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/infected-uninfected/20200413.C_bairdi.113.D9.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.113.D9.uninfected.cold.megan_R2.fq -o uninfected_01 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.113.D9.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.113.D9.uninfected.cold.megan_R2.fq } ### [ output ] => { uninfected_01 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to uninfected_01/logs [2020-04-25 20:13:19.341] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 20:13:19.341] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 20:13:19.341] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 20:13:19.341] [jointLog] [info] parsing read library format [2020-04-25 20:13:19.341] [jointLog] [info] There is 1 library. [2020-04-25 20:13:19.393] [jointLog] [info] Loading pufferfish index [2020-04-25 20:13:19.393] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 76.238 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 18.488 ms ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 11.667 ms ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 95.35 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 96.215 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 57.103 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 143.35 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 43.648 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 14.911 ms ----------------------------------------- [2020-04-25 20:13:19.986] [jointLog] [info] done [2020-04-25 20:13:19.986] [jointLog] [info] Index contained 40,435 targets [2020-04-25 20:13:20.011] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,588,136, hits per frag: 3.74432 processed 1,000,000 fragments hits: 3,173,653, hits per frag: 4.02466 processed 1,500,000 fragments hits: 4,765,763, hits per frag: 3.22662 processed 2,000,000 fragments hits: 6,348,370, hits per frag: 3.27161 [2020-04-25 20:13:26.499] [jointLog] [info] Computed 73,208 rich equivalence classes for further processing [2020-04-25 20:13:26.499] [jointLog] [info] Counted 2,278,269 total reads in the equivalence classes [2020-04-25 20:13:26.515] [jointLog] [info] Number of mappings discarded because of alignment score : 461,132 [2020-04-25 20:13:26.515] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,736 [2020-04-25 20:13:26.515] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 20:13:26.515] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,351 [2020-04-25 20:13:26.518] [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. [2020-04-25 20:13:26.518] [jointLog] [info] Mapping rate = 99.1406% [2020-04-25 20:13:26.518] [jointLog] [info] finished quantifyLibrary() [2020-04-25 20:13:26.520] [jointLog] [info] Starting optimizer [2020-04-25 20:13:26.543] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 20:13:26.548] [jointLog] [info] iteration = 0 | max rel diff. = 5253.15 [2020-04-25 20:13:26.832] [jointLog] [info] iteration = 100 | max rel diff. = 3.44095 [2020-04-25 20:13:27.107] [jointLog] [info] iteration = 200 | max rel diff. = 13.1233 [2020-04-25 20:13:27.379] [jointLog] [info] iteration = 300 | max rel diff. = 0.347319 [2020-04-25 20:13:27.650] [jointLog] [info] iteration = 400 | max rel diff. = 0.107838 [2020-04-25 20:13:27.924] [jointLog] [info] iteration = 500 | max rel diff. = 3.50026 [2020-04-25 20:13:28.202] [jointLog] [info] iteration = 600 | max rel diff. = 0.130658 [2020-04-25 20:13:28.482] [jointLog] [info] iteration = 700 | max rel diff. = 0.0500265 [2020-04-25 20:13:28.757] [jointLog] [info] iteration = 800 | max rel diff. = 0.0270105 [2020-04-25 20:13:28.942] [jointLog] [info] iteration = 868 | max rel diff. = 0.00943807 [2020-04-25 20:13:28.944] [jointLog] [info] Finished optimizer [2020-04-25 20:13:28.944] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl uninfected_01/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > uninfected_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/infected-uninfected/20200413.C_bairdi.118.D9.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.118.D9.infected.ambient.megan_R2.fq -o infected_01 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.118.D9.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.118.D9.infected.ambient.megan_R2.fq } ### [ output ] => { infected_01 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_01/logs [2020-04-25 20:21:59.304] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 20:21:59.304] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 20:21:59.304] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 20:21:59.304] [jointLog] [info] parsing read library format [2020-04-25 20:21:59.304] [jointLog] [info] There is 1 library. [2020-04-25 20:21:59.356] [jointLog] [info] Loading pufferfish index [2020-04-25 20:21:59.356] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 72.034 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 272.86 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 144.86 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 175.02 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 146 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 120 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 139.54 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 56.81 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 505.1 us ----------------------------------------- [2020-04-25 20:22:00.067] [jointLog] [info] done [2020-04-25 20:22:00.067] [jointLog] [info] Index contained 40,435 targets [2020-04-25 20:22:00.086] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,774,655, hits per frag: 6.09193 processed 1,000,000 fragments hits: 5,560,790, hits per frag: 5.81668 [2020-04-25 20:22:06.068] [jointLog] [info] Computed 68,086 rich equivalence classes for further processing [2020-04-25 20:22:06.068] [jointLog] [info] Counted 1,441,032 total reads in the equivalence classes [2020-04-25 20:22:06.089] [jointLog] [info] Number of mappings discarded because of alignment score : 600,984 [2020-04-25 20:22:06.089] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 15,865 [2020-04-25 20:22:06.089] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 20:22:06.089] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,603 [2020-04-25 20:22:06.093] [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. [2020-04-25 20:22:06.093] [jointLog] [info] Mapping rate = 98.8786% [2020-04-25 20:22:06.093] [jointLog] [info] finished quantifyLibrary() [2020-04-25 20:22:06.095] [jointLog] [info] Starting optimizer [2020-04-25 20:22:06.118] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 20:22:06.126] [jointLog] [info] iteration = 0 | max rel diff. = 3390.6 [2020-04-25 20:22:06.516] [jointLog] [info] iteration = 100 | max rel diff. = 20.3512 [2020-04-25 20:22:06.903] [jointLog] [info] iteration = 200 | max rel diff. = 6.02321 [2020-04-25 20:22:07.289] [jointLog] [info] iteration = 300 | max rel diff. = 0.0393583 [2020-04-25 20:22:07.677] [jointLog] [info] iteration = 400 | max rel diff. = 0.0447478 [2020-04-25 20:22:08.063] [jointLog] [info] iteration = 500 | max rel diff. = 0.0350777 [2020-04-25 20:22:08.445] [jointLog] [info] iteration = 600 | max rel diff. = 0.0463482 [2020-04-25 20:22:08.524] [jointLog] [info] iteration = 621 | max rel diff. = 0.0079067 [2020-04-25 20:22:08.526] [jointLog] [info] Finished optimizer [2020-04-25 20:22:08.526] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_01/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_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/infected-uninfected/20200413.C_bairdi.127.D9.infected.warm.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.127.D9.infected.warm.megan_R2.fq -o infected_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/infected-uninfected/20200413.C_bairdi.127.D9.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.127.D9.infected.warm.megan_R2.fq } ### [ output ] => { infected_02 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_02/logs [2020-04-25 20:30:39.229] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 20:30:39.229] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 20:30:39.229] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 20:30:39.229] [jointLog] [info] parsing read library format [2020-04-25 20:30:39.229] [jointLog] [info] There is 1 library. [2020-04-25 20:30:39.294] [jointLog] [info] Loading pufferfish index [2020-04-25 20:30:39.294] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 18.31 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 219.36 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 126.25 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 60.053 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 65.714 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 3.2388 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 122.79 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 67.198 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 650.62 us ----------------------------------------- [2020-04-25 20:30:39.633] [jointLog] [info] done [2020-04-25 20:30:39.633] [jointLog] [info] Index contained 40,435 targets [2020-04-25 20:30:39.655] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,736,942, hits per frag: 4.6705 processed 1,000,000 fragments hits: 3,476,400, hits per frag: 3.84027 processed 1,500,000 fragments hits: 5,222,884, hits per frag: 3.54844 processed 2,000,000 fragments hits: 6,963,670, hits per frag: 3.58763 [2020-04-25 20:30:45.874] [jointLog] [info] Computed 76,452 rich equivalence classes for further processing [2020-04-25 20:30:45.874] [jointLog] [info] Counted 2,319,185 total reads in the equivalence classes [2020-04-25 20:30:45.893] [jointLog] [info] Number of mappings discarded because of alignment score : 536,820 [2020-04-25 20:30:45.893] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,061 [2020-04-25 20:30:45.893] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 20:30:45.893] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,328 [2020-04-25 20:30:45.897] [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. [2020-04-25 20:30:45.897] [jointLog] [info] Mapping rate = 99.1791% [2020-04-25 20:30:45.897] [jointLog] [info] finished quantifyLibrary() [2020-04-25 20:30:45.899] [jointLog] [info] Starting optimizer [2020-04-25 20:30:45.920] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 20:30:45.925] [jointLog] [info] iteration = 0 | max rel diff. = 4684.76 [2020-04-25 20:30:46.219] [jointLog] [info] iteration = 100 | max rel diff. = 3.31511 [2020-04-25 20:30:46.502] [jointLog] [info] iteration = 200 | max rel diff. = 1.94852 [2020-04-25 20:30:46.789] [jointLog] [info] iteration = 300 | max rel diff. = 0.490505 [2020-04-25 20:30:47.075] [jointLog] [info] iteration = 400 | max rel diff. = 0.0589214 [2020-04-25 20:30:47.362] [jointLog] [info] iteration = 500 | max rel diff. = 0.302249 [2020-04-25 20:30:47.654] [jointLog] [info] iteration = 600 | max rel diff. = 0.155543 [2020-04-25 20:30:47.946] [jointLog] [info] iteration = 700 | max rel diff. = 0.059642 [2020-04-25 20:30:48.232] [jointLog] [info] iteration = 800 | max rel diff. = 0.13392 [2020-04-25 20:30:48.522] [jointLog] [info] iteration = 900 | max rel diff. = 0.00822358 [2020-04-25 20:30:48.526] [jointLog] [info] Finished optimizer [2020-04-25 20:30:48.526] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_02/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_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/infected-uninfected/20200413.C_bairdi.132.D9.