CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.113.D9.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.113.D9.uninfected.cold.megan_R2.fq -o D9_01 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.113.D9.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.113.D9.uninfected.cold.megan_R2.fq } ### [ output ] => { D9_01 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_01/logs [2020-04-25 23:43:57.153] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 23:43:57.153] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 23:43:57.153] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 23:43:57.153] [jointLog] [info] parsing read library format [2020-04-25 23:43:57.153] [jointLog] [info] There is 1 library. [2020-04-25 23:43:57.211] [jointLog] [info] Loading pufferfish index [2020-04-25 23:43:57.211] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.32 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 233.58 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 116.25 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.6773 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.089 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.3846 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 120.14 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.7748 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 143.1 us ----------------------------------------- [2020-04-25 23:43:57.386] [jointLog] [info] done [2020-04-25 23:43:57.386] [jointLog] [info] Index contained 40,435 targets [2020-04-25 23:43:57.400] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,588,153, hits per frag: 4.19053 processed 1,000,000 fragments hits: 3,173,384, hits per frag: 3.84353 processed 1,500,000 fragments hits: 4,766,014, hits per frag: 3.42514 processed 2,000,000 fragments hits: 6,347,857, hits per frag: 3.2346 [2020-04-25 23:44:03.970] [jointLog] [info] Computed 73,003 rich equivalence classes for further processing [2020-04-25 23:44:03.970] [jointLog] [info] Counted 2,278,267 total reads in the equivalence classes [2020-04-25 23:44:03.987] [jointLog] [info] Number of mappings discarded because of alignment score : 461,143 [2020-04-25 23:44:03.987] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,738 [2020-04-25 23:44:03.987] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 23:44:03.987] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,352 [2020-04-25 23:44:03.990] [jointLog] [warning] Only 2278267 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 23:44:03.990] [jointLog] [info] Mapping rate = 99.1405% [2020-04-25 23:44:03.990] [jointLog] [info] finished quantifyLibrary() [2020-04-25 23:44:03.992] [jointLog] [info] Starting optimizer [2020-04-25 23:44:04.013] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 23:44:04.017] [jointLog] [info] iteration = 0 | max rel diff. = 5253.93 [2020-04-25 23:44:04.302] [jointLog] [info] iteration = 100 | max rel diff. = 4.03124 [2020-04-25 23:44:04.580] [jointLog] [info] iteration = 200 | max rel diff. = 1.49539 [2020-04-25 23:44:04.853] [jointLog] [info] iteration = 300 | max rel diff. = 4.77244 [2020-04-25 23:44:05.124] [jointLog] [info] iteration = 400 | max rel diff. = 0.389465 [2020-04-25 23:44:05.402] [jointLog] [info] iteration = 500 | max rel diff. = 0.111154 [2020-04-25 23:44:05.677] [jointLog] [info] iteration = 600 | max rel diff. = 0.182056 [2020-04-25 23:44:05.947] [jointLog] [info] iteration = 700 | max rel diff. = 0.0837297 [2020-04-25 23:44:06.220] [jointLog] [info] iteration = 800 | max rel diff. = 0.0611069 [2020-04-25 23:44:06.302] [jointLog] [info] iteration = 831 | max rel diff. = 0.00377472 [2020-04-25 23:44:06.303] [jointLog] [info] Finished optimizer [2020-04-25 23:44:06.303] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_01/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_01/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.118.D9.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.118.D9.infected.ambient.megan_R2.fq -o D9_02 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.118.D9.