jointLog] [info] Starting optimizer [2020-02-07 11:04:47.455] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-02-07 11:04:47.457] [jointLog] [info] iteration = 0 | max rel diff. = 23273.5 [2020-02-07 11:04:47.631] [jointLog] [info] iteration = 100 | max rel diff. = 1.94389 [2020-02-07 11:04:47.793] [jointLog] [info] iteration = 200 | max rel diff. = 12.3524 [2020-02-07 11:04:47.955] [jointLog] [info] iteration = 300 | max rel diff. = 10.4115 [2020-02-07 11:04:48.117] [jointLog] [info] iteration = 400 | max rel diff. = 0.139701 [2020-02-07 11:04:48.279] [jointLog] [info] iteration = 500 | max rel diff. = 0.0372542 [2020-02-07 11:04:48.443] [jointLog] [info] iteration = 600 | max rel diff. = 0.0634977 [2020-02-07 11:04:48.604] [jointLog] [info] iteration = 700 | max rel diff. = 0.358358 [2020-02-07 11:04:48.653] [jointLog] [info] iteration = 731 | max rel diff. = 0.0071866 [2020-02-07 11:04:48.653] [jointLog] [info] Finished optimizer [2020-02-07 11:04:48.653] [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.329776.D26.infected.megan_R1.fq -2 /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200131.C_bairdi.329776.D26.infected.megan_R2.fq -o D26_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.329776.D26.infected.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200131.C_bairdi.329776.D26.infected.megan_R2.fq } ### [ output ] => { D26_infected_01 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D26_infected_01/logs [2020-02-07 11:13:18.756] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-02-07 11:13:18.756] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-02-07 11:13:18.756] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-02-07 11:13:18.756] [jointLog] [info] parsing read library format [2020-02-07 11:13:18.756] [jointLog] [info] There is 1 library. [2020-02-07 11:13:18.834] [jointLog] [info] Loading pufferfish index [2020-02-07 11:13:18.835] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 12.663 ms ----------------------------------------- size = 38529 ----------------------------------------- | Loading contig offsets | Time = 255.02 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 159.77 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 8.7581 ms ----------------------------------------- size = 13572252 Number of ones: 38528 Number of ones per inventory item: 512 Inventory entries filled: 76 ----------------------------------------- | Loading contig boundaries | Time = 41.355 ms ----------------------------------------- size = 13572252 ----------------------------------------- | Loading sequence | Time = 2.7637 ms ----------------------------------------- size = 12416412 ----------------------------------------- | Loading positions | Time = 22.335 ms ----------------------------------------- size = 19804148 ----------------------------------------- | Loading reference sequence | Time = 3.7881 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 185.66 us ----------------------------------------- [2020-02-07 11:13:18.927] [jointLog] [info] done [2020-02-07 11:13:18.927] [jointLog] [info] Index contained 19,670 targets [2020-02-07 11:13:18.937] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,102,907, hits per frag: 2.7153 processed 1,000,000 fragments hits: 2,203,598, hits per frag: 2.31822 processed 1,500,000 fragments hits: 3,316,371, hits per frag: 2.31705 processed 2,000,000 fragments hits: 4,431,805, hits per frag: 2.49969 processed 2,500,001 fragments hits: 5,540,730, hits per frag: 2.27478 processed 3,000,000 fragments hits: 6,646,775, hits per frag: 2.37718 processed 3,500,000 fragments hits: 7,755,620, hits per frag: 2.36729 processed 4,000,000 fragments hits: 8,858,474, hits per frag: 2.27466 processed 4,500,000 fragments hits: 9,965,207, hits per frag: 2.24883 processed 5,000,000 fragments hits: 11,083,304, hits per frag: 2.25424 processed 5,500,000 fragments hits: 12,199,320, hits per frag: 2.26244 processed 6,000,000 fragments hits: 13,296,398, hits per frag: 2.2397 [2020-02-07 11:13:36.866] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:13:36.872] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 11:13:36.873] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 11:13:36.886] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:13:36.886] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:13:36.891] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:13:36.894] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:13:36.895] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:13:36.899] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:13:36.903] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:13:36.905] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:13:36.908] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:13:36.909] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:13:36.913] [jointLog] [info] Thread saw mini-batch with a maximum of 0.13% zero probability fragments [2020-02-07 11:13:36.921] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:13:36.945] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:13:36.947] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 11:13:36.949] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:13:36.951] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:13:36.954] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:13:36.955] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 11:13:36.956] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 11:13:36.963] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 11:13:36.964] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:13:36.966] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 11:13:36.967] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:13:36.968] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 11:13:36.970] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 11:13:37.116] [jointLog] [info] Computed 59,752 rich equivalence classes for further processing [2020-02-07 11:13:37.116] [jointLog] [info] Counted 6,001,688 total reads in the equivalence classes [2020-02-07 11:13:37.131] [jointLog] [info] Number of mappings discarded because of alignment score : 580,149 [2020-02-07 11:13:37.131] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,872 [2020-02-07 11:13:37.131] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-02-07 11:13:37.131] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,290 [2020-02-07 11:13:37.131] [jointLog] [info] Mapping rate = 99.4936% [2020-02-07 11:13:37.131] [jointLog] [info] finished quantifyLibrary() [2020-02-07 11:13:37.132] [jointLog] [info] Starting optimizer [2020-02-07 11:13:37.152] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-02-07 11:13:37.154] [jointLog] [info] iteration = 0 | max rel diff. = 22279.9 [2020-02-07 11:13:37.342] [jointLog] [info] iteration = 100 | max rel diff. = 4.47678 [2020-02-07 11:13:37.507] [jointLog] [info] iteration = 200 | max rel diff. = 1.33114 [2020-02-07 11:13:37.671] [jointLog] [info] iteration = 300 | max rel diff. = 1.96155 [2020-02-07 11:13:37.835] [jointLog] [info] iteration = 400 | max rel diff. = 0.062511 [2020-02-07 11:13:38.000] [jointLog] [info] iteration = 500 | max rel diff. = 0.238749 [2020-02-07 11:13:38.164] [jointLog] [info] iteration = 600 | max rel diff. = 0.0848667 [2020-02-07 11:13:38.328] [jointLog] [info] iteration = 700 | max rel diff. = 0.0242495 [2020-02-07 11:13:38.493] [jointLog] [info] iteration = 800 | max rel diff. = 0.104385 [2020-02-07 11:13:38.657] [jointLog] [info] iteration = 900 | max rel diff. = 0.0214139 [2020-02-07 11:13:38.731] [jointLog] [info] iteration = 946 | max rel diff. = 0.00394748 [2020-02-07 11:13:38.732] [jointLog] [info] Finished optimizer [2020-02-07 11:13:38.732] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D26_infected_01/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200122.C_bairdi.megan.Trinity.fasta.gene_trans_map > D26_infected_01/quant.sf.genes