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.132.D9.infected.ambient.megan_R2.fq -o infected_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/infected-uninfected/20200413.C_bairdi.132.D9.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.132.D9.infected.ambient.megan_R2.fq } ### [ output ] => { infected_03 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_03/logs [2020-04-25 20:39:19.031] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 20:39:19.031] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 20:39:19.031] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 20:39:19.031] [jointLog] [info] parsing read library format [2020-04-25 20:39:19.031] [jointLog] [info] There is 1 library. [2020-04-25 20:39:19.090] [jointLog] [info] Loading pufferfish index [2020-04-25 20:39:19.090] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.245 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 193.52 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 110.11 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.8627 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.059 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4883 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 28.588 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.6936 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 193.5 us ----------------------------------------- [2020-04-25 20:39:19.173] [jointLog] [info] done [2020-04-25 20:39:19.173] [jointLog] [info] Index contained 40,435 targets [2020-04-25 20:39:19.186] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,222,639, hits per frag: 5.63447 processed 1,000,001 fragments hits: 4,445,522, hits per frag: 5.27024 processed 1,500,000 fragments hits: 6,667,711, hits per frag: 4.7746 [2020-04-25 20:39:24.890] [jointLog] [info] Computed 81,782 rich equivalence classes for further processing [2020-04-25 20:39:24.890] [jointLog] [info] Counted 1,745,454 total reads in the equivalence classes [2020-04-25 20:39:24.916] [jointLog] [info] Number of mappings discarded because of alignment score : 733,448 [2020-04-25 20:39:24.916] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,154 [2020-04-25 20:39:24.916] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 20:39:24.916] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,582 [2020-04-25 20:39:24.920] [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. [2020-04-25 20:39:24.920] [jointLog] [info] Mapping rate = 98.6937% [2020-04-25 20:39:24.920] [jointLog] [info] finished quantifyLibrary() [2020-04-25 20:39:24.922] [jointLog] [info] Starting optimizer [2020-04-25 20:39:24.950] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 20:39:24.957] [jointLog] [info] iteration = 0 | max rel diff. = 3746.91 [2020-04-25 20:39:25.319] [jointLog] [info] iteration = 100 | max rel diff. = 3.67314 [2020-04-25 20:39:25.676] [jointLog] [info] iteration = 200 | max rel diff. = 13.2264 [2020-04-25 20:39:26.036] [jointLog] [info] iteration = 300 | max rel diff. = 0.656034 [2020-04-25 20:39:26.293] [jointLog] [info] iteration = 374 | max rel diff. = 0.00980363 [2020-04-25 20:39:26.294] [jointLog] [info] Finished optimizer [2020-04-25 20:39:26.294] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_03/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_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/infected-uninfected/20200413.C_bairdi.151.D9.infected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.151.D9.infected.cold.megan_R2.fq -o infected_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/infected-uninfected/20200413.C_bairdi.151.D9.infected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.151.D9.infected.cold.megan_R2.fq } ### [ output ] => { infected_04 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_04/logs [2020-04-25 20:47:56.795] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 20:47:56.795] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 20:47:56.795] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 20:47:56.795] [jointLog] [info] parsing read library format [2020-04-25 20:47:56.795] [jointLog] [info] There is 1 library. [2020-04-25 20:47:56.852] [jointLog] [info] Loading pufferfish index [2020-04-25 20:47:56.852] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.089 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 192.67 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 111.84 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.6513 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.867 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.3163 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 29.721 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.4371 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 194.97 us ----------------------------------------- [2020-04-25 20:47:56.935] [jointLog] [info] done [2020-04-25 20:47:56.935] [jointLog] [info] Index contained 40,435 targets [2020-04-25 20:47:56.949] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,686,676, hits per frag: 3.72041 processed 1,000,000 fragments hits: 3,373,968, hits per frag: 3.78234 processed 1,500,000 fragments hits: 5,054,847, hits per frag: 3.72478 processed 2,000,000 fragments hits: 6,745,849, hits per frag: 3.49217 processed 2,500,000 fragments hits: 8,434,939, hits per frag: 3.49731 processed 3,000,000 fragments hits: 10,121,484, hits per frag: 3.49462 processed 3,500,000 fragments hits: 11,816,191, hits per frag: 3.45409 processed 4,000,000 fragments hits: 13,501,306, hits per frag: 3.45123 [2020-04-25 20:48:08.241] [jointLog] [info] Computed 99,575 rich equivalence classes for further processing [2020-04-25 20:48:08.241] [jointLog] [info] Counted 4,278,214 total reads in the equivalence classes [2020-04-25 20:48:08.260] [jointLog] [info] Number of mappings discarded because of alignment score : 1,083,052 [2020-04-25 20:48:08.260] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 31,025 [2020-04-25 20:48:08.260] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 20:48:08.260] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,876 [2020-04-25 20:48:08.264] [jointLog] [warning] Only 4278214 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-25 20:48:08.264] [jointLog] [info] Mapping rate = 99.2386% [2020-04-25 20:48:08.264] [jointLog] [info] finished quantifyLibrary() [2020-04-25 20:48:08.267] [jointLog] [info] Starting optimizer [2020-04-25 20:48:08.297] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 20:48:08.310] [jointLog] [info] iteration = 0 | max rel diff. = 9616.57 [2020-04-25 20:48:08.838] [jointLog] [info] iteration = 100 | max rel diff. = 7.91213 [2020-04-25 20:48:09.362] [jointLog] [info] iteration = 200 | max rel diff. = 2.55596 [2020-04-25 20:48:09.892] [jointLog] [info] iteration = 300 | max rel diff. = 0.305778 [2020-04-25 20:48:10.428] [jointLog] [info] iteration = 400 | max rel diff. = 0.567836 [2020-04-25 20:48:10.960] [jointLog] [info] iteration = 500 | max rel diff. = 0.12461 [2020-04-25 20:48:11.488] [jointLog] [info] iteration = 600 | max rel diff. = 0.170645 [2020-04-25 20:48:12.013] [jointLog] [info] iteration = 700 | max rel diff. = 0.0603391 [2020-04-25 20:48:12.544] [jointLog] [info] iteration = 800 | max rel diff. = 1.87193 [2020-04-25 20:48:12.824] [jointLog] [info] iteration = 854 | max rel diff. = 0.00396957 [2020-04-25 20:48:12.829] [jointLog] [info] Finished optimizer [2020-04-25 20:48:12.829] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_04/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_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/infected-uninfected/20200413.C_bairdi.173.D9.infected.warm.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.173.D9.infected.warm.megan_R2.fq -o infected_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/infected-uninfected/20200413.C_bairdi.173.D9.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.173.D9.infected.warm.megan_R2.fq } ### [ output ] => { infected_05 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_05/logs [2020-04-25 20:56:42.995] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 20:56:42.995] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 20:56:42.995] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 20:56:42.995] [jointLog] [info] parsing read library format [2020-04-25 20:56:42.995] [jointLog] [info] There is 1 library. ----------------------------------------- | Loading contig table | Time = 15.892 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 216.54 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 73.166 us ----------------------------------------- [2020-04-25 20:56:43.058] [jointLog] [info] Loading pufferfish index [2020-04-25 20:56:43.058] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading mphf table | Time = 6.3235 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.271 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.7448 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 193.77 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.9212 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 138.43 us ----------------------------------------- [2020-04-25 20:56:43.310] [jointLog] [info] done [2020-04-25 20:56:43.310] [jointLog] [info] Index contained 40,435 targets [2020-04-25 20:56:43.323] [jointLog] [info] Number of decoys : 0  processed 500,001 fragments hits: 2,221,245, hits per frag: 5.0779 processed 1,000,000 fragments hits: 4,449,777, hits per frag: 4.84111 [2020-04-25 20:56:48.292] [jointLog] [info] Computed 53,983 rich equivalence classes for further processing [2020-04-25 20:56:48.292] [jointLog] [info] Counted 1,453,008 total reads in the equivalence classes [2020-04-25 20:56:48.311] [jointLog] [info] Number of mappings discarded because of alignment score : 568,190 [2020-04-25 20:56:48.311] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,459 [2020-04-25 20:56:48.311] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 20:56:48.311] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,199 [2020-04-25 20:56:48.314] [jointLog] [warning] Only 1453008 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-25 20:56:48.314] [jointLog] [info] Mapping rate = 98.6029% [2020-04-25 20:56:48.314] [jointLog] [info] finished quantifyLibrary() [2020-04-25 20:56:48.316] [jointLog] [info] Starting optimizer [2020-04-25 20:56:48.336] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 20:56:48.341] [jointLog] [info] iteration = 0 | max rel diff. = 3116.13 [2020-04-25 20:56:48.592] [jointLog] [info] iteration = 100 | max rel diff. = 4.60584 [2020-04-25 20:56:48.845] [jointLog] [info] iteration = 200 | max rel diff. = 0.786872 [2020-04-25 20:56:49.093] [jointLog] [info] iteration = 300 | max rel diff. = 0.0689495 [2020-04-25 20:56:49.342] [jointLog] [info] iteration = 400 | max rel diff. = 0.183784 [2020-04-25 20:56:49.359] [jointLog] [info] iteration = 408 | max rel diff. = 0.00409956 [2020-04-25 20:56:49.360] [jointLog] [info] Finished optimizer [2020-04-25 20:56:49.360] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_05/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_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/infected-uninfected/20200413.C_bairdi.178.D9.