CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.113.D9.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.113.D9.uninfected.cold.megan_R2.fq -o D9_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/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.113.D9.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.113.D9.uninfected.cold.megan_R2.fq } ### [ output ] => { D9_01 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_01/logs [2020-04-26 02:22:38.177] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 02:22:38.178] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 02:22:38.178] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 02:22:38.178] [jointLog] [info] parsing read library format [2020-04-26 02:22:38.178] [jointLog] [info] There is 1 library. [2020-04-26 02:22:38.228] [jointLog] [info] Loading pufferfish index [2020-04-26 02:22:38.228] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 13.468 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 219.11 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 123.65 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.9904 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.724 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.315 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 116.03 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.9663 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 232.19 us ----------------------------------------- [2020-04-26 02:22:38.401] [jointLog] [info] done [2020-04-26 02:22:38.401] [jointLog] [info] Index contained 40,435 targets [2020-04-26 02:22:38.413] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,588,078, hits per frag: 3.51217 processed 1,000,000 fragments hits: 3,173,253, hits per frag: 3.64216 processed 1,500,000 fragments hits: 4,765,901, hits per frag: 3.34751 processed 2,000,001 fragments hits: 6,348,335, hits per frag: 3.30529 [2020-04-26 02:22:44.969] [jointLog] [info] Computed 72,803 rich equivalence classes for further processing [2020-04-26 02:22:44.969] [jointLog] [info] Counted 2,278,269 total reads in the equivalence classes [2020-04-26 02:22:44.986] [jointLog] [info] Number of mappings discarded because of alignment score : 461,137 [2020-04-26 02:22:44.986] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,736 [2020-04-26 02:22:44.986] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 02:22:44.986] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,352 [2020-04-26 02:22:44.989] [jointLog] [warning] Only 2278269 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 02:22:44.989] [jointLog] [info] Mapping rate = 99.1406% [2020-04-26 02:22:44.989] [jointLog] [info] finished quantifyLibrary() [2020-04-26 02:22:44.991] [jointLog] [info] Starting optimizer [2020-04-26 02:22:45.012] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 02:22:45.017] [jointLog] [info] iteration = 0 | max rel diff. = 5252.69 [2020-04-26 02:22:45.283] [jointLog] [info] iteration = 100 | max rel diff. = 3.94418 [2020-04-26 02:22:45.548] [jointLog] [info] iteration = 200 | max rel diff. = 0.477324 [2020-04-26 02:22:45.810] [jointLog] [info] iteration = 300 | max rel diff. = 0.25167 [2020-04-26 02:22:46.077] [jointLog] [info] iteration = 400 | max rel diff. = 0.108188 [2020-04-26 02:22:46.344] [jointLog] [info] iteration = 500 | max rel diff. = 0.0993165 [2020-04-26 02:22:46.609] [jointLog] [info] iteration = 600 | max rel diff. = 3.35828 [2020-04-26 02:22:46.878] [jointLog] [info] iteration = 700 | max rel diff. = 0.178284 [2020-04-26 02:22:47.154] [jointLog] [info] iteration = 800 | max rel diff. = 1.0699 [2020-04-26 02:22:47.265] [jointLog] [info] iteration = 841 | max rel diff. = 0.00762133 [2020-04-26 02:22:47.266] [jointLog] [info] Finished optimizer [2020-04-26 02:22:47.266] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_01/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_01/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.118.D9.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.118.D9.infected.ambient.megan_R2.fq -o D9_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/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.118.D9.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.118.D9.infected.ambient.megan_R2.fq } ### [ output ] => { D9_02 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_02/logs [2020-04-26 02:31:18.111] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 02:31:18.111] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 02:31:18.111] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 02:31:18.111] [jointLog] [info] parsing read library format [2020-04-26 02:31:18.111] [jointLog] [info] There is 1 library. [2020-04-26 02:31:18.166] [jointLog] [info] Loading pufferfish index [2020-04-26 02:31:18.166] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.244 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 198.27 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 113.83 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.2776 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.118 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.6183 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 119.6 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.7674 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 124.95 us ----------------------------------------- [2020-04-26 02:31:18.342] [jointLog] [info] done [2020-04-26 02:31:18.342] [jointLog] [info] Index contained 40,435 targets [2020-04-26 02:31:18.356] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,774,616, hits per frag: 6.96777 processed 1,000,000 fragments hits: 5,560,725, hits per frag: 5.86724 [2020-04-26 02:31:24.229] [jointLog] [info] Computed 68,053 rich equivalence classes for further processing [2020-04-26 02:31:24.229] [jointLog] [info] Counted 1,441,032 total reads in the equivalence classes [2020-04-26 02:31:24.252] [jointLog] [info] Number of mappings discarded because of alignment score : 600,985 [2020-04-26 02:31:24.252] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 15,865 [2020-04-26 02:31:24.252] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 02:31:24.252] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,603 [2020-04-26 02:31:24.256] [jointLog] [warning] Only 1441032 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 02:31:24.256] [jointLog] [info] Mapping rate = 98.8786% [2020-04-26 02:31:24.256] [jointLog] [info] finished quantifyLibrary() [2020-04-26 02:31:24.259] [jointLog] [info] Starting optimizer [2020-04-26 02:31:24.280] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 02:31:24.289] [jointLog] [info] iteration = 0 | max rel diff. = 3390.4 [2020-04-26 02:31:24.678] [jointLog] [info] iteration = 100 | max rel diff. = 16.2757 [2020-04-26 02:31:25.065] [jointLog] [info] iteration = 200 | max rel diff. = 0.739917 [2020-04-26 02:31:25.453] [jointLog] [info] iteration = 300 | max rel diff. = 0.029064 [2020-04-26 02:31:25.840] [jointLog] [info] iteration = 400 | max rel diff. = 0.0447917 [2020-04-26 02:31:26.228] [jointLog] [info] iteration = 500 | max rel diff. = 0.0356961 [2020-04-26 02:31:26.337] [jointLog] [info] iteration = 530 | max rel diff. = 0.00903985 [2020-04-26 02:31:26.338] [jointLog] [info] Finished optimizer [2020-04-26 02:31:26.338] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_02/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_02/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.127.D9.infected.warm.