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 [2020-02-07 06:29:45.123] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-02-07 06:29:45.123] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-02-07 06:29:45.123] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-02-07 06:29:45.123] [jointLog] [info] parsing read library format [2020-02-07 06:29:45.124] [jointLog] [info] There is 1 library. [2020-02-07 06:29:45.203] [jointLog] [info] Loading pufferfish index [2020-02-07 06:29:45.203] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 12.667 ms ----------------------------------------- size = 38529 ----------------------------------------- | Loading contig offsets | Time = 244.95 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 155.45 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 8.8682 ms ----------------------------------------- size = 13572252 Number of ones: 38528 Number of ones per inventory item: 512 Inventory entries filled: 76 ----------------------------------------- | Loading contig boundaries | Time = 55.556 ms ----------------------------------------- size = 13572252 ----------------------------------------- | Loading sequence | Time = 2.9404 ms ----------------------------------------- size = 12416412 ----------------------------------------- | Loading positions | Time = 24.123 ms ----------------------------------------- size = 19804148 ----------------------------------------- | Loading reference sequence | Time = 3.9268 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 193.18 us ----------------------------------------- [2020-02-07 06:29:45.312] [jointLog] [info] done [2020-02-07 06:29:45.312] [jointLog] [info] Index contained 19,670 targets [2020-02-07 06:29:45.322] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,151,340, hits per frag: 3.36376 processed 1,000,000 fragments hits: 2,302,704, hits per frag: 2.72515 processed 1,500,000 fragments hits: 3,459,257, hits per frag: 2.45616 processed 2,000,000 fragments hits: 4,625,216, hits per frag: 2.44285 processed 2,500,000 fragments hits: 5,787,007, hits per frag: 2.4099 processed 3,000,000 fragments hits: 6,931,214, hits per frag: 2.35266 processed 3,500,000 fragments hits: 8,087,485, hits per frag: 2.36647 processed 4,000,000 fragments hits: 9,236,750, hits per frag: 2.3779 processed 4,500,000 fragments hits: 10,389,802, hits per frag: 2.36344 processed 5,000,000 fragments hits: 11,551,194, hits per frag: 2.3996 processed 5,500,000 fragments hits: 12,713,486, hits per frag: 2.33313 processed 6,000,000 fragments hits: 13,858,969, hits per frag: 2.36005 [2020-02-07 06:30:03.687] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:30:03.688] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:30:03.693] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 06:30:03.698] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 06:30:03.707] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 06:30:03.709] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 06:30:03.714] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:30:03.721] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:30:03.721] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:30:03.725] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:30:03.727] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:30:03.730] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:30:03.746] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:30:03.765] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 06:30:03.766] [jointLog] [info] Thread saw mini-batch with a maximum of 0.22% zero probability fragments [2020-02-07 06:30:03.766] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 06:30:03.766] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments [2020-02-07 06:30:03.768] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 06:30:03.769] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:30:03.775] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 06:30:03.777] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:30:03.778] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 06:30:03.782] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 06:30:03.785] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 06:30:03.795] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 06:30:03.795] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:30:03.796] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:30:03.798] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments [2020-02-07 06:30:03.923] [jointLog] [info] Computed 46,457 rich equivalence classes for further processing [2020-02-07 06:30:03.923] [jointLog] [info] Counted 6,295,944 total reads in the equivalence classes [2020-02-07 06:30:03.938] [jointLog] [info] Number of mappings discarded because of alignment score : 725,182 [2020-02-07 06:30:03.938] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 20,693 [2020-02-07 06:30:03.938] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-02-07 06:30:03.938] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,422 [2020-02-07 06:30:03.938] [jointLog] [info] Mapping rate = 99.5528% [2020-02-07 06:30:03.938] [jointLog] [info] finished quantifyLibrary() [2020-02-07 06:30:03.940] [jointLog] [info] Starting optimizer [2020-02-07 06:30:03.953] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-02-07 06:30:03.955] [jointLog] [info] iteration = 0 | max rel diff. = 26946.6 [2020-02-07 06:30:04.112] [jointLog] [info] iteration = 100 | max rel diff. = 4.98452 [2020-02-07 06:30:04.262] [jointLog] [info] iteration = 200 | max rel diff. = 2.93961 [2020-02-07 06:30:04.412] [jointLog] [info] iteration = 300 | max rel diff. = 0.165184 [2020-02-07 06:30:04.562] [jointLog] [info] iteration = 400 | max rel diff. = 0.17632 [2020-02-07 06:30:04.712] [jointLog] [info] iteration = 500 | max rel diff. = 0.0485105 [2020-02-07 06:30:04.862] [jointLog] [info] iteration = 600 | max rel diff. = 0.0677893 [2020-02-07 06:30:04.977] [jointLog] [info] iteration = 677 | max rel diff. = 0.0098568 [2020-02-07 06:30:04.978] [jointLog] [info] Finished optimizer [2020-02-07 06:30:04.978] [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 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.329777.D26.uninfected.megan_R1.fq -2 /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200131.C_bairdi.329777.D26.uninfected.megan_R2.fq -o D26_uninfected -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.329777.D26.uninfected.