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.178.D9.infected.ambient.megan_R2.fq -o infected_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/infected-uninfected/20200413.C_bairdi.178.D9.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.178.D9.infected.ambient.megan_R2.fq } ### [ output ] => { infected_06 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_06/logs [2020-04-25 21:05:19.755] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 21:05:19.755] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 21:05:19.755] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 21:05:19.755] [jointLog] [info] parsing read library format [2020-04-25 21:05:19.755] [jointLog] [info] There is 1 library. [2020-04-25 21:05:19.807] [jointLog] [info] Loading pufferfish index [2020-04-25 21:05:19.807] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 10.965 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 203.32 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 115.4 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.4447 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.843 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.5387 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 168.64 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.2691 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 258.68 us ----------------------------------------- [2020-04-25 21:05:20.030] [jointLog] [info] done [2020-04-25 21:05:20.030] [jointLog] [info] Index contained 40,435 targets [2020-04-25 21:05:20.044] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,305,950, hits per frag: 5.54378 processed 1,000,000 fragments hits: 4,614,963, hits per frag: 4.76805 processed 1,500,000 fragments hits: 6,929,914, hits per frag: 5.02731 processed 2,000,001 fragments hits: 9,243,284, hits per frag: 4.76005 processed 2,500,000 fragments hits: 11,556,403, hits per frag: 4.72774 processed 3,000,000 fragments hits: 13,862,565, hits per frag: 4.72923 [2020-04-25 21:05:30.070] [jointLog] [info] Computed 93,649 rich equivalence classes for further processing [2020-04-25 21:05:30.070] [jointLog] [info] Counted 3,186,382 total reads in the equivalence classes [2020-04-25 21:05:30.090] [jointLog] [info] Number of mappings discarded because of alignment score : 1,265,422 [2020-04-25 21:05:30.090] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 26,413 [2020-04-25 21:05:30.090] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 21:05:30.090] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,312 [2020-04-25 21:05:30.093] [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. [2020-04-25 21:05:30.093] [jointLog] [info] Mapping rate = 99.1442% [2020-04-25 21:05:30.093] [jointLog] [info] finished quantifyLibrary() [2020-04-25 21:05:30.095] [jointLog] [info] Starting optimizer [2020-04-25 21:05:30.126] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 21:05:30.137] [jointLog] [info] iteration = 0 | max rel diff. = 7295.51 [2020-04-25 21:05:30.591] [jointLog] [info] iteration = 100 | max rel diff. = 13.9261 [2020-04-25 21:05:31.055] [jointLog] [info] iteration = 200 | max rel diff. = 0.947747 [2020-04-25 21:05:31.516] [jointLog] [info] iteration = 300 | max rel diff. = 0.331185 [2020-04-25 21:05:31.980] [jointLog] [info] iteration = 400 | max rel diff. = 0.387898 [2020-04-25 21:05:32.446] [jointLog] [info] iteration = 500 | max rel diff. = 0.201543 [2020-04-25 21:05:32.628] [jointLog] [info] iteration = 541 | max rel diff. = 0.00679113 [2020-04-25 21:05:32.630] [jointLog] [info] Finished optimizer [2020-04-25 21:05:32.630] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_06/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_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/infected-uninfected/20200413.C_bairdi.221.D12.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.221.D12.uninfected.cold.megan_R2.fq -o uninfected_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/infected-uninfected/20200413.C_bairdi.221.D12.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.221.D12.uninfected.cold.megan_R2.fq } ### [ output ] => { uninfected_02 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to uninfected_02/logs [2020-04-25 21:14:02.997] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 21:14:02.997] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 21:14:02.997] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 21:14:02.997] [jointLog] [info] parsing read library format [2020-04-25 21:14:02.997] [jointLog] [info] There is 1 library. [2020-04-25 21:14:03.054] [jointLog] [info] Loading pufferfish index [2020-04-25 21:14:03.054] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.502 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 200.56 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 112.93 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.5201 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.725 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4347 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 132.91 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.6701 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 230.91 us ----------------------------------------- [2020-04-25 21:14:03.243] [jointLog] [info] done [2020-04-25 21:14:03.243] [jointLog] [info] Index contained 40,435 targets [2020-04-25 21:14:03.257] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,242,729, hits per frag: 5.87594 processed 1,000,000 fragments hits: 4,487,987, hits per frag: 4.81723 processed 1,500,001 fragments hits: 6,734,490, hits per frag: 4.60999 processed 2,000,000 fragments hits: 8,978,507, hits per frag: 4.5423 processed 2,000,027 fragments hits: 8,978,598, hits per frag: 4.54947 processed 2,500,001 fragments hits: 11,219,487, hits per frag: 4.61136 [2020-04-25 21:14:11.308] [jointLog] [info] Computed 79,675 rich equivalence classes for further processing [2020-04-25 21:14:11.308] [jointLog] [info] Counted 2,609,007 total reads in the equivalence classes [2020-04-25 21:14:11.329] [jointLog] [info] Number of mappings discarded because of alignment score : 1,110,006 [2020-04-25 21:14:11.329] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,705 [2020-04-25 21:14:11.329] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 21:14:11.329] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,808 [2020-04-25 21:14:11.333] [jointLog] [warning] Only 2609007 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-25 21:14:11.333] [jointLog] [info] Mapping rate = 99.1136% [2020-04-25 21:14:11.333] [jointLog] [info] finished quantifyLibrary() [2020-04-25 21:14:11.335] [jointLog] [info] Starting optimizer [2020-04-25 21:14:11.357] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 21:14:11.366] [jointLog] [info] iteration = 0 | max rel diff. = 6036.62 [2020-04-25 21:14:11.760] [jointLog] [info] iteration = 100 | max rel diff. = 9.21536 [2020-04-25 21:14:12.149] [jointLog] [info] iteration = 200 | max rel diff. = 3.60178 [2020-04-25 21:14:12.540] [jointLog] [info] iteration = 300 | max rel diff. = 1.06344 [2020-04-25 21:14:12.931] [jointLog] [info] iteration = 400 | max rel diff. = 6.56335 [2020-04-25 21:14:13.116] [jointLog] [info] iteration = 448 | max rel diff. = 0.0086855 [2020-04-25 21:14:13.117] [jointLog] [info] Finished optimizer [2020-04-25 21:14:13.117] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl uninfected_02/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > uninfected_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/infected-uninfected/20200413.C_bairdi.222.D12.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.222.D12.uninfected.cold.megan_R2.fq -o uninfected_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/infected-uninfected/20200413.C_bairdi.222.D12.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.222.D12.uninfected.cold.megan_R2.fq } ### [ output ] => { uninfected_03 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to uninfected_03/logs [2020-04-25 21:22:43.193] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 21:22:43.193] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 21:22:43.193] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 21:22:43.193] [jointLog] [info] parsing read library format [2020-04-25 21:22:43.193] [jointLog] [info] There is 1 library. [2020-04-25 21:22:43.246] [jointLog] [info] Loading pufferfish index [2020-04-25 21:22:43.246] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.946 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 245.26 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 132.97 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 7.0434 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.58 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.2907 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 21.813 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.521 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 207.47 us ----------------------------------------- [2020-04-25 21:22:43.323] [jointLog] [info] done [2020-04-25 21:22:43.323] [jointLog] [info] Index contained 40,435 targets [2020-04-25 21:22:43.334] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,585,908, hits per frag: 3.73175 processed 1,000,000 fragments hits: 3,171,606, hits per frag: 3.63377 [2020-04-25 21:22:47.461] [jointLog] [info] Computed 59,769 rich equivalence classes for further processing [2020-04-25 21:22:47.461] [jointLog] [info] Counted 1,344,958 total reads in the equivalence classes [2020-04-25 