CMD: salmon quant -i /gscratch/srlab/sam/data/Hematodinium/transcriptomes/20200122.hemat.megan.Trinity.fasta.salmon.idx -l ISR -1 /gscratch/srlab/sam/data/Hematodinium/RNAseq/20200131.Hematodinium.329774.D12.infected.megan_R1.fq -2 /gscratch/srlab/sam/data/Hematodinium/RNAseq/20200131.Hematodinium.329774.D12.infected.megan_R2.fq -o D12_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/Hematodinium/transcriptomes/20200122.hemat.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /gscratch/srlab/sam/data/Hematodinium/RNAseq/20200131.Hematodinium.329774.D12.infected.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/Hematodinium/RNAseq/20200131.Hematodinium.329774.D12.infected.megan_R2.fq } ### [ output ] => { D12_01 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D12_01/logs [2020-04-06 17:23:20.517] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-06 17:23:20.517] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-06 17:23:20.517] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-06 17:23:20.517] [jointLog] [info] parsing read library format [2020-04-06 17:23:20.517] [jointLog] [info] There is 1 library. ----------------------------------------- | Loading contig table | Time = 1.4399 ms ----------------------------------------- size = 7179 ----------------------------------------- | Loading contig offsets | Time = 132.31 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 61.319 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 1.6522 ms ----------------------------------------- size = 3327413 Number of ones: 7178 Number of ones per inventory item: 512 Inventory entries filled: 15 ----------------------------------------- | Loading contig boundaries | Time = 8.2994 ms ----------------------------------------- size = 3327413 ----------------------------------------- | Loading sequence | Time = 782.91 us ----------------------------------------- size = 3112073 [2020-04-06 17:23:20.583] [jointLog] [info] Loading pufferfish index [2020-04-06 17:23:20.583] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading positions | Time = 4.5129 ms ----------------------------------------- size = 3816332 ----------------------------------------- | Loading reference sequence | Time = 904.78 us ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 78.349 us ----------------------------------------- [2020-04-06 17:23:20.601] [jointLog] [info] done [2020-04-06 17:23:20.601] [jointLog] [info] Index contained 5,183 targets [2020-04-06 17:23:20.604] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 988,622, hits per frag: 2.80694[2020-04-06 17:23:22.734] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:23:22.763] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:23:22.772] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments [2020-04-06 17:23:22.783] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:23:22.800] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:23:22.819] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments [2020-04-06 17:23:22.828] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:23:22.837] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:23:22.844] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:23:22.858] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:23:22.873] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments [2020-04-06 17:23:22.881] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:23:22.883] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments [2020-04-06 17:23:22.903] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:23:22.906] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-04-06 17:23:22.906] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:23:22.907] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments [2020-04-06 17:23:22.908] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments [2020-04-06 17:23:22.908] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments [2020-04-06 17:23:22.914] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:23:22.918] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:23:22.921] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:23:22.921] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments [2020-04-06 17:23:22.923] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:23:22.925] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments [2020-04-06 17:23:23.124] [jointLog] [info] Computed 9,691 rich equivalence classes for further processing [2020-04-06 17:23:23.124] [jointLog] [info] Counted 707,579 total reads in the equivalence classes [2020-04-06 17:23:23.137] [jointLog] [info] Number of mappings discarded because of alignment score : 26,250 [2020-04-06 17:23:23.137] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 5,962 [2020-04-06 17:23:23.137] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-06 17:23:23.137] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 57 [2020-04-06 17:23:23.137] [jointLog] [warning] Only 707579 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-06 17:23:23.137] [jointLog] [info] Mapping rate = 98.8607% [2020-04-06 17:23:23.137] [jointLog] [info] finished quantifyLibrary() [2020-04-06 17:23:23.138] [jointLog] [info] Starting optimizer [2020-04-06 17:23:23.144] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-06 17:23:23.145] [jointLog] [info] iteration = 0 | max rel diff. = 7173.08 [2020-04-06 17:23:23.179] [jointLog] [info] iteration = 100 | max rel diff. = 0.337263 [2020-04-06 17:23:23.210] [jointLog] [info] iteration = 200 | max rel diff. = 0.0168808 [2020-04-06 17:23:23.240] [jointLog] [info] iteration = 300 | max rel diff. = 0.0832982 [2020-04-06 17:23:23.255] [jointLog] [info] iteration = 357 | max rel diff. = 0.00142306 [2020-04-06 17:23:23.255] [jointLog] [info] Finished optimizer [2020-04-06 17:23:23.255] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D12_01/quant.sf /gscratch/srlab/sam/data/Hematodinium/transcriptomes/20200122.hemat.megan.Trinity.fasta.gene_trans_map > D12_01/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/Hematodinium/transcriptomes/20200122.hemat.megan.Trinity.fasta.salmon.idx -l ISR -1 /gscratch/srlab/sam/data/Hematodinium/RNAseq/20200131.Hematodinium.329776.D26.infected.megan_R1.fq -2 /gscratch/srlab/sam/data/Hematodinium/RNAseq/20200131.Hematodinium.329776.D26.infected.megan_R2.fq -o D26_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/Hematodinium/transcriptomes/20200122.hemat.