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.127.D9.infected.warm.megan_R2.fq -o D9_03 -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/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.127.D9.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.127.D9.infected.warm.megan_R2.fq } ### [ output ] => { D9_03 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_03/logs [2020-04-26 02:39:56.262] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 02:39:56.262] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 02:39:56.262] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 02:39:56.262] [jointLog] [info] parsing read library format [2020-04-26 02:39:56.262] [jointLog] [info] There is 1 library. [2020-04-26 02:39:56.315] [jointLog] [info] Loading pufferfish index [2020-04-26 02:39:56.315] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.337 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 206.88 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 118.82 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.3871 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.732 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.3818 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 139.29 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.1058 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 233.11 us ----------------------------------------- [2020-04-26 02:39:56.508] [jointLog] [info] done [2020-04-26 02:39:56.508] [jointLog] [info] Index contained 40,435 targets [2020-04-26 02:39:56.520] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,736,570, hits per frag: 4.57983 processed 1,500,000 fragments hits: 5,222,446, hits per frag: 3.80291 processed 2,000,000 fragments hits: 6,963,372, hits per frag: 3.69985 [2020-04-26 02:40:03.430] [jointLog] [info] Computed 76,366 rich equivalence classes for further processing [2020-04-26 02:40:03.430] [jointLog] [info] Counted 2,319,185 total reads in the equivalence classes [2020-04-26 02:40:03.448] [jointLog] [info] Number of mappings discarded because of alignment score : 536,822 [2020-04-26 02:40:03.448] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,061 [2020-04-26 02:40:03.448] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 02:40:03.448] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,328 [2020-04-26 02:40:03.451] [jointLog] [warning] Only 2319185 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 02:40:03.451] [jointLog] [info] Mapping rate = 99.1791% [2020-04-26 02:40:03.451] [jointLog] [info] finished quantifyLibrary() [2020-04-26 02:40:03.452] [jointLog] [info] Starting optimizer [2020-04-26 02:40:03.474] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 02:40:03.479] [jointLog] [info] iteration = 0 | max rel diff. = 4684.72 [2020-04-26 02:40:03.767] [jointLog] [info] iteration = 100 | max rel diff. = 4.44958 [2020-04-26 02:40:04.049] [jointLog] [info] iteration = 200 | max rel diff. = 5.04084 [2020-04-26 02:40:04.332] [jointLog] [info] iteration = 300 | max rel diff. = 0.57508 [2020-04-26 02:40:04.617] [jointLog] [info] iteration = 400 | max rel diff. = 0.247405 [2020-04-26 02:40:04.896] [jointLog] [info] iteration = 500 | max rel diff. = 0.034264 [2020-04-26 02:40:05.173] [jointLog] [info] iteration = 600 | max rel diff. = 0.0973451 [2020-04-26 02:40:05.461] [jointLog] [info] iteration = 700 | max rel diff. = 0.0636478 [2020-04-26 02:40:05.746] [jointLog] [info] iteration = 800 | max rel diff. = 0.0262892 [2020-04-26 02:40:06.032] [jointLog] [info] iteration = 900 | max rel diff. = 0.0158562 [2020-04-26 02:40:06.316] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0172616 [2020-04-26 02:40:06.490] [jointLog] [info] iteration = 1,062 | max rel diff. = 0.00190054 [2020-04-26 02:40:06.491] [jointLog] [info] Finished optimizer [2020-04-26 02:40:06.491] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_03/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_03/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.132.D9.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.132.D9.infected.ambient.megan_R2.fq -o D9_04 -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/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.132.D9.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.132.D9.infected.ambient.megan_R2.fq } ### [ output ] => { D9_04 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_04/logs [2020-04-26 02:48:36.456] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 02:48:36.456] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 02:48:36.456] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 02:48:36.456] [jointLog] [info] parsing read library format [2020-04-26 02:48:36.456] [jointLog] [info] There is 1 library. [2020-04-26 02:48:36.516] [jointLog] [info] Loading pufferfish index [2020-04-26 02:48:36.516] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.541 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 197.14 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 117.64 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.5654 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.837 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4934 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 66.32 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.2974 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 222.26 us ----------------------------------------- [2020-04-26 02:48:36.638] [jointLog] [info] done [2020-04-26 02:48:36.638] [jointLog] [info] Index contained 40,435 targets [2020-04-26 02:48:36.652] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,222,581, hits per frag: 5.10121 processed 1,000,000 fragments hits: 4,444,740, hits per frag: 5.02998 processed 1,500,000 fragments hits: 6,667,108, hits per frag: 4.543 [2020-04-26 02:48:42.359] [jointLog] [info] Computed 81,660 rich equivalence classes for further processing [2020-04-26 02:48:42.359] [jointLog] [info] Counted 1,745,454 total reads in the equivalence classes [2020-04-26 02:48:42.379] [jointLog] [info] Number of mappings discarded because of alignment score : 733,451 [2020-04-26 02:48:42.379] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,154 [2020-04-26 02:48:42.379] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 02:48:42.379] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,582 [2020-04-26 02:48:42.383] [jointLog] [warning] Only 1745454 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 02:48:42.383] [jointLog] [info] Mapping rate = 98.6937% [2020-04-26 02:48:42.383] [jointLog] [info] finished quantifyLibrary() [2020-04-26 02:48:42.385] [jointLog] [info] Starting optimizer [2020-04-26 02:48:42.411] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 02:48:42.416] [jointLog] [info] iteration = 0 | max rel diff. = 3746.67 [2020-04-26 02:48:42.772] [jointLog] [info] iteration = 100 | max rel diff. = 4.45373 [2020-04-26 02:48:43.120] [jointLog] [info] iteration = 200 | max rel diff. = 13.6858 [2020-04-26 02:48:43.465] [jointLog] [info] iteration = 300 | max rel diff. = 0.675412 [2020-04-26 02:48:43.813] [jointLog] [info] iteration = 400 | max rel diff. = 0.0738747 [2020-04-26 02:48:44.166] [jointLog] [info] iteration = 500 | max rel diff. = 0.0218468 [2020-04-26 02:48:44.510] [jointLog] [info] iteration = 600 | max rel diff. = 0.235416 [2020-04-26 02:48:44.530] [jointLog] [info] iteration = 607 | max rel diff. = 0.00447046 [2020-04-26 02:48:44.532] [jointLog] [info] Finished optimizer [2020-04-26 02:48:44.532] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_04/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_04/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.151.D9.infected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.151.D9.infected.cold.megan_R2.fq -o D9_05 -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/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.151.D9.infected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.151.D9.infected.cold.megan_R2.fq } ### [ output ] => { D9_05 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_05/logs [2020-04-26 02:57:14.596] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 02:57:14.596] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 02:57:14.596] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 02:57:14.596] [jointLog] [info] parsing read library format [2020-04-26 02:57:14.596] [jointLog] [info] There is 1 library. ----------------------------------------- | Loading contig table | Time = 11.182 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 190.03 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 114.26 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.7615 ms ----------------------------------------- size = 21703191 [2020-04-26 02:57:14.657] [jointLog] [info] Loading pufferfish index Number of ones: 98889 Number of ones per inventory item: 512 [2020-04-26 02:57:14.657] [jointLog] [info] Loading dense pufferfish index. Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.036 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.3904 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 127.04 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.8265 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 218.11 us ----------------------------------------- [2020-04-26 02:57:14.838] [jointLog] [info] done [2020-04-26 02:57:14.838] [jointLog] [info] Index contained 40,435 targets [2020-04-26 02:57:14.852] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,686,655, hits per frag: 4.09182 processed 1,000,000 fragments hits: 3,373,613, hits per frag: 3.51108 processed 1,500,000 fragments hits: 5,055,038, hits per frag: 3.56197 processed 2,000,000 fragments hits: 6,746,121, hits per frag: 3.54472 processed 2,500,000 fragments hits: 8,435,484, hits per frag: 3.42969 processed 3,000,000 fragments hits: 10,121,367, hits per frag: 3.44555 processed 3,500,001 fragments hits: 11,815,831, hits per frag: 3.47862 processed 4,000,000 fragments hits: 13,501,118, hits per frag: 3.46238 [2020-04-26 02:57:26.391] [jointLog] [info] Computed 99,524 rich equivalence classes for further processing [2020-04-26 02:57:26.391] [jointLog] [info] Counted 4,278,215 total reads in the equivalence classes [2020-04-26 02:57:26.412] [jointLog] [info] Number of mappings discarded because of alignment score : 1,083,048 [2020-04-26 02:57:26.412] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 31,024 [2020-04-26 02:57:26.412] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 02:57:26.412] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,876 [2020-04-26 02:57:26.415] [jointLog] [warning] Only 4278215 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 02:57:26.415] [jointLog] [info] Mapping rate = 99.2387% [2020-04-26 02:57:26.415] [jointLog] [info] finished quantifyLibrary() [2020-04-26 02:57:26.417] [jointLog] [info] Starting optimizer [2020-04-26 02:57:26.454] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 02:57:26.465] [jointLog] [info] iteration = 0 | max rel diff. = 9620.68 [2020-04-26 02:57:26.963] [jointLog] [info] iteration = 100 | max rel diff. = 6.22337 [2020-04-26 02:57:27.467] [jointLog] [info] iteration = 200 | max rel diff. = 3.62951 [2020-04-26 02:57:27.971] [jointLog] [info] iteration = 300 | max rel diff. = 0.322306 [2020-04-26 02:57:28.474] [jointLog] [info] iteration = 400 | max rel diff. = 0.195409 [2020-04-26 02:57:28.980] [jointLog] [info] iteration = 500 | max rel diff. = 0.216216 [2020-04-26 02:57:29.485] [jointLog] [info] iteration = 600 | max rel diff. = 0.27544 [2020-04-26 02:57:29.989] [jointLog] [info] iteration = 700 | max rel diff. = 0.0640185 [2020-04-26 02:57:30.492] [jointLog] [info] iteration = 800 | max rel diff. = 0.0904471 [2020-04-26 02:57:30.750] [jointLog] [info] iteration = 852 | max rel diff. = 0.00831655 [2020-04-26 02:57:30.754] [jointLog] [info] Finished optimizer [2020-04-26 02:57:30.754] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_05/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_05/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.173.D9.infected.warm.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.173.D9.infected.warm.megan_R2.fq -o D9_06 -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/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.173.D9.