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.118.D9.infected.ambient.megan_R2.fq } ### [ output ] => { D9_02 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_02/logs [2020-04-25 23:52:36.960] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-25 23:52:36.960] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-25 23:52:36.960] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-25 23:52:36.960] [jointLog] [info] parsing read library format [2020-04-25 23:52:36.960] [jointLog] [info] There is 1 library. [2020-04-25 23:52:37.019] [jointLog] [info] Loading pufferfish index [2020-04-25 23:52:37.019] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 10.768 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 156.09 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 95.845 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.7795 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.098 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.3608 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 186.73 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 6.4401 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 261.28 us ----------------------------------------- [2020-04-25 23:52:37.261] [jointLog] [info] done [2020-04-25 23:52:37.261] [jointLog] [info] Index contained 40,435 targets [2020-04-25 23:52:37.276] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,774,972, hits per frag: 6.33894 processed 1,000,000 fragments hits: 5,560,567, hits per frag: 5.93121 [2020-04-25 23:52:43.368] [jointLog] [info] Computed 68,103 rich equivalence classes for further processing [2020-04-25 23:52:43.368] [jointLog] [info] Counted 1,441,032 total reads in the equivalence classes [2020-04-25 23:52:43.390] [jointLog] [info] Number of mappings discarded because of alignment score : 600,985 [2020-04-25 23:52:43.390] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 15,865 [2020-04-25 23:52:43.390] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-25 23:52:43.390] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,603 [2020-04-25 23:52:43.395] [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 23:52:43.395] [jointLog] [info] Mapping rate = 98.8786% [2020-04-25 23:52:43.395] [jointLog] [info] finished quantifyLibrary() [2020-04-25 23:52:43.396] [jointLog] [info] Starting optimizer [2020-04-25 23:52:43.419] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-25 23:52:43.428] [jointLog] [info] iteration = 0 | max rel diff. = 3389.57 [2020-04-25 23:52:43.804] [jointLog] [info] iteration = 100 | max rel diff. = 1.22199 [2020-04-25 23:52:44.190] [jointLog] [info] iteration = 200 | max rel diff. = 0.107501 [2020-04-25 23:52:44.576] [jointLog] [info] iteration = 300 | max rel diff. = 0.0774432 [2020-04-25 23:52:44.954] [jointLog] [info] iteration = 400 | max rel diff. = 0.043996 [2020-04-25 23:52:45.347] [jointLog] [info] iteration = 500 | max rel diff. = 0.0359073 [2020-04-25 23:52:45.731] [jointLog] [info] iteration = 599 | max rel diff. = 0.00158506 [2020-04-25 23:52:45.733] [jointLog] [info] Finished optimizer [2020-04-25 23:52:45.733] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_02/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_02/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.127.D9.infected.warm.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.127.D9.infected.warm.megan_R2.fq -o D9_03 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.127.D9.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.127.D9.infected.warm.megan_R2.fq } ### [ output ] => { D9_03 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_03/logs [2020-04-26 00:01:16.256] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 00:01:16.256] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 00:01:16.256] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 00:01:16.256] [jointLog] [info] parsing read library format [2020-04-26 00:01:16.256] [jointLog] [info] There is 1 library. [2020-04-26 00:01:16.314] [jointLog] [info] Loading pufferfish index [2020-04-26 00:01:16.314] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.374 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 191.58 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 107.55 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.6051 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.63 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.1197 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 140.26 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.4953 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 267.03 us ----------------------------------------- [2020-04-26 00:01:16.509] [jointLog] [info] done [2020-04-26 00:01:16.509] [jointLog] [info] Index contained 40,435 targets [2020-04-26 00:01:16.522] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,738,023, hits per frag: 5.20711 processed 1,000,000 fragments hits: 3,476,078, hits per frag: 3.73338 processed 1,500,000 fragments hits: 5,222,965, hits per frag: 3.74827 processed 2,000,000 fragments hits: 6,963,783, hits per frag: 3.5582 [2020-04-26 00:01:22.869] [jointLog] [info] Computed 76,483 rich equivalence classes for further processing [2020-04-26 00:01:22.869] [jointLog] [info] Counted 2,319,185 total reads in the equivalence classes [2020-04-26 