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_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_01 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D12_01/logs [2020-02-07 05:48:14.915] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-02-07 05:48:14.915] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-02-07 05:48:14.915] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-02-07 05:48:14.915] [jointLog] [info] parsing read library format [2020-02-07 05:48:14.916] [jointLog] [info] There is 1 library. [2020-02-07 05:48:14.992] [jointLog] [info] Loading pufferfish index [2020-02-07 05:48:15.004] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 61.515 ms ----------------------------------------- size = 38529 ----------------------------------------- | Loading contig offsets | Time = 785.86 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 209.1 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 115.87 ms ----------------------------------------- size = 13572252 Number of ones: 38528 Number of ones per inventory item: 512 Inventory entries filled: 76 ----------------------------------------- | Loading contig boundaries | Time = 97.982 ms ----------------------------------------- size = 13572252 ----------------------------------------- | Loading sequence | Time = 64.78 ms ----------------------------------------- size = 12416412 ----------------------------------------- | Loading positions | Time = 154.06 ms ----------------------------------------- size = 19804148 ----------------------------------------- | Loading reference sequence | Time = 128.34 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 319.39 us ----------------------------------------- [2020-02-07 05:48:15.664] [jointLog] [info] done [2020-02-07 05:48:15.665] [jointLog] [info] Index contained 19,670 targets [2020-02-07 05:48:15.682] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,052,842, hits per frag: 2.84117 processed 1,000,000 fragments hits: 2,107,162, hits per frag: 2.45969 processed 1,500,000 fragments hits: 3,165,361, hits per frag: 2.25153 processed 2,000,000 fragments hits: 4,232,855, hits per frag: 2.26411 processed 2,500,000 fragments hits: 5,295,434, hits per frag: 2.21915 processed 3,000,000 fragments hits: 6,348,177, hits per frag: 2.20611 processed 3,500,000 fragments hits: 7,407,182, hits per frag: 2.19926 processed 4,000,000 fragments hits: 8,461,243, hits per frag: 2.17988 processed 4,500,000 fragments hits: 9,518,833, hits per frag: 2.16835 processed 5,000,001 fragments hits: 10,582,640, hits per frag: 2.18537 processed 5,500,001 fragments hits: 11,646,071, hits per frag: 2.15565 processed 6,000,000 fragments hits: 12,701,393, hits per frag: 2.13847[2020-02-07 05:48:33.301] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:48:33.302] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:48:33.307] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:48:33.318] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:48:33.319] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:48:33.334] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:48:33.342] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:48:33.342] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:48:33.343] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 05:48:33.350] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:48:33.355] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:48:33.356] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:48:33.357] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:48:33.366] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:48:33.370] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:48:33.374] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:48:33.379] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:48:33.391] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:48:33.393] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 05:48:33.393] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:48:33.396] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:48:33.400] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:48:33.404] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:48:33.408] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:48:33.409] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:48:33.409] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments [2020-02-07 05:48:33.409] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:48:33.411] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 05:48:33.533] [jointLog] [info] Computed 65,439 rich equivalence classes for further processing [2020-02-07 05:48:33.533] [jointLog] [info] Counted 6,338,345 total reads in the equivalence classes [2020-02-07 05:48:33.547] [jointLog] [info] Number of mappings discarded because of alignment score : 662,283 [2020-02-07 05:48:33.547] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 32,252 [2020-02-07 05:48:33.547] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-02-07 05:48:33.547] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,647 [2020-02-07 05:48:33.547] [jointLog] [info] Mapping rate = 99.3513% [2020-02-07 05:48:33.547] [jointLog] [info] finished quantifyLibrary() [2020-02-07 