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /gscratch/srlab/sam/data/Hematodinium/RNAseq/20200131.Hematodinium.329776.D26.infected.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/Hematodinium/RNAseq/20200131.Hematodinium.329776.D26.infected.megan_R2.fq } ### [ output ] => { D26_01 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D26_01/logs [2020-04-06 17:31:52.889] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-06 17:31:52.889] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-06 17:31:52.889] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-06 17:31:52.889] [jointLog] [info] parsing read library format [2020-04-06 17:31:52.889] [jointLog] [info] There is 1 library. ----------------------------------------- | Loading contig table | Time = 1.4698 ms ----------------------------------------- size = 7179 ----------------------------------------- | Loading contig offsets | Time = 109.56 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 53.989 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 1.552 ms ----------------------------------------- size = 3327413 Number of ones: 7178 Number of ones per inventory item: 512 Inventory entries filled: 15 ----------------------------------------- | Loading contig boundaries | Time = 8.7939 ms ----------------------------------------- size = 3327413 ----------------------------------------- | Loading sequence | Time = 781.27 us ----------------------------------------- size = 3112073 [2020-04-06 17:31:52.953] [jointLog] [info] Loading pufferfish index [2020-04-06 17:31:52.953] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading positions | Time = 5.2882 ms ----------------------------------------- size = 3816332 ----------------------------------------- | Loading reference sequence | Time = 905.17 us ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 76.387 us ----------------------------------------- [2020-04-06 17:31:52.972] [jointLog] [info] done [2020-04-06 17:31:52.972] [jointLog] [info] Index contained 5,183 targets [2020-04-06 17:31:52.975] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,082,823, hits per frag: 2.62102[2020-04-06 17:31:55.123] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.212] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments [2020-04-06 17:31:55.212] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.245] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments [2020-04-06 17:31:55.252] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.252] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments [2020-04-06 17:31:55.268] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.271] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.278] [jointLog] [info] Thread saw mini-batch with a maximum of 0.06% zero probability fragments [2020-04-06 17:31:55.288] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments [2020-04-06 17:31:55.302] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments [2020-04-06 17:31:55.305] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.305] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.306] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.314] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.317] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.327] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.329] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.334] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.339] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.340] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments [2020-04-06 17:31:55.343] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.345] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.345] [jointLog] [info] Thread saw mini-batch with a maximum of 0.04% zero probability fragments [2020-04-06 17:31:55.346] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.347] [jointLog] [info] Thread saw mini-batch with a maximum of 0.02% zero probability fragments [2020-04-06 17:31:55.590] [jointLog] [info] Computed 9,130 rich equivalence classes for further processing [2020-04-06 17:31:55.590] [jointLog] [info] Counted 639,747 total reads in the equivalence classes [2020-04-06 17:31:55.603] [jointLog] [info] Number of mappings discarded because of alignment score : 27,472 [2020-04-06 17:31:55.603] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 5,748 [2020-04-06 17:31:55.603] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-06 17:31:55.603] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 23 [2020-04-06 17:31:55.604] [jointLog] [warning] Only 639747 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-06 17:31:55.604] [jointLog] [info] Mapping rate = 98.8296% [2020-04-06 17:31:55.604] [jointLog] [info] finished quantifyLibrary() [2020-04-06 17:31:55.605] [jointLog] [info] Starting optimizer [2020-04-06 17:31:55.611] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-06 17:31:55.612] [jointLog] [info] iteration = 0 | max rel diff. = 11003.1 [2020-04-06 17:31:55.645] [jointLog] [info] iteration = 100 | max rel diff. = 0.270096 [2020-04-06 17:31:55.674] [jointLog] [info] iteration = 200 | max rel diff. = 0.80245 [2020-04-06 17:31:55.701] [jointLog] [info] iteration = 300 | max rel diff. = 0.0157792 [2020-04-06 17:31:55.727] [jointLog] [info] iteration = 400 | max rel diff. = 0.0982042 [2020-04-06 17:31:55.751] [jointLog] [info] iteration = 500 | max rel diff. = 0.0321339 [2020-04-06 17:31:55.770] [jointLog] [info] iteration = 584 | max rel diff. = 0.00078143 [2020-04-06 17:31:55.770] [jointLog] [info] Finished optimizer [2020-04-06 17:31:55.770] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D26_01/quant.sf /gscratch/srlab/sam/data/Hematodinium/transcriptomes/20200122.hemat.megan.Trinity.fasta.gene_trans_map > D26_01/quant.sf.genes