00:01:22.887] [jointLog] [info] Number of mappings discarded because of alignment score : 536,826 [2020-04-26 00:01:22.887] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,061 [2020-04-26 00:01:22.887] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 00:01:22.887] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,328 [2020-04-26 00:01:22.890] [jointLog] [warning] Only 2319185 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 00:01:22.890] [jointLog] [info] Mapping rate = 99.1791% [2020-04-26 00:01:22.890] [jointLog] [info] finished quantifyLibrary() [2020-04-26 00:01:22.892] [jointLog] [info] Starting optimizer [2020-04-26 00:01:22.916] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 00:01:22.922] [jointLog] [info] iteration = 0 | max rel diff. = 4684.51 [2020-04-26 00:01:23.217] [jointLog] [info] iteration = 100 | max rel diff. = 4.41794 [2020-04-26 00:01:23.508] [jointLog] [info] iteration = 200 | max rel diff. = 2.96994 [2020-04-26 00:01:23.799] [jointLog] [info] iteration = 300 | max rel diff. = 0.713546 [2020-04-26 00:01:24.093] [jointLog] [info] iteration = 400 | max rel diff. = 0.224459 [2020-04-26 00:01:24.392] [jointLog] [info] iteration = 500 | max rel diff. = 0.106728 [2020-04-26 00:01:24.685] [jointLog] [info] iteration = 600 | max rel diff. = 1.1458 [2020-04-26 00:01:24.972] [jointLog] [info] iteration = 700 | max rel diff. = 0.0266081 [2020-04-26 00:01:25.250] [jointLog] [info] iteration = 800 | max rel diff. = 0.0567766 [2020-04-26 00:01:25.512] [jointLog] [info] iteration = 894 | max rel diff. = 0.00747066 [2020-04-26 00:01:25.513] [jointLog] [info] Finished optimizer [2020-04-26 00:01:25.513] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_03/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_03/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.132.D9.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.132.D9.infected.ambient.megan_R2.fq -o D9_04 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.132.D9.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.132.D9.infected.ambient.megan_R2.fq } ### [ output ] => { D9_04 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_04/logs [2020-04-26 00:09:56.066] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 00:09:56.066] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 00:09:56.066] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 00:09:56.066] [jointLog] [info] parsing read library format [2020-04-26 00:09:56.066] [jointLog] [info] There is 1 library. [2020-04-26 00:09:56.119] [jointLog] [info] Loading pufferfish index [2020-04-26 00:09:56.119] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.157 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 198.74 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 117.85 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.3861 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.263 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.5263 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 22.128 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.6134 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 209.92 us ----------------------------------------- [2020-04-26 00:09:56.195] [jointLog] [info] done [2020-04-26 00:09:56.195] [jointLog] [info] Index contained 40,435 targets [2020-04-26 00:09:56.207] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,222,373, hits per frag: 5.39652 processed 1,000,000 fragments hits: 4,444,761, hits per frag: 4.84918 processed 1,500,000 fragments hits: 6,667,712, hits per frag: 4.58649 [2020-04-26 00:10:01.918] [jointLog] [info] Computed 81,772 rich equivalence classes for further processing [2020-04-26 00:10:01.918] [jointLog] [info] Counted 1,745,454 total reads in the equivalence classes [2020-04-26 00:10:01.940] [jointLog] [info] Number of mappings discarded because of alignment score : 733,448 [2020-04-26 00:10:01.940] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,154 [2020-04-26 00:10:01.940] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 00:10:01.940] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,582 [2020-04-26 00:10:01.943] [jointLog] [warning] Only 1745454 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 00:10:01.943] [jointLog] [info] Mapping rate = 98.6937% [2020-04-26 00:10:01.943] [jointLog] [info] finished quantifyLibrary() [2020-04-26 00:10:01.945] [jointLog] [info] Starting optimizer [2020-04-26 00:10:01.967] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 00:10:01.974] [jointLog] [info] iteration = 0 | max rel diff. = 3747.53 [2020-04-26 00:10:02.335] [jointLog] [info] iteration = 100 | max rel diff. = 4.41432 [2020-04-26 00:10:02.693] [jointLog] [info] iteration = 200 | max rel diff. = 5.26484 [2020-04-26 00:10:03.050] [jointLog] [info] iteration = 300 | max rel diff. = 1.30696 [2020-04-26 00:10:03.408] [jointLog] [info] iteration = 400 | max rel diff. = 0.0219816 [2020-04-26 00:10:03.766] [jointLog] [info] iteration = 500 | max rel diff. = 0.0962094 [2020-04-26 00:10:04.125] [jointLog] [info] iteration = 600 | max rel diff. = 0.488996 [2020-04-26 00:10:04.136] [jointLog] [info] iteration = 604 | max rel diff. = 0.00683818 [2020-04-26 00:10:04.137] [jointLog] [info] Finished optimizer [2020-04-26 00:10:04.137] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_04/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_04/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.151.D9.infected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.151.D9.infected.cold.megan_R2.fq -o D9_05 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.151.D9.infected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.151.D9.infected.cold.megan_R2.fq } ### [ output ] => { D9_05 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_05/logs [2020-04-26 00:18:34.720] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 00:18:34.720] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 00:18:34.720] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 00:18:34.720] [jointLog] [info] parsing read library format [2020-04-26 00:18:34.720] [jointLog] [info] There is 1 library. [2020-04-26 00:18:34.770] [jointLog] [info] Loading pufferfish index [2020-04-26 00:18:34.770] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.256 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 208.56 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 120.14 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.4153 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.86 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.5464 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 21.652 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.5253 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 220.89 us ----------------------------------------- [2020-04-26 00:18:34.845] [jointLog] [info] done [2020-04-26 00:18:34.845] [jointLog] [info] Index contained 40,435 targets [2020-04-26 00:18:34.857] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,685,960, hits per frag: 3.98113 processed 1,000,000 fragments hits: 3,373,719, hits per frag: 3.58301 processed 1,500,000 fragments hits: 5,055,067, hits per frag: 3.88828 processed 2,000,000 fragments hits: 6,745,763, hits per frag: 3.48987 processed 2,500,000 fragments hits: 8,434,128, hits per frag: 3.44946 processed 3,000,000 fragments hits: 10,121,653, hits per frag: 3.49772 processed 3,500,000 fragments hits: 11,816,398, hits per frag: 3.54772 processed 4,000,000 fragments hits: 13,501,447, hits per frag: 3.45531 [2020-04-26 00:18:46.267] [jointLog] [info] Computed 99,603 rich equivalence classes for further processing [2020-04-26 00:18:46.267] [jointLog] [info] Counted 4,278,214 total reads in the equivalence classes [2020-04-26 00:18:46.285] [jointLog] [info] Number of mappings discarded because of alignment score : 1,083,055 [2020-04-26 00:18:46.285] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 31,025 [2020-04-26 00:18:46.285] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 00:18:46.285] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,876 [2020-04-26 00:18:46.289] [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. [2020-04-26 00:18:46.289] [jointLog] [info] Mapping rate = 99.2386% [2020-04-26 00:18:46.289] [jointLog] [info] finished quantifyLibrary() [2020-04-26 00:18:46.290] [jointLog] [info] Starting optimizer [2020-04-26 00:18:46.321] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 00:18:46.333] [jointLog] [info] iteration = 0 | max rel diff. = 9618.61 [2020-04-26 00:18:46.846] [jointLog] [info] iteration = 100 | max rel diff. = 6.9739 [2020-04-26 00:18:47.361] [jointLog] [info] iteration = 200 | max rel diff. = 4.22364 [2020-04-26 00:18:47.873] [jointLog] [info] iteration = 300 | max rel diff. = 0.295972 [2020-04-26 00:18:48.384] [jointLog] [info] iteration = 400 | max rel diff. = 0.455904 [2020-04-26 00:18:48.897] [jointLog] [info] iteration = 500 | max rel diff. = 0.130512 [2020-04-26 00:18:49.405] [jointLog] [info] iteration = 600 | max rel diff. = 5.60665 [2020-04-26 00:18:49.903] [jointLog] [info] iteration = 700 | max rel diff. = 0.0593442 [2020-04-26 00:18:50.410] [jointLog] [info] iteration = 800 | max rel diff. = 0.0590919 [2020-04-26 00:18:50.682] [jointLog] [info] iteration = 855 | max rel diff. = 0.00642465 [2020-04-26 00:18:50.684] [jointLog] [info] Finished optimizer [2020-04-26 00:18:50.684] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_05/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_05/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.173.D9.infected.warm.