05:48:33.548] [jointLog] [info] Starting optimizer [2020-02-07 05:48:33.565] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-02-07 05:48:33.567] [jointLog] [info] iteration = 0 | max rel diff. = 23254.5 [2020-02-07 05:48:33.735] [jointLog] [info] iteration = 100 | max rel diff. = 6.12481 [2020-02-07 05:48:33.891] [jointLog] [info] iteration = 200 | max rel diff. = 1.62517 [2020-02-07 05:48:34.047] [jointLog] [info] iteration = 300 | max rel diff. = 10.8648 [2020-02-07 05:48:34.204] [jointLog] [info] iteration = 400 | max rel diff. = 0.250715 [2020-02-07 05:48:34.360] [jointLog] [info] iteration = 500 | max rel diff. = 0.084418 [2020-02-07 05:48:34.516] [jointLog] [info] iteration = 600 | max rel diff. = 0.174293 [2020-02-07 05:48:34.673] [jointLog] [info] iteration = 700 | max rel diff. = 0.0544346 [2020-02-07 05:48:34.831] [jointLog] [info] iteration = 800 | max rel diff. = 0.0330384 [2020-02-07 05:48:34.987] [jointLog] [info] iteration = 900 | max rel diff. = 0.0371923 [2020-02-07 05:48:35.032] [jointLog] [info] iteration = 930 | max rel diff. = 0.00789576 [2020-02-07 05:48:35.033] [jointLog] [info] Finished optimizer [2020-02-07 05:48:35.033] [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/C_bairdi/transcriptomes/20200122.C_bairdi.megan.Trinity.fasta.gene_trans_map > D12_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_02 -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_02 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D12_02/logs [2020-02-07 05:57:04.806] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-02-07 05:57:04.806] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-02-07 05:57:04.806] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-02-07 05:57:04.806] [jointLog] [info] parsing read library format [2020-02-07 05:57:04.806] [jointLog] [info] There is 1 library. [2020-02-07 05:57:04.884] [jointLog] [info] Loading pufferfish index [2020-02-07 05:57:04.884] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 14.361 ms ----------------------------------------- size = 38529 ----------------------------------------- | Loading contig offsets | Time = 234.47 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 157.3 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 55.489 ms ----------------------------------------- size = 13572252 Number of ones: 38528 Number of ones per inventory item: 512 Inventory entries filled: 76 ----------------------------------------- | Loading contig boundaries | Time = 60.534 ms ----------------------------------------- size = 13572252 ----------------------------------------- | Loading sequence | Time = 7.682 ms ----------------------------------------- size = 12416412 ----------------------------------------- | Loading positions | Time = 137.38 ms ----------------------------------------- size = 19804148 ----------------------------------------- | Loading reference sequence | Time = 53.02 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 291.22 us ----------------------------------------- [2020-02-07 05:57:05.214] [jointLog] [info] done [2020-02-07 05:57:05.214] [jointLog] [info] Index contained 19,670 targets [2020-02-07 05:57:05.229] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,151,353, hits per frag: 3.21104 processed 1,000,000 fragments hits: 2,302,629, hits per frag: 2.55427 processed 1,500,001 fragments hits: 3,459,304, hits per frag: 2.56077 processed 2,000,000 fragments hits: 4,625,137, hits per frag: 2.43303 processed 2,500,000 fragments hits: 5,787,148, hits per frag: 2.42576 processed 3,000,000 fragments hits: 6,931,157, hits per frag: 2.36235 processed 3,500,000 fragments hits: 8,086,823, hits per frag: 2.39435 processed 4,000,000 fragments hits: 9,237,234, hits per frag: 2.39209 processed 4,500,000 fragments hits: 10,390,028, hits per frag: 2.37779 processed 5,000,000 fragments hits: 11,551,410, hits per frag: 2.39201 processed 5,500,000 fragments hits: 12,713,840, hits per frag: 2.34436 processed 6,000,001 fragments hits: 13,858,885, hits per frag: 2.32164 [2020-02-07 05:57:21.330] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 05:57:21.331] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:57:21.346] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 05:57:21.353] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 05:57:21.353] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 05:57:21.356] [jointLog] [info] Thread saw mini-batch with a maximum of 0.18% zero probability fragments [2020-02-07 05:57:21.361] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:57:21.374] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:57:21.382] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:57:21.384] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 05:57:21.386] [jointLog] [info] Thread saw mini-batch with a maximum of 0.22% zero probability fragments [2020-02-07 05:57:21.388] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 05:57:21.401] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:57:21.409] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 05:57:21.417] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:57:21.422] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:57:21.425] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 