21:22:47.477] [jointLog] [info] Number of mappings discarded because of alignment score : 339,466 [2020-04-25 21:22:47.477] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 14,114 [2020-04-25 21:22:47.477] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 21:22:47.477] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,729 [2020-04-25 21:22:47.480] [jointLog] [warning] Only 1344958 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-25 21:22:47.480] [jointLog] [info] Mapping rate = 98.8393% [2020-04-25 21:22:47.480] [jointLog] [info] finished quantifyLibrary() [2020-04-25 21:22:47.482] [jointLog] [info] Starting optimizer [2020-04-25 21:22:47.503] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 21:22:47.507] [jointLog] [info] iteration = 0 | max rel diff. = 3203.89 [2020-04-25 21:22:47.755] [jointLog] [info] iteration = 100 | max rel diff. = 17.446 [2020-04-25 21:22:47.994] [jointLog] [info] iteration = 200 | max rel diff. = 0.481976 [2020-04-25 21:22:48.224] [jointLog] [info] iteration = 300 | max rel diff. = 0.0383367 [2020-04-25 21:22:48.467] [jointLog] [info] iteration = 400 | max rel diff. = 0.0657569 [2020-04-25 21:22:48.710] [jointLog] [info] iteration = 500 | max rel diff. = 0.148109 [2020-04-25 21:22:48.923] [jointLog] [info] iteration = 589 | max rel diff. = 0.00750462 [2020-04-25 21:22:48.924] [jointLog] [info] Finished optimizer [2020-04-25 21:22:48.924] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl uninfected_03/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > uninfected_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/infected-uninfected/20200413.C_bairdi.254.D12.infected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.254.D12.infected.cold.megan_R2.fq -o infected_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/infected-uninfected/20200413.C_bairdi.254.D12.infected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.254.D12.infected.cold.megan_R2.fq } ### [ output ] => { infected_07 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_07/logs [2020-04-25 21:31:19.311] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 21:31:19.311] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 21:31:19.311] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 21:31:19.311] [jointLog] [info] parsing read library format [2020-04-25 21:31:19.311] [jointLog] [info] There is 1 library. [2020-04-25 21:31:19.363] [jointLog] [info] Loading pufferfish index [2020-04-25 21:31:19.363] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 10.996 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 201.38 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 115.16 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.3844 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.959 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.5955 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 21.776 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.5797 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 210.67 us ----------------------------------------- [2020-04-25 21:31:19.438] [jointLog] [info] done [2020-04-25 21:31:19.438] [jointLog] [info] Index contained 40,435 targets [2020-04-25 21:31:19.449] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,790,082, hits per frag: 3.7582 processed 1,000,000 fragments hits: 3,579,369, hits per frag: 3.76674 processed 1,500,000 fragments hits: 5,369,719, hits per frag: 3.8528 [2020-04-25 21:31:25.759] [jointLog] [info] Computed 65,127 rich equivalence classes for further processing [2020-04-25 21:31:25.759] [jointLog] [info] Counted 1,951,686 total reads in the equivalence classes [2020-04-25 21:31:25.776] [jointLog] [info] Number of mappings discarded because of alignment score : 660,574 [2020-04-25 21:31:25.776] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 21,117 [2020-04-25 21:31:25.776] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 21:31:25.776] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,559 [2020-04-25 21:31:25.779] [jointLog] [warning] Only 1951686 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-25 21:31:25.779] [jointLog] [info] Mapping rate = 98.8965% [2020-04-25 21:31:25.779] [jointLog] [info] finished quantifyLibrary() [2020-04-25 21:31:25.781] [jointLog] [info] Starting optimizer [2020-04-25 21:31:25.801] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 21:31:25.809] [jointLog] [info] iteration = 0 | max rel diff. = 4061.37 [2020-04-25 21:31:26.233] [jointLog] [info] iteration = 100 | max rel diff. = 4.37046 [2020-04-25 21:31:26.657] [jointLog] [info] iteration = 200 | max rel diff. = 6.982 [2020-04-25 21:31:27.076] [jointLog] [info] iteration = 300 | max rel diff. = 0.26176 [2020-04-25 21:31:27.449] [jointLog] [info] iteration = 390 | max rel diff. = 0.00775314 [2020-04-25 21:31:27.449] [jointLog] [info] Finished optimizer [2020-04-25 21:31:27.449] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_07/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_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/infected-uninfected/20200413.C_bairdi.272.D12.infected.warm.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.272.D12.infected.warm.megan_R2.fq -o infected_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/infected-uninfected/20200413.C_bairdi.272.D12.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.272.D12.infected.warm.megan_R2.fq } ### [ output ] => { infected_08 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_08/logs [2020-04-25 21:39:57.965] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 21:39:57.965] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 21:39:57.965] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 21:39:57.965] [jointLog] [info] parsing read library format [2020-04-25 21:39:57.965] [jointLog] [info] There is 1 library. [2020-04-25 21:39:58.017] [jointLog] [info] Loading pufferfish index [2020-04-25 21:39:58.017] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.145 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 199.76 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 120.11 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.2853 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 42.525 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 3.3373 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 22.996 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.7389 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 229.07 us ----------------------------------------- [2020-04-25 21:39:58.108] [jointLog] [info] done [2020-04-25 21:39:58.108] [jointLog] [info] Index contained 40,435 targets [2020-04-25 21:39:58.120] [jointLog] [info] Number of decoys : 0 [2020-04-25 21:40:00.004] [jointLog] [info] Computed 34,339 rich equivalence classes for further processing [2020-04-25 21:40:00.004] [jointLog] [info] Counted 379,958 total reads in the equivalence classes [2020-04-25 21:40:00.043] [jointLog] [info] Number of mappings discarded because of alignment score : 250,108 [2020-04-25 21:40:00.043] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,667 [2020-04-25 21:40:00.043] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 21:40:00.043] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 899 [2020-04-25 21:40:00.047] [jointLog] [warning] Only 379958 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-25 21:40:00.047] [jointLog] [info] Mapping rate = 94.4906% [2020-04-25 21:40:00.047] [jointLog] [info] finished quantifyLibrary() [2020-04-25 21:40:00.048] [jointLog] [info] Starting optimizer [2020-04-25 21:40:00.065] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 21:40:00.069] [jointLog] [info] iteration = 0 | max rel diff. = 901.869 [2020-04-25 21:40:00.267] [jointLog] [info] iteration = 100 | max rel diff. = 11.4617 [2020-04-25 21:40:00.455] [jointLog] [info] iteration = 200 | max rel diff. = 0.0678074 [2020-04-25 21:40:00.646] [jointLog] [info] iteration = 300 | max rel diff. = 0.0417858 [2020-04-25 21:40:00.836] [jointLog] [info] iteration = 400 | max rel diff. = 0.0183644 [2020-04-25 21:40:01.034] [jointLog] [info] iteration = 500 | max rel diff. = 0.0863831 [2020-04-25 21:40:01.060] [jointLog] [info] iteration = 515 | max rel diff. = 0.000644268 [2020-04-25 21:40:01.061] [jointLog] [info] Finished optimizer [2020-04-25 21:40:01.061] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_08/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_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/infected-uninfected/20200413.C_bairdi.280.D12.infected.warm.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.280.D12.infected.warm.megan_R2.fq -o infected_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/infected-uninfected/20200413.C_bairdi.280.D12.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.280.D12.infected.warm.megan_R2.fq } ### [ output ] => { infected_09 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_09/logs [2020-04-25 21:48:31.230] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 21:48:31.230] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 21:48:31.230] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 21:48:31.230] [jointLog] [info] parsing read library format [2020-04-25 21:48:31.230] [jointLog] [info] There is 1 library. ----------------------------------------- | Loading contig table | Time = 11.773 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 209.32 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 119.8 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.5655 ms ----------------------------------------- size = 21703191 [2020-04-25 21:48:31.291] [jointLog] [info] Loading pufferfish index [2020-04-25 21:48:31.291] [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 = 29.666 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4282 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 28.396 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.4026 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 92.003 us ----------------------------------------- [2020-04-25 21:48:31.375] [jointLog] [info] done [2020-04-25 21:48:31.375] [jointLog] [info] Index contained 40,435 targets [2020-04-25 21:48:31.389] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,858,863, hits per frag: 3.96519 [2020-04-25 21:48:34.041] [jointLog] [info] Computed 61,194 rich equivalence classes for further processing [2020-04-25 21:48:34.041] [jointLog] [info] Counted 792,532 total reads in the equivalence classes [2020-04-25 21:48:34.059] [jointLog] [info] Number of mappings discarded because of alignment score : 329,168 [2020-04-25 21:48:34.059] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,419 [2020-04-25 21:48:34.059] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 21:48:34.059] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,914 [2020-04-25 21:48:34.062] [jointLog] [warning] Only 792532 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-25 21:48:34.062] [jointLog] [info] Mapping rate = 97.2166% [2020-04-25 21:48:34.062] [jointLog] [info] finished quantifyLibrary() [2020-04-25 21:48:34.064] [jointLog] [info] Starting optimizer [2020-04-25 21:48:34.084] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 21:48:34.088] [jointLog] [info] iteration = 0 | max rel diff. = 1897.92 [2020-04-25 21:48:34.316] [jointLog] [info] iteration = 100 | max rel diff. = 0.659093 [2020-04-25 21:48:34.539] [jointLog] [info] iteration = 200 | max rel diff. = 7.7275 [2020-04-25 21:48:34.765] [jointLog] [info] iteration = 300 | max rel diff. = 0.0121327 [2020-04-25 21:48:34.983] [jointLog] [info] iteration = 400 | max rel diff. = 0.00540614 [2020-04-25 21:48:34.984] [jointLog] [info] Finished optimizer [2020-04-25 21:48:34.984] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_09/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_09/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/infected-uninfected/20200413.C_bairdi.294.D12.infected.warm.