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.173.D9.infected.warm.megan_R2.fq } ### [ output ] => { D9_06 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_06/logs [2020-04-26 03:06:01.010] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 03:06:01.010] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 03:06:01.010] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 03:06:01.010] [jointLog] [info] parsing read library format [2020-04-26 03:06:01.010] [jointLog] [info] There is 1 library. [2020-04-26 03:06:01.070] [jointLog] [info] Loading pufferfish index [2020-04-26 03:06:01.070] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.717 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 190.98 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 109.22 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.758 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.802 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.5175 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 115.23 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.6568 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 204.12 us ----------------------------------------- [2020-04-26 03:06:01.239] [jointLog] [info] done [2020-04-26 03:06:01.239] [jointLog] [info] Index contained 40,435 targets [2020-04-26 03:06:01.253] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,220,996, hits per frag: 5.06942 processed 1,000,001 fragments hits: 4,449,942, hits per frag: 4.98068 [2020-04-26 03:06:06.237] [jointLog] [info] Computed 53,980 rich equivalence classes for further processing [2020-04-26 03:06:06.237] [jointLog] [info] Counted 1,453,010 total reads in the equivalence classes [2020-04-26 03:06:06.256] [jointLog] [info] Number of mappings discarded because of alignment score : 568,187 [2020-04-26 03:06:06.256] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,457 [2020-04-26 03:06:06.256] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 03:06:06.256] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,199 [2020-04-26 03:06:06.260] [jointLog] [warning] Only 1453010 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 03:06:06.260] [jointLog] [info] Mapping rate = 98.6031% [2020-04-26 03:06:06.260] [jointLog] [info] finished quantifyLibrary() [2020-04-26 03:06:06.262] [jointLog] [info] Starting optimizer [2020-04-26 03:06:06.279] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 03:06:06.285] [jointLog] [info] iteration = 0 | max rel diff. = 3116.02 [2020-04-26 03:06:06.539] [jointLog] [info] iteration = 100 | max rel diff. = 4.49759 [2020-04-26 03:06:06.785] [jointLog] [info] iteration = 200 | max rel diff. = 4.80523 [2020-04-26 03:06:07.031] [jointLog] [info] iteration = 300 | max rel diff. = 1.3627 [2020-04-26 03:06:07.282] [jointLog] [info] iteration = 400 | max rel diff. = 0.155924 [2020-04-26 03:06:07.470] [jointLog] [info] iteration = 477 | max rel diff. = 0.00364994 [2020-04-26 03:06:07.471] [jointLog] [info] Finished optimizer [2020-04-26 03:06:07.471] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_06/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_06/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.178.D9.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.178.D9.infected.ambient.megan_R2.fq -o D9_07 -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/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.178.D9.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.178.D9.infected.ambient.megan_R2.fq } ### [ output ] => { D9_07 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_07/logs [2020-04-26 03:14:38.048] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 03:14:38.048] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 03:14:38.048] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 03:14:38.048] [jointLog] [info] parsing read library format [2020-04-26 03:14:38.048] [jointLog] [info] There is 1 library. [2020-04-26 03:14:38.101] [jointLog] [info] Loading pufferfish index [2020-04-26 03:14:38.101] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.24 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 209.77 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 115.73 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.4353 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.957 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4145 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 154.37 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.7926 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 252.5 us ----------------------------------------- [2020-04-26 03:14:38.310] [jointLog] [info] done [2020-04-26 03:14:38.310] [jointLog] [info] Index contained 40,435 targets [2020-04-26 03:14:38.323] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,306,114, hits per frag: 6.46264 processed 1,000,000 fragments hits: 4,614,616, hits per frag: 5.30207 processed 1,500,001 fragments hits: 6,929,800, hits per frag: 5.10379 processed 2,000,000 fragments hits: 9,242,901, hits per frag: 4.94117 processed 2,500,000 fragments hits: 11,556,117, hits per frag: 4.87967 processed 3,000,000 fragments hits: 13,862,633, hits per frag: 4.75254 [2020-04-26 03:14:48.071] [jointLog] [info] Computed 93,477 rich equivalence classes for further processing [2020-04-26 03:14:48.071] [jointLog] [info] Counted 3,186,382 total reads in the equivalence classes [2020-04-26 03:14:48.091] [jointLog] [info] Number of mappings discarded because of alignment score : 1,265,424 [2020-04-26 03:14:48.091] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 26,413 [2020-04-26 03:14:48.091] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 03:14:48.091] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,312 [2020-04-26 03:14:48.095] [jointLog] [warning] Only 3186382 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 03:14:48.095] [jointLog] [info] Mapping rate = 99.1442% [2020-04-26 03:14:48.095] [jointLog] [info] finished quantifyLibrary() [2020-04-26 03:14:48.096] [jointLog] [info] Starting optimizer [2020-04-26 03:14:48.121] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 03:14:48.131] [jointLog] [info] iteration = 0 | max rel diff. = 7296.02 [2020-04-26 03:14:48.605] [jointLog] [info] iteration = 100 | max rel diff. = 13.497 [2020-04-26 03:14:49.068] [jointLog] [info] iteration = 200 | max rel diff. = 1.61723 [2020-04-26 03:14:49.526] [jointLog] [info] iteration = 300 | max rel diff. = 0.29557 [2020-04-26 03:14:49.989] [jointLog] [info] iteration = 400 | max rel diff. = 1.25413 [2020-04-26 03:14:50.456] [jointLog] [info] iteration = 500 | max rel diff. = 0.13444 [2020-04-26 03:14:50.629] [jointLog] [info] iteration = 539 | max rel diff. = 0.00644757 [2020-04-26 03:14:50.630] [jointLog] [info] Finished optimizer [2020-04-26 03:14:50.630] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_07/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_07/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.425.D26.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.425.D26.uninfected.cold.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/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.425.D26.