05:57:21.427] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 05:57:21.428] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:57:21.429] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 05:57:21.433] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 05:57:21.434] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:57:21.437] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 05:57:21.443] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 05:57:21.443] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:57:21.447] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:57:21.450] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:57:21.450] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 05:57:21.574] [jointLog] [info] Computed 46,323 rich equivalence classes for further processing [2020-02-07 05:57:21.574] [jointLog] [info] Counted 6,295,939 total reads in the equivalence classes [2020-02-07 05:57:21.589] [jointLog] [info] Number of mappings discarded because of alignment score : 724,371 [2020-02-07 05:57:21.589] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 20,687 [2020-02-07 05:57:21.589] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-02-07 05:57:21.589] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,421 [2020-02-07 05:57:21.589] [jointLog] [info] Mapping rate = 99.5528% [2020-02-07 05:57:21.589] [jointLog] [info] finished quantifyLibrary() [2020-02-07 05:57:21.590] [jointLog] [info] Starting optimizer [2020-02-07 05:57:21.605] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-02-07 05:57:21.607] [jointLog] [info] iteration = 0 | max rel diff. = 26942.5 [2020-02-07 05:57:21.772] [jointLog] [info] iteration = 100 | max rel diff. = 5.44918 [2020-02-07 05:57:21.919] [jointLog] [info] iteration = 200 | max rel diff. = 2.7389 [2020-02-07 05:57:22.067] [jointLog] [info] iteration = 300 | max rel diff. = 0.193153 [2020-02-07 05:57:22.215] [jointLog] [info] iteration = 400 | max rel diff. = 15.0176 [2020-02-07 05:57:22.363] [jointLog] [info] iteration = 500 | max rel diff. = 0.0485858 [2020-02-07 05:57:22.512] [jointLog] [info] iteration = 600 | max rel diff. = 0.0401607 [2020-02-07 05:57:22.621] [jointLog] [info] iteration = 674 | max rel diff. = 0.00985215 [2020-02-07 05:57:22.621] [jointLog] [info] Finished optimizer [2020-02-07 05:57:22.621] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D12_02/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200122.C_bairdi.megan.Trinity.fasta.gene_trans_map > D12_02/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_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_01 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D26_01/logs [2020-02-07 06:05:52.932] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-02-07 06:05:52.932] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-02-07 06:05:52.932] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-02-07 06:05:52.932] [jointLog] [info] parsing read library format [2020-02-07 06:05:52.932] [jointLog] [info] There is 1 library. [2020-02-07 06:05:53.008] [jointLog] [info] Loading pufferfish index [2020-02-07 06:05:53.008] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 15.002 ms ----------------------------------------- size = 38529 ----------------------------------------- | Loading contig offsets | Time = 242.93 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 135.85 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 7.4382 ms ----------------------------------------- size = 13572252 Number of ones: 38528 Number of ones per inventory item: 512 Inventory entries filled: 76 ----------------------------------------- | Loading contig boundaries | Time = 58.546 ms ----------------------------------------- size = 13572252 ----------------------------------------- | Loading sequence | Time = 3.3485 ms ----------------------------------------- size = 12416412 ----------------------------------------- | Loading positions | Time = 146.76 ms ----------------------------------------- size = 19804148 ----------------------------------------- | Loading reference sequence | Time = 5.4526 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 307.29 us ----------------------------------------- [2020-02-07 06:05:53.246] [jointLog] [info] done [2020-02-07 06:05:53.246] [jointLog] [info] Index contained 19,670 targets [2020-02-07 06:05:53.263] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,102,804, hits per frag: 2.49739 processed 1,000,000 fragments hits: 2,203,519, hits per frag: 2.67269 processed 1,500,000 fragments hits: 3,316,606, hits per frag: 2.33362 processed 2,000,000 fragments hits: 4,432,013, hits per frag: 2.30753 processed 2,500,000 fragments hits: 5,541,059, hits per frag: 2.29749 processed 3,000,000 fragments hits: 6,646,663, hits per frag: 2.33588 processed 3,500,000 fragments hits: 7,755,789, hits per frag: 2.32245 processed 4,000,000 fragments hits: 8,858,608, hits per frag: 2.27339 processed 4,500,000 fragments hits: 9,965,549, hits per frag: 2.26014 processed 5,000,000 fragments hits: 11,083,529, hits per frag: 2.29778 processed 5,500,000 fragments hits: 12,199,812, hits per frag: 2.24698 processed 6,000,001 fragments hits: 13,296,325, hits per frag: 2.24789[2020-02-07 