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.294.D12.infected.warm.megan_R2.fq -o infected_10 -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/infected-uninfected/20200413.C_bairdi.294.D12.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.294.D12.infected.warm.megan_R2.fq } ### [ output ] => { infected_10 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_10/logs [2020-04-25 21:57:05.535] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 21:57:05.535] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 21:57:05.535] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 21:57:05.535] [jointLog] [info] parsing read library format [2020-04-25 21:57:05.535] [jointLog] [info] There is 1 library. [2020-04-25 21:57:05.594] [jointLog] [info] Loading pufferfish index [2020-04-25 21:57:05.594] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.312 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 199.14 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 111.07 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.5978 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.781 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.2935 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 28.982 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.3398 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 192.22 us ----------------------------------------- [2020-04-25 21:57:05.676] [jointLog] [info] done [2020-04-25 21:57:05.676] [jointLog] [info] Index contained 40,435 targets [2020-04-25 21:57:05.690] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,737,058, hits per frag: 4.13112 processed 1,000,000 fragments hits: 3,474,215, hits per frag: 3.64778 processed 1,500,001 fragments hits: 5,217,675, hits per frag: 3.66032 processed 2,000,000 fragments hits: 6,965,411, hits per frag: 3.51209 processed 2,500,000 fragments hits: 8,705,758, hits per frag: 3.6829 processed 3,000,000 fragments hits: 10,449,954, hits per frag: 3.62678 [2020-04-25 21:57:14.545] [jointLog] [info] Computed 81,616 rich equivalence classes for further processing [2020-04-25 21:57:14.545] [jointLog] [info] Counted 3,165,463 total reads in the equivalence classes [2020-04-25 21:57:14.564] [jointLog] [info] Number of mappings discarded because of alignment score : 937,204 [2020-04-25 21:57:14.564] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 23,634 [2020-04-25 21:57:14.564] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 21:57:14.564] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,170 [2020-04-25 21:57:14.568] [jointLog] [warning] Only 3165463 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-25 21:57:14.568] [jointLog] [info] Mapping rate = 99.2286% [2020-04-25 21:57:14.568] [jointLog] [info] finished quantifyLibrary() [2020-04-25 21:57:14.569] [jointLog] [info] Starting optimizer [2020-04-25 21:57:14.591] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 21:57:14.599] [jointLog] [info] iteration = 0 | max rel diff. = 7007.65 [2020-04-25 21:57:14.998] [jointLog] [info] iteration = 100 | max rel diff. = 11.0592 [2020-04-25 21:57:15.391] [jointLog] [info] iteration = 200 | max rel diff. = 1.19924 [2020-04-25 21:57:15.802] [jointLog] [info] iteration = 300 | max rel diff. = 0.112575 [2020-04-25 21:57:16.217] [jointLog] [info] iteration = 400 | max rel diff. = 0.878347 [2020-04-25 21:57:16.634] [jointLog] [info] iteration = 500 | max rel diff. = 0.0352689 [2020-04-25 21:57:17.043] [jointLog] [info] iteration = 600 | max rel diff. = 0.00307668 [2020-04-25 21:57:17.047] [jointLog] [info] Finished optimizer [2020-04-25 21:57:17.047] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_10/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_10/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/infected-uninfected/20200413.C_bairdi.334.D12.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.334.D12.infected.ambient.megan_R2.fq -o infected_11 -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/infected-uninfected/20200413.C_bairdi.334.D12.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.334.D12.infected.ambient.megan_R2.fq } ### [ output ] => { infected_11 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_11/logs [2020-04-25 22:05:47.633] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 22:05:47.633] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 22:05:47.633] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 22:05:47.633] [jointLog] [info] parsing read library format [2020-04-25 22:05:47.633] [jointLog] [info] There is 1 library. [2020-04-25 22:05:47.692] [jointLog] [info] Loading pufferfish index [2020-04-25 22:05:47.692] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.272 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 192.8 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 109.9 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.7268 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.824 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.1633 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 28.938 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.4999 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 198.21 us ----------------------------------------- [2020-04-25 22:05:47.774] [jointLog] [info] done [2020-04-25 22:05:47.774] [jointLog] [info] Index contained 40,435 targets [2020-04-25 22:05:47.788] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,645,485, hits per frag: 5.91392 processed 1,000,000 fragments hits: 5,295,835, hits per frag: 5.81157 [2020-04-25 22:05:52.254] [jointLog] [info] Computed 60,283 rich equivalence classes for further processing [2020-04-25 22:05:52.254] [jointLog] [info] Counted 1,107,449 total reads in the equivalence classes [2020-04-25 22:05:52.273] [jointLog] [info] Number of mappings discarded because of alignment score : 485,229 [2020-04-25 22:05:52.273] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 12,163 [2020-04-25 22:05:52.273] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 22:05:52.273] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,777 [2020-04-25 22:05:52.277] [jointLog] [warning] Only 1107449 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-25 22:05:52.277] [jointLog] [info] Mapping rate = 98.8795% [2020-04-25 22:05:52.277] [jointLog] [info] finished quantifyLibrary() [2020-04-25 22:05:52.279] [jointLog] [info] Starting optimizer [2020-04-25 22:05:52.297] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 22:05:52.302] [jointLog] [info] iteration = 0 | max rel diff. = 2447.97 [2020-04-25 22:05:52.606] [jointLog] [info] iteration = 100 | max rel diff. = 0.344132 [2020-04-25 22:05:52.916] [jointLog] [info] iteration = 200 | max rel diff. = 0.850319 [2020-04-25 22:05:53.222] [jointLog] [info] iteration = 300 | max rel diff. = 0.50341 [2020-04-25 22:05:53.525] [jointLog] [info] iteration = 400 | max rel diff. = 0.277981 [2020-04-25 22:05:53.672] [jointLog] [info] iteration = 449 | max rel diff. = 0.0022278 [2020-04-25 22:05:53.673] [jointLog] [info] Finished optimizer [2020-04-25 22:05:53.673] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_11/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_11/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/infected-uninfected/20200413.C_bairdi.349.D12.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.349.D12.infected.ambient.megan_R2.fq -o infected_12 -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/infected-uninfected/20200413.C_bairdi.349.D12.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.349.D12.infected.ambient.megan_R2.fq } ### [ output ] => { infected_12 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_12/logs [2020-04-25 22:14:23.887] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 22:14:23.887] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 22:14:23.887] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 22:14:23.887] [jointLog] [info] parsing read library format [2020-04-25 22:14:23.887] [jointLog] [info] There is 1 library. [2020-04-25 22:14:23.941] [jointLog] [info] Loading pufferfish index [2020-04-25 22:14:23.941] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.395 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 205.53 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 120.62 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.324 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.004 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.7228 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 22.041 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.584 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 211.89 us ----------------------------------------- [2020-04-25 22:14:24.017] [jointLog] [info] done [2020-04-25 22:14:24.017] [jointLog] [info] Index contained 40,435 targets [2020-04-25 22:14:24.028] [jointLog] [info] Number of decoys : 0 [2020-04-25 22:14:24.753] [jointLog] [info] Computed 21,365 rich equivalence classes for further processing [2020-04-25 22:14:24.753] [jointLog] [info] Counted 79,374 total reads in the equivalence classes [2020-04-25 22:14:24.772] [jointLog] [info] Number of mappings discarded because of alignment score : 85,738 [2020-04-25 22:14:24.772] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 8,610 [2020-04-25 22:14:24.772] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 22:14:24.772] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 338 [2020-04-25 22:14:24.775] [jointLog] [warning] Only 79374 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-25 22:14:24.775] [jointLog] [info] Mapping rate = 86.6396% [2020-04-25 22:14:24.775] [jointLog] [info] finished quantifyLibrary() [2020-04-25 22:14:24.776] [jointLog] [info] Starting optimizer [2020-04-25 22:14:24.790] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 22:14:24.793] [jointLog] [info] iteration = 0 | max rel diff. = 190.219 [2020-04-25 22:14:24.908] [jointLog] [info] iteration = 100 | max rel diff. = 0.229335 [2020-04-25 22:14:24.987] [jointLog] [info] iteration = 176 | max rel diff. = 0.00993408 [2020-04-25 22:14:24.987] [jointLog] [info] Finished optimizer [2020-04-25 22:14:24.987] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_12/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_12/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/infected-uninfected/20200413.C_bairdi.359.D12.