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.425.D26.uninfected.cold.megan_R2.fq } ### [ output ] => { D26_01 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D26_01/logs [2020-04-26 03:23:20.799] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 03:23:20.799] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 03:23:20.799] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 03:23:20.799] [jointLog] [info] parsing read library format [2020-04-26 03:23:20.800] [jointLog] [info] There is 1 library. [2020-04-26 03:23:20.859] [jointLog] [info] Loading pufferfish index [2020-04-26 03:23:20.859] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.654 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 203.13 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 111.82 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.4916 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.753 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4464 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 110.98 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.3005 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 224.61 us ----------------------------------------- [2020-04-26 03:23:21.025] [jointLog] [info] done [2020-04-26 03:23:21.025] [jointLog] [info] Index contained 40,435 targets [2020-04-26 03:23:21.039] [jointLog] [info] Number of decoys : 0 [2020-04-26 03:23:21.826] [jointLog] [info] Computed 12,723 rich equivalence classes for further processing [2020-04-26 03:23:21.826] [jointLog] [info] Counted 75,333 total reads in the equivalence classes [2020-04-26 03:23:21.858] [jointLog] [info] Number of mappings discarded because of alignment score : 63,773 [2020-04-26 03:23:21.858] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,953 [2020-04-26 03:23:21.858] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 03:23:21.858] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 724 [2020-04-26 03:23:21.861] [jointLog] [warning] Only 75333 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 03:23:21.861] [jointLog] [info] Mapping rate = 95.7059% [2020-04-26 03:23:21.861] [jointLog] [info] finished quantifyLibrary() [2020-04-26 03:23:21.862] [jointLog] [info] Starting optimizer [2020-04-26 03:23:21.874] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 03:23:21.875] [jointLog] [info] iteration = 0 | max rel diff. = 164.855 [2020-04-26 03:23:21.969] [jointLog] [info] iteration = 100 | max rel diff. = 0.0556853 [2020-04-26 03:23:22.023] [jointLog] [info] iteration = 161 | max rel diff. = 0.00154717 [2020-04-26 03:23:22.023] [jointLog] [info] Finished optimizer [2020-04-26 03:23:22.023] [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/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D26_01/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.427.D26.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.427.D26.uninfected.cold.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/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.427.D26.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.427.D26.uninfected.cold.megan_R2.fq } ### [ output ] => { D26_02 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D26_02/logs [2020-04-26 03:31:52.547] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 03:31:52.547] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 03:31:52.547] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 03:31:52.547] [jointLog] [info] parsing read library format [2020-04-26 03:31:52.547] [jointLog] [info] There is 1 library. ----------------------------------------- | Loading contig table | Time = 11.496 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 203.56 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 107.08 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.3672 ms ----------------------------------------- size = 21703191 [2020-04-26 03:31:52.609] [jointLog] [info] Loading pufferfish index [2020-04-26 03:31:52.609] [jointLog] [info] Loading dense pufferfish index. Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.964 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.3497 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 64.519 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.4192 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 91.034 us ----------------------------------------- [2020-04-26 03:31:52.726] [jointLog] [info] done [2020-04-26 03:31:52.726] [jointLog] [info] Index contained 40,435 targets [2020-04-26 03:31:52.740] [jointLog] [info] Number of decoys : 0 [2020-04-26 03:31:53.555] [jointLog] [info] Computed 8,621 rich equivalence classes for further processing [2020-04-26 03:31:53.556] [jointLog] [info] Counted 49,503 total reads in the equivalence classes [2020-04-26 03:31:53.590] [jointLog] [info] Number of mappings discarded because of alignment score : 49,151 [2020-04-26 03:31:53.590] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,787 [2020-04-26 03:31:53.590] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 03:31:53.590] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 268 [2020-04-26 03:31:53.593] [jointLog] [warning] Only 49503 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 03:31:53.593] [jointLog] [info] Mapping rate = 87.3115% [2020-04-26 03:31:53.593] [jointLog] [info] finished quantifyLibrary() [2020-04-26 03:31:53.595] [jointLog] [info] Starting optimizer [2020-04-26 03:31:53.606] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 03:31:53.610] [jointLog] [info] iteration = 0 | max rel diff. = 119.489 [2020-04-26 03:31:53.683] [jointLog] [info] iteration = 100 | max rel diff. = 0.230932 [2020-04-26 03:31:53.749] [jointLog] [info] iteration = 200 | max rel diff. = 0.330031 [2020-04-26 03:31:53.818] [jointLog] [info] iteration = 300 | max rel diff. = 0.0206814 [2020-04-26 03:31:53.841] [jointLog] [info] iteration = 336 | max rel diff. = 0.00983168 [2020-04-26 03:31:53.842] [jointLog] [info] Finished optimizer [2020-04-26 03:31:53.842] [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/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D26_02/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.445.D26.infected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.445.D26.infected.cold.megan_R2.fq -o D26_03 -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/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.445.D26.infected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.445.D26.infected.cold.megan_R2.fq } ### [ output ] => { D26_03 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D26_03/logs [2020-04-26 03:40:24.289] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 03:40:24.289] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 03:40:24.289] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 03:40:24.289] [jointLog] [info] parsing read library format [2020-04-26 03:40:24.289] [jointLog] [info] There is 1 library. ----------------------------------------- | Loading contig table | Time = 11.202 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 190.01 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 106.55 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.5044 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 [2020-04-26 03:40:24.351] [jointLog] [info] Loading pufferfish index [2020-04-26 03:40:24.351] [jointLog] [info] Loading dense pufferfish index. Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.442 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4322 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 84.109 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.6021 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 197.67 us ----------------------------------------- [2020-04-26 03:40:24.488] [jointLog] [info] done [2020-04-26 03:40:24.488] [jointLog] [info] Index contained 40,435 targets [2020-04-26 03:40:24.502] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,949,187, hits per frag: 4.81441 processed 1,000,000 fragments hits: 3,892,862, hits per frag: 4.20613 processed 1,500,001 fragments hits: 5,841,920, hits per frag: 4.04376 processed 2,000,000 fragments hits: 7,778,536, hits per frag: 4.15987 processed 2,500,000 fragments hits: 9,722,277, hits per frag: 3.97552 [2020-04-26 03:40:31.641] [jointLog] [info] Computed 81,264 rich equivalence classes for further processing [2020-04-26 03:40:31.641] [jointLog] [info] Counted 2,537,571 total reads in the equivalence classes [2020-04-26 03:40:31.661] [jointLog] [info] Number of mappings discarded because of alignment score : 763,753 [2020-04-26 03:40:31.661] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 25,277 [2020-04-26 03:40:31.661] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 03:40:31.661] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,111 [2020-04-26 03:40:31.665] [jointLog] [warning] Only 2537571 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 03:40:31.665] [jointLog] [info] Mapping rate = 98.9787% [2020-04-26 03:40:31.665] [jointLog] [info] finished quantifyLibrary() [2020-04-26 03:40:31.667] [jointLog] [info] Starting optimizer [2020-04-26 03:40:31.690] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 03:40:31.695] [jointLog] [info] iteration = 0 | max rel diff. = 5796.83 [2020-04-26 03:40:32.015] [jointLog] [info] iteration = 100 | max rel diff. = 8.1899 [2020-04-26 03:40:32.329] [jointLog] [info] iteration = 200 | max rel diff. = 3.8306 [2020-04-26 03:40:32.652] [jointLog] [info] iteration = 300 | max rel diff. = 7.41525 [2020-04-26 03:40:32.975] [jointLog] [info] iteration = 400 | max rel diff. = 3.06393 [2020-04-26 03:40:33.295] [jointLog] [info] iteration = 500 | max rel diff. = 0.139388 [2020-04-26 03:40:33.615] [jointLog] [info] iteration = 600 | max rel diff. = 0.0488443 [2020-04-26 03:40:33.941] [jointLog] [info] iteration = 700 | max rel diff. = 0.0278767 [2020-04-26 03:40:34.242] [jointLog] [info] iteration = 797 | max rel diff. = 0.00852398 [2020-04-26 03:40:34.243] [jointLog] [info] Finished optimizer [2020-04-26 03:40:34.243] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D26_03/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D26_03/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.463.D26.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.463.D26.infected.ambient.megan_R2.fq -o D26_04 -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/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.463.D26.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.463.D26.infected.ambient.megan_R2.fq } ### [ output ] => { D26_04 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D26_04/logs [2020-04-26 03:49:04.991] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 03:49:04.991] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 03:49:04.991] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 03:49:04.991] [jointLog] [info] parsing read library format [2020-04-26 03:49:04.991] [jointLog] [info] There is 1 library. [2020-04-26 03:49:05.051] [jointLog] [info] Loading pufferfish index [2020-04-26 03:49:05.051] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.459 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 187.25 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 105.69 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.6651 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.9 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.2291 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 163.25 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.272 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 231.8 us ----------------------------------------- [2020-04-26 03:49:05.268] [jointLog] [info] done [2020-04-26 03:49:05.268] [jointLog] [info] Index contained 40,435 targets [2020-04-26 03:49:05.283] [jointLog] [info] Number of decoys : 0 [2020-04-26 03:49:06.811] [jointLog] [info] Computed 4,767 rich equivalence classes for further processing [2020-04-26 03:49:06.811] [jointLog] [info] Counted 26,916 total reads in the equivalence classes [2020-04-26 03:49:06.852] [jointLog] [info] Number of mappings discarded because of alignment score : 21,743 [2020-04-26 03:49:06.852] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,769 [2020-04-26 03:49:06.852] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 03:49:06.852] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 79 [2020-04-26 03:49:06.856] [jointLog] [warning] Only 26916 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 03:49:06.856] [jointLog] [info] Mapping rate = 89.1878% [2020-04-26 03:49:06.856] [jointLog] [info] finished quantifyLibrary() [2020-04-26 03:49:06.857] [jointLog] [info] Starting optimizer [2020-04-26 03:49:06.871] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 03:49:06.873] [jointLog] [info] iteration = 0 | max rel diff. = 64.4271 [2020-04-26 03:49:06.938] [jointLog] [info] iteration = 100 | max rel diff. = 0.00287292 [2020-04-26 03:49:06.939] [jointLog] [info] Finished optimizer [2020-04-26 03:49:06.939] [jointLog] [info] writing output [2020-04-26 03:49:06.992] [jointLog] [warning] NOTE: Read Lib [[ /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.463.D26.infected.ambient.megan_R1.fq, /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.463.D26.infected.ambient.megan_R2.fq]] : Detected a *potential* strand bias > 1% in an unstranded protocol check the file: D26_04/lib_format_counts.json for details CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D26_04/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D26_04/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.481.D26.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.481.D26.infected.ambient.megan_R2.fq -o D26_05 -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/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.481.D26.