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.173.D9.infected.warm.megan_R2.fq -o D9_06 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.173.D9.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.173.D9.infected.warm.megan_R2.fq } ### [ output ] => { D9_06 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_06/logs [2020-04-26 00:27:21.569] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 00:27:21.569] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 00:27:21.569] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 00:27:21.569] [jointLog] [info] parsing read library format [2020-04-26 00:27:21.569] [jointLog] [info] There is 1 library. [2020-04-26 00:27:21.627] [jointLog] [info] Loading pufferfish index [2020-04-26 00:27:21.627] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.314 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 201.47 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 115.14 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.5044 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.871 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.5578 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 188.7 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 6.4402 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 268.88 us ----------------------------------------- [2020-04-26 00:27:21.873] [jointLog] [info] done [2020-04-26 00:27:21.873] [jointLog] [info] Index contained 40,435 targets [2020-04-26 00:27:21.887] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,221,613, hits per frag: 5.78188 processed 1,000,000 fragments hits: 4,449,678, hits per frag: 4.546 [2020-04-26 00:27:27.125] [jointLog] [info] Computed 53,966 rich equivalence classes for further processing [2020-04-26 00:27:27.125] [jointLog] [info] Counted 1,453,008 total reads in the equivalence classes [2020-04-26 00:27:27.144] [jointLog] [info] Number of mappings discarded because of alignment score : 568,190 [2020-04-26 00:27:27.144] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,459 [2020-04-26 00:27:27.144] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 00:27:27.144] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,199 [2020-04-26 00:27:27.148] [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. [2020-04-26 00:27:27.148] [jointLog] [info] Mapping rate = 98.6029% [2020-04-26 00:27:27.148] [jointLog] [info] finished quantifyLibrary() [2020-04-26 00:27:27.149] [jointLog] [info] Starting optimizer [2020-04-26 00:27:27.170] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 00:27:27.175] [jointLog] [info] iteration = 0 | max rel diff. = 3115.12 [2020-04-26 00:27:27.428] [jointLog] [info] iteration = 100 | max rel diff. = 4.71009 [2020-04-26 00:27:27.676] [jointLog] [info] iteration = 200 | max rel diff. = 0.712976 [2020-04-26 00:27:27.925] [jointLog] [info] iteration = 300 | max rel diff. = 0.0734371 [2020-04-26 00:27:28.173] [jointLog] [info] iteration = 400 | max rel diff. = 0.0212116 [2020-04-26 00:27:28.421] [jointLog] [info] iteration = 500 | max rel diff. = 0.0918102 [2020-04-26 00:27:28.447] [jointLog] [info] iteration = 512 | max rel diff. = 0.00949391 [2020-04-26 00:27:28.449] [jointLog] [info] Finished optimizer [2020-04-26 00:27:28.449] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_06/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_06/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.178.D9.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.178.D9.infected.ambient.megan_R2.fq -o D9_07 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.178.D9.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.178.D9.infected.ambient.megan_R2.fq } ### [ output ] => { D9_07 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_07/logs [2020-04-26 00:35:58.688] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 00:35:58.688] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 00:35:58.688] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 00:35:58.688] [jointLog] [info] parsing read library format [2020-04-26 00:35:58.688] [jointLog] [info] There is 1 library. [2020-04-26 00:35:58.742] [jointLog] [info] Loading pufferfish index [2020-04-26 00:35:58.742] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.074 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 207.69 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 62.918 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.7845 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 = 2.7509 