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.359.D12.infected.ambient.megan_R2.fq -o infected_13 -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/infected-uninfected/20200413.C_bairdi.359.D12.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.359.D12.infected.ambient.megan_R2.fq } ### [ output ] => { infected_13 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_13/logs [2020-04-25 22:22:55.244] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 22:22:55.244] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 22:22:55.244] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 22:22:55.244] [jointLog] [info] parsing read library format [2020-04-25 22:22:55.244] [jointLog] [info] There is 1 library. ----------------------------------------- | Loading contig table | Time = 11.351 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 199.45 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 112.57 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.5332 ms ----------------------------------------- size = 21703191 [2020-04-25 22:22:55.306] [jointLog] [info] Loading pufferfish index [2020-04-25 22:22:55.306] [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 = 29.052 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.5182 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 32.82 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.2548 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 217.84 us ----------------------------------------- [2020-04-25 22:22:55.394] [jointLog] [info] done [2020-04-25 22:22:55.394] [jointLog] [info] Index contained 40,435 targets [2020-04-25 22:22:55.408] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,086,998, hits per frag: 4.36356 processed 1,000,001 fragments hits: 4,174,296, hits per frag: 4.46636 processed 1,500,000 fragments hits: 6,264,988, hits per frag: 4.27417 processed 2,000,000 fragments hits: 8,361,344, hits per frag: 4.47185 processed 2,500,000 fragments hits: 10,452,280, hits per frag: 4.34302 processed 3,000,000 fragments hits: 12,534,794, hits per frag: 4.28734 [2020-04-25 22:23:06.009] [jointLog] [info] Computed 95,726 rich equivalence classes for further processing [2020-04-25 22:23:06.009] [jointLog] [info] Counted 3,196,425 total reads in the equivalence classes [2020-04-25 22:23:06.031] [jointLog] [info] Number of mappings discarded because of alignment score : 1,080,608 [2020-04-25 22:23:06.031] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 24,486 [2020-04-25 22:23:06.031] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 22:23:06.031] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,462 [2020-04-25 22:23:06.035] [jointLog] [warning] Only 3196425 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-25 22:23:06.035] [jointLog] [info] Mapping rate = 99.2016% [2020-04-25 22:23:06.035] [jointLog] [info] finished quantifyLibrary() [2020-04-25 22:23:06.037] [jointLog] [info] Starting optimizer [2020-04-25 22:23:06.063] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 22:23:06.072] [jointLog] [info] iteration = 0 | max rel diff. = 7373.95 [2020-04-25 22:23:06.455] [jointLog] [info] iteration = 100 | max rel diff. = 16.8416 [2020-04-25 22:23:06.829] [jointLog] [info] iteration = 200 | max rel diff. = 18.6212 [2020-04-25 22:23:07.208] [jointLog] [info] iteration = 300 | max rel diff. = 2.74986 [2020-04-25 22:23:07.584] [jointLog] [info] iteration = 400 | max rel diff. = 0.414992 [2020-04-25 22:23:07.963] [jointLog] [info] iteration = 500 | max rel diff. = 0.151488 [2020-04-25 22:23:08.238] [jointLog] [info] iteration = 574 | max rel diff. = 0.0084751 [2020-04-25 22:23:08.239] [jointLog] [info] Finished optimizer [2020-04-25 22:23:08.239] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_13/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_13/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/infected-uninfected/20200413.C_bairdi.425.D26.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.425.D26.uninfected.cold.megan_R2.fq -o uninfected_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/infected-uninfected/20200413.C_bairdi.425.D26.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.425.D26.uninfected.cold.megan_R2.fq } ### [ output ] => { uninfected_04 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to uninfected_04/logs [2020-04-25 22:31:38.772] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 22:31:38.772] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 22:31:38.772] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 22:31:38.772] [jointLog] [info] parsing read library format [2020-04-25 22:31:38.772] [jointLog] [info] There is 1 library. [2020-04-25 22:31:38.831] [jointLog] [info] Loading pufferfish index [2020-04-25 22:31:38.831] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.689 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 197.53 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 116.81 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.8611 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.645 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.1162 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 30.298 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.5254 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 197.97 us ----------------------------------------- [2020-04-25 22:31:38.915] [jointLog] [info] done [2020-04-25 22:31:38.915] [jointLog] [info] Index contained 40,435 targets [2020-04-25 22:31:38.929] [jointLog] [info] Number of decoys : 0 [2020-04-25 22:31:39.651] [jointLog] [info] Computed 12,723 rich equivalence classes for further processing [2020-04-25 22:31:39.651] [jointLog] [info] Counted 75,333 total reads in the equivalence classes [2020-04-25 22:31:39.682] [jointLog] [info] Number of mappings discarded because of alignment score : 63,773 [2020-04-25 22:31:39.682] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,953 [2020-04-25 22:31:39.682] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 22:31:39.682] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 724 [2020-04-25 22:31:39.685] [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. [2020-04-25 22:31:39.685] [jointLog] [info] Mapping rate = 95.7059% [2020-04-25 22:31:39.685] [jointLog] [info] finished quantifyLibrary() [2020-04-25 22:31:39.687] [jointLog] [info] Starting optimizer [2020-04-25 22:31:39.701] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 22:31:39.704] [jointLog] [info] iteration = 0 | max rel diff. = 146.141 [2020-04-25 22:31:39.796] [jointLog] [info] iteration = 100 | max rel diff. = 0.0561517 [2020-04-25 22:31:39.852] [jointLog] [info] iteration = 165 | max rel diff. = 0.00960637 [2020-04-25 22:31:39.852] [jointLog] [info] Finished optimizer [2020-04-25 22:31:39.852] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl uninfected_04/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > uninfected_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/infected-uninfected/20200413.C_bairdi.427.D26.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.427.D26.uninfected.cold.megan_R2.fq -o uninfected_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/infected-uninfected/20200413.C_bairdi.427.D26.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.427.D26.uninfected.cold.megan_R2.fq } ### [ output ] => { uninfected_05 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to uninfected_05/logs [2020-04-25 22:40:09.966] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 22:40:09.966] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 22:40:09.966] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 22:40:09.966] [jointLog] [info] parsing read library format [2020-04-25 22:40:09.966] [jointLog] [info] There is 1 library. [2020-04-25 22:40:10.022] [jointLog] [info] Loading pufferfish index [2020-04-25 22:40:10.022] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 10.897 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 200.64 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 106.9 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.0398 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.693 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.0067 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 28.802 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.3275 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 185.04 us ----------------------------------------- [2020-04-25 22:40:10.104] [jointLog] [info] done [2020-04-25 22:40:10.104] [jointLog] [info] Index contained 40,435 targets [2020-04-25 22:40:10.117] [jointLog] [info] Number of decoys : 0 [2020-04-25 22:40:11.011] [jointLog] [info] Computed 8,592 rich equivalence classes for further processing [2020-04-25 22:40:11.011] [jointLog] [info] Counted 49,503 total reads in the equivalence classes [2020-04-25 22:40:11.046] [jointLog] [info] Number of mappings discarded because of alignment score : 49,151 [2020-04-25 22:40:11.046] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,787 [2020-04-25 22:40:11.046] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 22:40:11.046] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 268 [2020-04-25 22:40:11.049] [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. [2020-04-25 22:40:11.049] [jointLog] [info] Mapping rate = 87.3115% [2020-04-25 22:40:11.049] [jointLog] [info] finished quantifyLibrary() [2020-04-25 22:40:11.050] [jointLog] [info] Starting optimizer [2020-04-25 22:40:11.065] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 22:40:11.067] [jointLog] [info] iteration = 0 | max rel diff. = 119.435 [2020-04-25 22:40:11.141] [jointLog] [info] iteration = 100 | max rel diff. = 0.883259 [2020-04-25 22:40:11.209] [jointLog] [info] iteration = 200 | max rel diff. = 0.276108 [2020-04-25 22:40:11.216] [jointLog] [info] iteration = 212 | max rel diff. = 0.00763359 [2020-04-25 22:40:11.217] [jointLog] [info] Finished optimizer [2020-04-25 22:40:11.217] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl uninfected_05/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > uninfected_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/infected-uninfected/20200413.C_bairdi.445.D26.infected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.445.D26.infected.cold.megan_R2.fq -o infected_14 -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/infected-uninfected/20200413.C_bairdi.445.D26.infected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.445.D26.infected.cold.megan_R2.fq } ### [ output ] => { infected_14 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_14/logs [2020-04-25 22:48:41.221] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 22:48:41.221] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 22:48:41.221] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 22:48:41.221] [jointLog] [info] parsing read library format [2020-04-25 22:48:41.221] [jointLog] [info] There is 1 library. [2020-04-25 22:48:41.278] [jointLog] [info] Loading pufferfish index [2020-04-25 22:48:41.278] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.149 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 189.53 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 111.67 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.387 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.372 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4137 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 28.886 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.3632 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 88.746 us ----------------------------------------- [2020-04-25 22:48:41.359] [jointLog] [info] done [2020-04-25 22:48:41.359] [jointLog] [info] Index contained 40,435 targets [2020-04-25 22:48:41.373] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,948,250, hits per frag: 5.21743 processed 1,000,001 fragments hits: 3,892,406, hits per frag: 3.99913 processed 1,500,000 fragments hits: 5,841,962, hits per frag: 4.1537 processed 2,000,000 fragments hits: 7,777,466, hits per frag: 4.04278 processed 2,500,000 fragments hits: 9,722,449, hits per frag: 4.01779 [2020-04-25 22:48:49.131] [jointLog] [info] Computed 81,404 rich equivalence classes for further processing [2020-04-25 22:48:49.131] [jointLog] [info] Counted 2,537,570 total reads in the equivalence classes [2020-04-25 22:48:49.153] [jointLog] [info] Number of mappings discarded because of alignment score : 763,754 [2020-04-25 22:48:49.153] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 25,278 [2020-04-25 22:48:49.153] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 22:48:49.153] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,111 [2020-04-25 22:48:49.157] [jointLog] [warning] Only 2537570 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-25 22:48:49.157] [jointLog] [info] Mapping rate = 98.9786% [2020-04-25 22:48:49.157] [jointLog] [info] finished quantifyLibrary() [2020-04-25 22:48:49.158] [jointLog] [info] Starting optimizer [2020-04-25 22:48:49.187] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 22:48:49.194] [jointLog] [info] iteration = 0 | max rel diff. = 5795.65 [2020-04-25 22:48:49.529] [jointLog] [info] iteration = 100 | max rel diff. = 8.26659 [2020-04-25 22:48:49.861] [jointLog] [info] iteration = 200 | max rel diff. = 13.2913 [2020-04-25 22:48:50.191] [jointLog] [info] iteration = 300 | max rel diff. = 0.671813 [2020-04-25 22:48:50.520] [jointLog] [info] iteration = 400 | max rel diff. = 0.0579421 [2020-04-25 22:48:50.841] [jointLog] [info] iteration = 500 | max rel diff. = 0.275643 [2020-04-25 22:48:51.166] [jointLog] [info] iteration = 600 | max rel diff. = 0.395018 [2020-04-25 22:48:51.478] [jointLog] [info] iteration = 696 | max rel diff. = 0.0086757 [2020-04-25 22:48:51.482] [jointLog] [info] Finished optimizer [2020-04-25 22:48:51.482] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_14/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_14/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/infected-uninfected/20200413.C_bairdi.463.D26.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.463.D26.infected.ambient.megan_R2.fq -o infected_15 -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/infected-uninfected/20200413.C_bairdi.463.D26.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.463.D26.infected.ambient.megan_R2.fq } ### [ output ] => { infected_15 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_15/logs [2020-04-25 22:57:22.031] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 22:57:22.031] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 22:57:22.031] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 22:57:22.031] [jointLog] [info] parsing read library format [2020-04-25 22:57:22.031] [jointLog] [info] There is 1 library. [2020-04-25 22:57:22.086] [jointLog] [info] Loading pufferfish index [2020-04-25 22:57:22.086] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.182 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 189.65 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 108.34 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.8446 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.715 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.5287 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 149.33 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.6405 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 207.14 us ----------------------------------------- [2020-04-25 22:57:22.289] [jointLog] [info] done [2020-04-25 22:57:22.289] [jointLog] [info] Index contained 40,435 targets [2020-04-25 22:57:22.303] [jointLog] [info] Number of decoys : 0 [2020-04-25 22:57:23.860] [jointLog] [info] Computed 4,767 rich equivalence classes for further processing [2020-04-25 22:57:23.860] [jointLog] [info] Counted 26,916 total reads in the equivalence classes [2020-04-25 22:57:23.902] [jointLog] [info] Number of mappings discarded because of alignment score : 21,743 [2020-04-25 22:57:23.902] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,769 [2020-04-25 22:57:23.902] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 22:57:23.902] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 79 [2020-04-25 22:57:23.907] [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. [2020-04-25 22:57:23.907] [jointLog] [info] Mapping rate = 89.1878% [2020-04-25 22:57:23.907] [jointLog] [info] finished quantifyLibrary() [2020-04-25 22:57:23.908] [jointLog] [info] Starting optimizer [2020-04-25 22:57:23.917] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 22:57:23.920] [jointLog] [info] iteration = 0 | max rel diff. = 64.4773 [2020-04-25 22:57:23.986] [jointLog] [info] iteration = 100 | max rel diff. = 0.00287446 [2020-04-25 22:57:23.986] [jointLog] [info] Finished optimizer [2020-04-25 22:57:23.987] [jointLog] [info] writing output [2020-04-25 22:57:24.035] [jointLog] [warning] NOTE: Read Lib [[ /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.463.D26.infected.ambient.megan_R1.fq, /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.463.D26.infected.ambient.megan_R2.fq]] : Detected a *potential* strand bias > 1% in an unstranded protocol check the file: infected_15/lib_format_counts.json for details CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_15/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_15/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/infected-uninfected/20200413.C_bairdi.481.D26.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.481.D26.infected.ambient.megan_R2.fq -o infected_16 -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/infected-uninfected/20200413.C_bairdi.481.D26.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.481.D26.infected.ambient.megan_R2.fq } ### [ output ] => { infected_16 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_16/logs [2020-04-25 23:05:54.416] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 23:05:54.416] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 23:05:54.416] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 23:05:54.416] [jointLog] [info] parsing read library format [2020-04-25 23:05:54.416] [jointLog] [info] There is 1 library. [2020-04-25 23:05:54.474] [jointLog] [info] Loading pufferfish index [2020-04-25 23:05:54.474] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.622 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 197.71 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 105.76 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.6227 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.65 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.2223 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 29.095 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.3894 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 187.31 us ----------------------------------------- [2020-04-25 23:05:54.556] [jointLog] [info] done [2020-04-25 23:05:54.556] [jointLog] [info] Index contained 40,435 targets [2020-04-25 23:05:54.570] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,629,968, hits per frag: 4.27521 processed 1,000,001 fragments hits: 3,259,760, hits per frag: 3.39287 [2020-04-25 23:05:58.695] [jointLog] [info] Computed 70,045 rich equivalence classes for further processing [2020-04-25 23:05:58.695] [jointLog] [info] Counted 1,295,949 total reads in the equivalence classes [2020-04-25 23:05:58.712] [jointLog] [info] Number of mappings discarded because of alignment score : 406,726 [2020-04-25 23:05:58.712] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,982 [2020-04-25 23:05:58.712] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 23:05:58.712] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,002 [2020-04-25 23:05:58.716] [jointLog] [warning] Only 1295949 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-25 23:05:58.716] [jointLog] [info] Mapping rate = 98.1522% [2020-04-25 23:05:58.716] [jointLog] [info] finished quantifyLibrary() [2020-04-25 23:05:58.718] [jointLog] [info] Starting optimizer [2020-04-25 23:05:58.738] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 23:05:58.742] [jointLog] [info] iteration = 0 | max rel diff. = 3061.97 [2020-04-25 23:05:58.984] [jointLog] [info] iteration = 100 | max rel diff. = 8.23365 [2020-04-25 23:05:59.229] [jointLog] [info] iteration = 200 | max rel diff. = 2.37361 [2020-04-25 23:05:59.471] [jointLog] [info] iteration = 300 | max rel diff. = 0.160402 [2020-04-25 23:05:59.705] [jointLog] [info] iteration = 400 | max rel diff. = 2.00434 [2020-04-25 23:05:59.940] [jointLog] [info] iteration = 500 | max rel diff. = 0.12409 [2020-04-25 23:06:00.180] [jointLog] [info] iteration = 600 | max rel diff. = 0.0371456 [2020-04-25 23:06:00.417] [jointLog] [info] iteration = 700 | max rel diff. = 0.0181668 [2020-04-25 23:06:00.542] [jointLog] [info] iteration = 752 | max rel diff. = 0.00805883 [2020-04-25 23:06:00.543] [jointLog] [info] Finished optimizer [2020-04-25 23:06:00.543] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_16/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_16/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/infected-uninfected/20200413.C_bairdi.485.D26.