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.481.D26.infected.ambient.megan_R2.fq } ### [ output ] => { D26_05 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D26_05/logs [2020-04-26 03:57:37.504] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 03:57:37.504] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 03:57:37.504] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 03:57:37.504] [jointLog] [info] parsing read library format [2020-04-26 03:57:37.504] [jointLog] [info] There is 1 library. ----------------------------------------- | Loading contig table | Time = 10.576 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 191.41 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 105 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.8908 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 [2020-04-26 03:57:37.565] [jointLog] [info] Loading pufferfish index [2020-04-26 03:57:37.565] [jointLog] [info] Loading dense pufferfish index. Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.548 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.109 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 29.788 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.4614 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 196.97 us ----------------------------------------- [2020-04-26 03:57:37.648] [jointLog] [info] done [2020-04-26 03:57:37.648] [jointLog] [info] Index contained 40,435 targets [2020-04-26 03:57:37.661] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,629,882, hits per frag: 3.55543 processed 1,000,000 fragments hits: 3,259,678, hits per frag: 3.84357 [2020-04-26 03:57:41.607] [jointLog] [info] Computed 70,026 rich equivalence classes for further processing [2020-04-26 03:57:41.607] [jointLog] [info] Counted 1,295,947 total reads in the equivalence classes [2020-04-26 03:57:41.624] [jointLog] [info] Number of mappings discarded because of alignment score : 406,709 [2020-04-26 03:57:41.624] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,984 [2020-04-26 03:57:41.624] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 03:57:41.624] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,002 [2020-04-26 03:57:41.628] [jointLog] [warning] Only 1295947 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 03:57:41.628] [jointLog] [info] Mapping rate = 98.1521% [2020-04-26 03:57:41.628] [jointLog] [info] finished quantifyLibrary() [2020-04-26 03:57:41.629] [jointLog] [info] Starting optimizer [2020-04-26 03:57:41.651] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 03:57:41.655] [jointLog] [info] iteration = 0 | max rel diff. = 3060.57 [2020-04-26 03:57:41.889] [jointLog] [info] iteration = 100 | max rel diff. = 7.40287 [2020-04-26 03:57:42.122] [jointLog] [info] iteration = 200 | max rel diff. = 0.190008 [2020-04-26 03:57:42.355] [jointLog] [info] iteration = 300 | max rel diff. = 0.241952 [2020-04-26 03:57:42.588] [jointLog] [info] iteration = 400 | max rel diff. = 2.06599 [2020-04-26 03:57:42.806] [jointLog] [info] iteration = 500 | max rel diff. = 15.6906 [2020-04-26 03:57:42.824] [jointLog] [info] iteration = 509 | max rel diff. = 0.00650112 [2020-04-26 03:57:42.825] [jointLog] [info] Finished optimizer [2020-04-26 03:57:42.825] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D26_05/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D26_05/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.485.D26.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.485.D26.infected.ambient.megan_R2.fq -o D26_06 -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/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.485.D26.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.485.D26.infected.ambient.megan_R2.fq } ### [ output ] => { D26_06 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D26_06/logs [2020-04-26 04:06:13.344] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 04:06:13.344] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 04:06:13.344] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 04:06:13.344] [jointLog] [info] parsing read library format [2020-04-26 04:06:13.344] [jointLog] [info] There is 1 library. [2020-04-26 04:06:13.404] [jointLog] [info] Loading pufferfish index [2020-04-26 04:06:13.404] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.159 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 187.79 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 106.31 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.5367 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.252 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4851 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 99.796 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.7866 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 217.98 us ----------------------------------------- [2020-04-26 04:06:13.558] [jointLog] [info] done [2020-04-26 04:06:13.558] [jointLog] [info] Index contained 40,435 targets [2020-04-26 04:06:13.572] [jointLog] [info] Number of decoys : 0  processed 500,001 fragments hits: 2,018,579, hits per frag: 5.01737 processed 1,000,000 fragments hits: 4,039,833, hits per frag: 4.50368 processed 1,500,000 fragments hits: 6,060,456, hits per frag: 4.19469 [2020-04-26 04:06:19.574] [jointLog] [info] Computed 62,758 rich equivalence classes for further processing [2020-04-26 04:06:19.574] [jointLog] [info] Counted 1,711,628 total reads in the equivalence classes [2020-04-26 04:06:19.594] [jointLog] [info] Number of mappings discarded because of alignment score : 553,509 [2020-04-26 04:06:19.594] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 16,872 [2020-04-26 04:06:19.594] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 04:06:19.594] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,511 [2020-04-26 04:06:19.597] [jointLog] [warning] Only 1711628 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 04:06:19.597] [jointLog] [info] Mapping rate = 98.9712% [2020-04-26 04:06:19.597] [jointLog] [info] finished quantifyLibrary() [2020-04-26 04:06:19.599] [jointLog] [info] Starting optimizer [2020-04-26 04:06:19.622] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 04:06:19.627] [jointLog] [info] iteration = 0 | max rel diff. = 4011.83 [2020-04-26 04:06:19.891] [jointLog] [info] iteration = 100 | max rel diff. = 0.988338 [2020-04-26 04:06:20.150] [jointLog] [info] iteration = 200 | max rel diff. = 2.29269 [2020-04-26 04:06:20.407] [jointLog] [info] iteration = 300 | max rel diff. = 0.655287 [2020-04-26 04:06:20.661] [jointLog] [info] iteration = 400 | max rel diff. = 0.0802813 [2020-04-26 04:06:20.917] [jointLog] [info] iteration = 500 | max rel diff. = 0.455623 [2020-04-26 04:06:20.925] [jointLog] [info] iteration = 504 | max rel diff. = 0.00401271 [2020-04-26 04:06:20.926] [jointLog] [info] Finished optimizer [2020-04-26 04:06:20.926] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D26_06/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D26_06/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.72.D9.infected.warm.