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200131.C_bairdi.329777.D26.uninfected.megan_R2.fq } ### [ output ] => { D26_uninfected } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D26_uninfected/logs [2020-02-07 06:38:35.171] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-02-07 06:38:35.171] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-02-07 06:38:35.171] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-02-07 06:38:35.171] [jointLog] [info] parsing read library format [2020-02-07 06:38:35.171] [jointLog] [info] There is 1 library. [2020-02-07 06:38:35.248] [jointLog] [info] Loading pufferfish index [2020-02-07 06:38:35.249] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 78.059 ms ----------------------------------------- size = 38529 ----------------------------------------- | Loading contig offsets | Time = 285.32 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 169.39 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 123.98 ms ----------------------------------------- size = 13572252 Number of ones: 38528 Number of ones per inventory item: 512 Inventory entries filled: 76 ----------------------------------------- | Loading contig boundaries | Time = 116.47 ms ----------------------------------------- size = 13572252 ----------------------------------------- | Loading sequence | Time = 50.481 ms ----------------------------------------- size = 12416412 ----------------------------------------- | Loading positions | Time = 241.63 ms ----------------------------------------- size = 19804148 ----------------------------------------- | Loading reference sequence | Time = 88.46 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 310.26 us ----------------------------------------- [2020-02-07 06:38:35.949] [jointLog] [info] done [2020-02-07 06:38:35.949] [jointLog] [info] Index contained 19,670 targets [2020-02-07 06:38:35.966] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,118,466, hits per frag: 2.56178 processed 1,000,000 fragments hits: 2,240,194, hits per frag: 2.38627 processed 1,500,000 fragments hits: 3,356,976, hits per frag: 2.50285 processed 2,000,000 fragments hits: 4,501,497, hits per frag: 2.37167 processed 2,500,000 fragments hits: 5,646,687, hits per frag: 2.3653 processed 3,000,000 fragments hits: 6,769,851, hits per frag: 2.37264 processed 3,500,000 fragments hits: 7,903,745, hits per frag: 2.29023 processed 4,000,001 fragments hits: 9,030,203, hits per frag: 2.40412 processed 4,500,000 fragments hits: 10,148,657, hits per frag: 2.30901 processed 5,000,000 fragments hits: 11,269,128, hits per frag: 2.33264 processed 5,500,001 fragments hits: 12,405,228, hits per frag: 2.2804 processed 6,000,000 fragments hits: 13,548,863, hits per frag: 2.31176 processed 6,500,000 fragments hits: 14,673,322, hits per frag: 2.27752 [2020-02-07 06:38:52.806] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:38:52.807] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:38:52.809] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:38:52.812] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:38:52.817] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:38:52.820] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:38:52.825] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:38:52.827] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:38:52.848] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 06:38:52.848] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:38:52.852] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:38:52.858] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:38:52.870] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:38:52.882] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:38:52.883] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:38:52.890] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:38:52.896] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:38:52.904] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:38:52.906] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:38:52.907] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:38:52.908] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:38:52.916] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:38:52.918] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:38:52.918] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:38:52.919] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 06:38:52.919] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 06:38:52.920] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 06:38:52.921] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:38:53.048] [jointLog] [info] Computed 55,920 rich equivalence classes for further processing [2020-02-07 06:38:53.048] [jointLog] [info] Counted 6,861,138 total reads in the equivalence classes [2020-02-07 06:38:53.064] [jointLog] [info] Number of mappings discarded because of alignment score : 914,634 [2020-02-07 06:38:53.065] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 23,613 [2020-02-07 06:38:53.065] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-02-07 06:38:53.065] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,043 [2020-02-07 06:38:53.065] [jointLog] [info] Mapping rate = 99.5867% [2020-02-07 06:38:53.065] [jointLog] [info] finished quantifyLibrary() [2020-02-07 06:38:53.066] [jointLog] [info] Starting optimizer [2020-02-07 06:38:53.083] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-02-07 06:38:53.086] [jointLog] [info] iteration = 0 | max rel diff. = 29797.6 [2020-02-07 06:38:53.337] [jointLog] [info] iteration = 100 | max rel diff. = 4.72741 [2020-02-07 06:38:53.574] [jointLog] [info] iteration = 200 | max rel diff. = 0.527137 [2020-02-07 06:38:53.811] [jointLog] [info] iteration = 300 | max rel diff. = 1.27619 [2020-02-07 06:38:54.048] [jointLog] [info] iteration = 400 | max rel diff. = 0.0284666 [2020-02-07 06:38:54.284] [jointLog] [info] iteration = 500 | max rel diff. = 0.358911 [2020-02-07 06:38:54.521] [jointLog] [info] iteration = 600 | max rel diff. = 0.0455363 [2020-02-07 06:38:54.756] [jointLog] [info] iteration = 700 | max rel diff. = 0.0317149 [2020-02-07 06:38:54.840] [jointLog] [info] iteration = 736 | max rel diff. = 0.0054179 [2020-02-07 06:38:54.841] [jointLog] [info] Finished optimizer [2020-02-07 06:38:54.841] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D26_uninfected/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200122.C_bairdi.megan.Trinity.fasta.gene_trans_map > D26_uninfected/quant.sf.genes