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.485.D26.infected.ambient.megan_R2.fq -o infected_17 -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/infected-uninfected/20200413.C_bairdi.485.D26.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.485.D26.infected.ambient.megan_R2.fq } ### [ output ] => { infected_17 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_17/logs [2020-04-25 23:14:31.165] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 23:14:31.165] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 23:14:31.165] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 23:14:31.165] [jointLog] [info] parsing read library format [2020-04-25 23:14:31.165] [jointLog] [info] There is 1 library. [2020-04-25 23:14:31.218] [jointLog] [info] Loading pufferfish index [2020-04-25 23:14:31.218] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.224 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 204.09 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 116.36 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.5434 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.109 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.8058 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 82.521 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.6427 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 223.2 us ----------------------------------------- [2020-04-25 23:14:31.355] [jointLog] [info] done [2020-04-25 23:14:31.355] [jointLog] [info] Index contained 40,435 targets [2020-04-25 23:14:31.367] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,018,243, hits per frag: 4.65259 processed 1,000,000 fragments hits: 4,039,664, hits per frag: 4.26646 processed 1,500,000 fragments hits: 6,060,388, hits per frag: 4.21065 [2020-04-25 23:14:37.136] [jointLog] [info] Computed 62,815 rich equivalence classes for further processing [2020-04-25 23:14:37.136] [jointLog] [info] Counted 1,711,628 total reads in the equivalence classes [2020-04-25 23:14:37.154] [jointLog] [info] Number of mappings discarded because of alignment score : 553,510 [2020-04-25 23:14:37.154] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 16,872 [2020-04-25 23:14:37.154] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 23:14:37.154] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,511 [2020-04-25 23:14:37.158] [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. [2020-04-25 23:14:37.158] [jointLog] [info] Mapping rate = 98.9712% [2020-04-25 23:14:37.158] [jointLog] [info] finished quantifyLibrary() [2020-04-25 23:14:37.159] [jointLog] [info] Starting optimizer [2020-04-25 23:14:37.179] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 23:14:37.185] [jointLog] [info] iteration = 0 | max rel diff. = 4011.45 [2020-04-25 23:14:37.447] [jointLog] [info] iteration = 100 | max rel diff. = 0.969857 [2020-04-25 23:14:37.705] [jointLog] [info] iteration = 200 | max rel diff. = 0.964476 [2020-04-25 23:14:37.965] [jointLog] [info] iteration = 300 | max rel diff. = 0.758371 [2020-04-25 23:14:38.221] [jointLog] [info] iteration = 400 | max rel diff. = 0.0535222 [2020-04-25 23:14:38.480] [jointLog] [info] iteration = 500 | max rel diff. = 0.400617 [2020-04-25 23:14:38.491] [jointLog] [info] iteration = 505 | max rel diff. = 0.00563125 [2020-04-25 23:14:38.492] [jointLog] [info] Finished optimizer [2020-04-25 23:14:38.492] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_17/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_17/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/infected-uninfected/20200413.C_bairdi.72.D9.infected.warm.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.72.D9.infected.warm.megan_R2.fq -o infected_18 -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/infected-uninfected/20200413.C_bairdi.72.D9.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.72.D9.infected.warm.megan_R2.fq } ### [ output ] => { infected_18 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to infected_18/logs [2020-04-25 23:23:08.914] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 23:23:08.914] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 23:23:08.914] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 23:23:08.914] [jointLog] [info] parsing read library format [2020-04-25 23:23:08.914] [jointLog] [info] There is 1 library. [2020-04-25 23:23:08.972] [jointLog] [info] Loading pufferfish index [2020-04-25 23:23:08.973] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.348 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 200.96 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 120.38 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.6105 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.74 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4231 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 149.87 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.8243 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 235.01 us ----------------------------------------- [2020-04-25 23:23:09.178] [jointLog] [info] done [2020-04-25 23:23:09.178] [jointLog] [info] Index contained 40,435 targets [2020-04-25 23:23:09.193] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,671,630, hits per frag: 5.66332 processed 1,000,000 fragments hits: 5,358,189, hits per frag: 6.21779 processed 1,500,000 fragments hits: 8,041,166, hits per frag: 5.69928 [2020-04-25 23:23:15.148] [jointLog] [info] Computed 63,989 rich equivalence classes for further processing [2020-04-25 23:23:15.148] [jointLog] [info] Counted 1,547,156 total reads in the equivalence classes [2020-04-25 23:23:15.169] [jointLog] [info] Number of mappings discarded because of alignment score : 744,608 [2020-04-25 23:23:15.169] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 20,255 [2020-04-25 23:23:15.169] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 23:23:15.169] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,061 [2020-04-25 23:23:15.173] [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. [2020-04-25 23:23:15.173] [jointLog] [info] Mapping rate = 98.6772% [2020-04-25 23:23:15.173] [jointLog] [info] finished quantifyLibrary() [2020-04-25 23:23:15.174] [jointLog] [info] Starting optimizer [2020-04-25 23:23:15.197] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 23:23:15.204] [jointLog] [info] iteration = 0 | max rel diff. = 3445.26 [2020-04-25 23:23:15.534] [jointLog] [info] iteration = 100 | max rel diff. = 1.74427 [2020-04-25 23:23:15.857] [jointLog] [info] iteration = 200 | max rel diff. = 2.34535 [2020-04-25 23:23:16.181] [jointLog] [info] iteration = 300 | max rel diff. = 0.0146923 [2020-04-25 23:23:16.507] [jointLog] [info] iteration = 400 | max rel diff. = 0.0433253 [2020-04-25 23:23:16.831] [jointLog] [info] iteration = 500 | max rel diff. = 0.0212253 [2020-04-25 23:23:16.973] [jointLog] [info] iteration = 544 | max rel diff. = 0.00267322 [2020-04-25 23:23:16.974] [jointLog] [info] Finished optimizer [2020-04-25 23:23:16.974] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl infected_18/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > infected_18/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/infected-uninfected/20200413.C_bairdi.73.D9.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.73.D9.uninfected.cold.megan_R2.fq -o uninfected_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/infected-uninfected/20200413.C_bairdi.73.D9.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/infected-uninfected/20200413.C_bairdi.73.D9.uninfected.cold.megan_R2.fq } ### [ output ] => { uninfected_06 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to uninfected_06/logs [2020-04-25 23:31:47.192] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 23:31:47.192] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 23:31:47.192] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 23:31:47.192] [jointLog] [info] parsing read library format [2020-04-25 23:31:47.192] [jointLog] [info] There is 1 library. [2020-04-25 23:31:47.249] [jointLog] [info] Loading pufferfish index [2020-04-25 23:31:47.249] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.221 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 189.56 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 110.63 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.707 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.062 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4735 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 93.451 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.7992 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 210.86 us ----------------------------------------- [2020-04-25 23:31:47.397] [jointLog] [info] done [2020-04-25 23:31:47.397] [jointLog] [info] Index contained 40,435 targets [2020-04-25 23:31:47.411] [jointLog] [info] Number of decoys : 0 [2020-04-25 23:31:48.638] [jointLog] [info] Computed 8,701 rich equivalence classes for further processing [2020-04-25 23:31:48.638] [jointLog] [info] Counted 91,344 total reads in the equivalence classes [2020-04-25 23:31:48.663] [jointLog] [info] Number of mappings discarded because of alignment score : 98,787 [2020-04-25 23:31:48.663] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 9,280 [2020-04-25 23:31:48.663] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 23:31:48.663] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 518 [2020-04-25 23:31:48.666] [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. [2020-04-25 23:31:48.666] [jointLog] [info] Mapping rate = 89.7518% [2020-04-25 23:31:48.666] [jointLog] [info] finished quantifyLibrary() [2020-04-25 23:31:48.668] [jointLog] [info] Starting optimizer [2020-04-25 23:31:48.683] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 23:31:48.685] [jointLog] [info] iteration = 0 | max rel diff. = 223.403 [2020-04-25 23:31:48.780] [jointLog] [info] iteration = 100 | max rel diff. = 0.164675 [2020-04-25 23:31:48.867] [jointLog] [info] iteration = 200 | max rel diff. = 0.0355829 [2020-04-25 23:31:48.910] [jointLog] [info] iteration = 253 | max rel diff. = 0.00668343 [2020-04-25 23:31:48.911] [jointLog] [info] Finished optimizer [2020-04-25 23:31:48.911] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl uninfected_06/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > uninfected_06/quant.sf.genes