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.72.D9.infected.warm.megan_R2.fq -o D9_08 -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/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.72.D9.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.72.D9.infected.warm.megan_R2.fq } ### [ output ] => { D9_08 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_08/logs [2020-04-26 04:14:51.493] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 04:14:51.494] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 04:14:51.494] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 04:14:51.494] [jointLog] [info] parsing read library format [2020-04-26 04:14:51.494] [jointLog] [info] There is 1 library. [2020-04-26 04:14:51.551] [jointLog] [info] Loading pufferfish index [2020-04-26 04:14:51.551] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 10.638 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 188.61 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 106.18 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.6077 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.905 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.3678 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 123.31 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.7219 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 210.96 us ----------------------------------------- [2020-04-26 04:14:51.728] [jointLog] [info] done [2020-04-26 04:14:51.728] [jointLog] [info] Index contained 40,435 targets [2020-04-26 04:14:51.741] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,671,487, hits per frag: 5.6683 processed 1,000,000 fragments hits: 5,359,046, hits per frag: 5.47942 processed 1,500,000 fragments hits: 8,040,822, hits per frag: 5.43076 [2020-04-26 04:14:57.623] [jointLog] [info] Computed 63,901 rich equivalence classes for further processing [2020-04-26 04:14:57.623] [jointLog] [info] Counted 1,547,156 total reads in the equivalence classes [2020-04-26 04:14:57.649] [jointLog] [info] Number of mappings discarded because of alignment score : 744,606 [2020-04-26 04:14:57.649] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 20,255 [2020-04-26 04:14:57.649] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 04:14:57.649] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,061 [2020-04-26 04:14:57.653] [jointLog] [warning] Only 1547156 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 04:14:57.653] [jointLog] [info] Mapping rate = 98.6772% [2020-04-26 04:14:57.653] [jointLog] [info] finished quantifyLibrary() [2020-04-26 04:14:57.654] [jointLog] [info] Starting optimizer [2020-04-26 04:14:57.674] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 04:14:57.680] [jointLog] [info] iteration = 0 | max rel diff. = 3444.94 [2020-04-26 04:14:58.003] [jointLog] [info] iteration = 100 | max rel diff. = 1.73415 [2020-04-26 04:14:58.319] [jointLog] [info] iteration = 200 | max rel diff. = 0.246043 [2020-04-26 04:14:58.640] [jointLog] [info] iteration = 300 | max rel diff. = 1.2273 [2020-04-26 04:14:58.956] [jointLog] [info] iteration = 400 | max rel diff. = 0.0154456 [2020-04-26 04:14:59.276] [jointLog] [info] iteration = 500 | max rel diff. = 0.0224559 [2020-04-26 04:14:59.565] [jointLog] [info] iteration = 592 | max rel diff. = 0.0026684 [2020-04-26 04:14:59.566] [jointLog] [info] Finished optimizer [2020-04-26 04:14:59.566] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_08/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_08/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.73.D9.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.73.D9.uninfected.cold.megan_R2.fq -o D9_09 -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/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.73.D9.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D26/20200413.C_bairdi.73.D9.uninfected.cold.megan_R2.fq } ### [ output ] => { D9_09 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_09/logs [2020-04-26 04:23:29.633] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 04:23:29.633] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 04:23:29.633] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 04:23:29.633] [jointLog] [info] parsing read library format [2020-04-26 04:23:29.633] [jointLog] [info] There is 1 library. [2020-04-26 04:23:29.686] [jointLog] [info] Loading pufferfish index [2020-04-26 04:23:29.686] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.087 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 205.91 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 117.59 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.9081 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.751 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4378 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 76.878 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.8232 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 112.22 us ----------------------------------------- [2020-04-26 04:23:29.816] [jointLog] [info] done [2020-04-26 04:23:29.816] [jointLog] [info] Index contained 40,435 targets [2020-04-26 04:23:29.827] [jointLog] [info] Number of decoys : 0 [2020-04-26 04:23:30.968] [jointLog] [info] Computed 8,752 rich equivalence classes for further processing [2020-04-26 04:23:30.968] [jointLog] [info] Counted 91,344 total reads in the equivalence classes [2020-04-26 04:23:30.988] [jointLog] [info] Number of mappings discarded because of alignment score : 98,787 [2020-04-26 04:23:30.988] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 9,280 [2020-04-26 04:23:30.988] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 04:23:30.988] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 518 [2020-04-26 04:23:30.991] [jointLog] [warning] Only 91344 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 04:23:30.991] [jointLog] [info] Mapping rate = 89.7518% [2020-04-26 04:23:30.991] [jointLog] [info] finished quantifyLibrary() [2020-04-26 04:23:30.993] [jointLog] [info] Starting optimizer [2020-04-26 04:23:31.006] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 04:23:31.008] [jointLog] [info] iteration = 0 | max rel diff. = 223.417 [2020-04-26 04:23:31.099] [jointLog] [info] iteration = 100 | max rel diff. = 0.173575 [2020-04-26 04:23:31.156] [jointLog] [info] iteration = 167 | max rel diff. = 0.0070097 [2020-04-26 04:23:31.157] [jointLog] [info] Finished optimizer [2020-04-26 04:23:31.157] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_09/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_09/quant.sf.genes