06:06:11.710] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:06:11.715] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 06:06:11.716] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:06:11.729] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:06:11.732] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:06:11.736] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:06:11.741] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:06:11.742] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:06:11.743] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:06:11.744] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:06:11.746] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:06:11.761] [jointLog] [info] Thread saw mini-batch with a maximum of 0.13% zero probability fragments [2020-02-07 06:06:11.765] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 06:06:11.765] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:06:11.795] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 06:06:11.809] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:06:11.810] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:06:11.811] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:06:11.815] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:06:11.817] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:06:11.820] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:06:11.821] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:06:11.824] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:06:11.824] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:06:11.826] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:06:11.827] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 06:06:11.827] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:06:11.828] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:06:11.949] [jointLog] [info] Computed 59,859 rich equivalence classes for further processing [2020-02-07 06:06:11.949] [jointLog] [info] Counted 6,001,679 total reads in the equivalence classes [2020-02-07 06:06:11.963] [jointLog] [info] Number of mappings discarded because of alignment score : 580,291 [2020-02-07 06:06:11.963] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,871 [2020-02-07 06:06:11.963] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-02-07 06:06:11.963] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,293 [2020-02-07 06:06:11.963] [jointLog] [info] Mapping rate = 99.4934% [2020-02-07 06:06:11.963] [jointLog] [info] finished quantifyLibrary() [2020-02-07 06:06:11.964] [jointLog] [info] Starting optimizer [2020-02-07 06:06:11.980] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-02-07 06:06:11.983] [jointLog] [info] iteration = 0 | max rel diff. = 22288.5 [2020-02-07 06:06:12.173] [jointLog] [info] iteration = 100 | max rel diff. = 5.81382 [2020-02-07 06:06:12.350] [jointLog] [info] iteration = 200 | max rel diff. = 1.42077 [2020-02-07 06:06:12.527] [jointLog] [info] iteration = 300 | max rel diff. = 1.66594 [2020-02-07 06:06:12.704] [jointLog] [info] iteration = 400 | max rel diff. = 0.0851054 [2020-02-07 06:06:12.881] [jointLog] [info] iteration = 500 | max rel diff. = 0.202441 [2020-02-07 06:06:13.058] [jointLog] [info] iteration = 600 | max rel diff. = 1.1212 [2020-02-07 06:06:13.235] [jointLog] [info] iteration = 700 | max rel diff. = 0.0507354 [2020-02-07 06:06:13.411] [jointLog] [info] iteration = 800 | max rel diff. = 0.132915 [2020-02-07 06:06:13.521] [jointLog] [info] iteration = 863 | max rel diff. = 0.00857531 [2020-02-07 06:06:13.522] [jointLog] [info] Finished optimizer [2020-02-07 06:06:13.522] [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/C_bairdi/transcriptomes/20200122.C_bairdi.megan.Trinity.fasta.gene_trans_map > D26_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_02 -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_02 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D26_02/logs [2020-02-07 06:14:43.364] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-02-07 06:14:43.364] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-02-07 06:14:43.364] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-02-07 06:14:43.364] [jointLog] [info] parsing read library format [2020-02-07 06:14:43.364] [jointLog] [info] There is 1 library. [2020-02-07 06:14:43.443] [jointLog] [info] Loading pufferfish index [2020-02-07 06:14:43.443] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.616 ms ----------------------------------------- size = 38529 ----------------------------------------- | Loading contig offsets | Time = 171.36 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 86.26 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 7.3969 ms ----------------------------------------- size = 13572252 Number of ones: 38528 Number of ones per inventory item: 512 Inventory entries filled: 76 ----------------------------------------- | Loading contig boundaries | Time = 49.748 ms ----------------------------------------- size = 13572252 ----------------------------------------- | Loading sequence | Time = 2.4824 ms ----------------------------------------- size = 12416412 ----------------------------------------- | Loading positions | Time = 21.508 ms ----------------------------------------- size = 19804148 ----------------------------------------- | Loading reference sequence | Time = 3.6707 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 103.04 us ----------------------------------------- [2020-02-07 06:14:43.540] [jointLog] [info] done [2020-02-07 06:14:43.540] [jointLog] [info] Index contained 19,670 targets [2020-02-07 06:14:43.549] [jointLog] [info] Number of decoys : 0  processed 500,001 fragments hits: 1,118,394, hits per frag: 2.63553 processed 1,000,000 fragments hits: 2,239,929, hits per frag: 2.78226 processed 1,500,000 fragments hits: 3,356,822, hits per frag: 2.61463 processed 2,000,001 fragments hits: 4,501,533, hits per frag: 2.53137 processed 2,500,000 fragments hits: 5,646,857, hits per frag: 2.45723 processed 3,000,000 fragments hits: 6,771,121, hits per frag: 2.4312 processed 3,500,000 fragments hits: 7,904,595, hits per frag: 2.31387 processed 4,000,000 fragments hits: 9,030,141, hits per frag: 2.38772 processed 4,500,000 fragments hits: 10,149,142, hits per frag: 2.35873 processed 5,000,000 fragments hits: 11,269,415, hits per frag: 2.29318 processed 5,500,002 fragments hits: 12,405,828, hits per frag: 2.2957 processed 6,000,000 fragments hits: 13,549,692, hits per frag: 2.29818 processed 6,500,000 fragments hits: 14,673,988, hits per frag: 2.28889[2020-02-07 06:15:02.229] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:15:02.234] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:15:02.241] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:15:02.243] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:15:02.251] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:15:02.252] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:15:02.258] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:15:02.260] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:15:02.265] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:15:02.274] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:15:02.282] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 06:15:02.282] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:15:02.297] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:15:02.314] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:15:02.319] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:15:02.326] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:15:02.331] [jointLog] [info] Thread saw mini-batch with a maximum of 0.16% zero probability fragments [2020-02-07 06:15:02.335] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:15:02.345] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 06:15:02.347] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:15:02.348] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:15:02.353] [jointLog] [info] Thread saw mini-batch with a maximum of 0.12% zero probability fragments [2020-02-07 06:15:02.355] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:15:02.355] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 06:15:02.355] [jointLog] [info] Thread saw mini-batch with a maximum of 0.10% zero probability fragments [2020-02-07 06:15:02.355] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:15:02.356] [jointLog] [info] Thread saw mini-batch with a maximum of 0.14% zero probability fragments [2020-02-07 06:15:02.358] [jointLog] [info] Thread saw mini-batch with a maximum of 0.08% zero probability fragments [2020-02-07 06:15:02.473] [jointLog] [info] Computed 56,040 rich equivalence classes for further processing [2020-02-07 06:15:02.473] [jointLog] [info] Counted 6,861,144 total reads in the equivalence classes [2020-02-07 06:15:02.489] [jointLog] [info] Number of mappings discarded because of alignment score : 914,422 [2020-02-07 06:15:02.489] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 23,608 [2020-02-07 06:15:02.489] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-02-07 06:15:02.489] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,055 [2020-02-07 06:15:02.489] [jointLog] [info] Mapping rate = 99.5868% [2020-02-07 06:15:02.489] [jointLog] [info] finished quantifyLibrary() [2020-02-07 06:15:02.490] [jointLog] [info] Starting optimizer [2020-02-07 06:15:02.509] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-02-07 06:15:02.512] [jointLog] [info] iteration = 0 | max rel diff. = 29792.4 [2020-02-07 06:15:02.758] [jointLog] [info] iteration = 100 | max rel diff. = 3.57875 [2020-02-07 06:15:02.987] [jointLog] [info] iteration = 200 | max rel diff. = 0.389661 [2020-02-07 06:15:03.214] [jointLog] [info] iteration = 300 | max rel diff. = 0.421193 [2020-02-07 06:15:03.442] [jointLog] [info] iteration = 400 | max rel diff. = 0.126702 [2020-02-07 06:15:03.670] [jointLog] [info] iteration = 500 | max rel diff. = 0.367529 [2020-02-07 06:15:03.899] [jointLog] [info] iteration = 600 | max rel diff. = 0.132982 [2020-02-07 06:15:04.126] [jointLog] [info] iteration = 700 | max rel diff. = 0.0901902 [2020-02-07 06:15:04.231] [jointLog] [info] iteration = 747 | max rel diff. = 0.00660845 [2020-02-07 06:15:04.231] [jointLog] [info] Finished optimizer [2020-02-07 06:15:04.231] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D26_02/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200122.C_bairdi.megan.Trinity.fasta.gene_trans_map > D26_02/quant.sf.genes