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 98.49 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.6178 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 108.77 us ----------------------------------------- [2020-04-26 00:35:58.893] [jointLog] [info] done [2020-04-26 00:35:58.893] [jointLog] [info] Index contained 40,435 targets [2020-04-26 00:35:58.905] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,305,765, hits per frag: 5.98196 processed 1,000,001 fragments hits: 4,613,944, hits per frag: 5.32412 processed 1,500,001 fragments hits: 6,930,474, hits per frag: 4.69025 processed 2,000,001 fragments hits: 9,242,974, hits per frag: 4.94132 processed 2,500,000 fragments hits: 11,557,206, hits per frag: 4.7308 processed 3,000,000 fragments hits: 13,862,937, hits per frag: 4.78717 [2020-04-26 00:36:08.851] [jointLog] [info] Computed 93,696 rich equivalence classes for further processing [2020-04-26 00:36:08.851] [jointLog] [info] Counted 3,186,382 total reads in the equivalence classes [2020-04-26 00:36:08.873] [jointLog] [info] Number of mappings discarded because of alignment score : 1,265,419 [2020-04-26 00:36:08.873] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 26,413 [2020-04-26 00:36:08.873] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 00:36:08.873] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,312 [2020-04-26 00:36:08.877] [jointLog] [warning] Only 3186382 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 00:36:08.877] [jointLog] [info] Mapping rate = 99.1442% [2020-04-26 00:36:08.877] [jointLog] [info] finished quantifyLibrary() [2020-04-26 00:36:08.878] [jointLog] [info] Starting optimizer [2020-04-26 00:36:08.924] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 00:36:08.937] [jointLog] [info] iteration = 0 | max rel diff. = 7295.02 [2020-04-26 00:36:09.395] [jointLog] [info] iteration = 100 | max rel diff. = 18.4472 [2020-04-26 00:36:09.852] [jointLog] [info] iteration = 200 | max rel diff. = 0.374987 [2020-04-26 00:36:10.306] [jointLog] [info] iteration = 300 | max rel diff. = 0.321835 [2020-04-26 00:36:10.764] [jointLog] [info] iteration = 400 | max rel diff. = 0.595385 [2020-04-26 00:36:11.219] [jointLog] [info] iteration = 500 | max rel diff. = 0.216722 [2020-04-26 00:36:11.386] [jointLog] [info] iteration = 539 | max rel diff. = 0.00667356 [2020-04-26 00:36:11.388] [jointLog] [info] Finished optimizer [2020-04-26 00:36:11.388] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_07/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_07/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.221.D12.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.221.D12.uninfected.cold.megan_R2.fq -o D12_01 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.221.D12.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.221.D12.uninfected.cold.megan_R2.fq } ### [ output ] => { D12_01 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D12_01/logs [2020-04-26 00:44:41.439] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 00:44:41.439] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 00:44:41.439] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 00:44:41.439] [jointLog] [info] parsing read library format [2020-04-26 00:44:41.439] [jointLog] [info] There is 1 library. [2020-04-26 00:44:41.498] [jointLog] [info] Loading pufferfish index [2020-04-26 00:44:41.498] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 10.761 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 172.95 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 110.07 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.6515 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.674 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.3468 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 33.243 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.9842 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 105.96 us ----------------------------------------- [2020-04-26 00:44:41.585] [jointLog] [info] done [2020-04-26 00:44:41.585] [jointLog] [info] Index contained 40,435 targets [2020-04-26 00:44:41.599] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,243,637, hits per frag: 5.53123 processed 1,000,000 fragments hits: 4,487,680, hits per frag: 4.85924 processed 1,500,000 fragments hits: 6,734,568, hits per frag: 4.77338 processed 2,000,000 fragments hits: 8,977,938, hits per frag: 4.53937 processed 2,500,000 fragments hits: 11,219,097, hits per frag: 4.53112 [2020-04-26 00:44:50.396] [jointLog] [info] Computed 79,755 rich equivalence classes for further processing [2020-04-26 00:44:50.396] [jointLog] [info] Counted 2,609,007 total reads in the equivalence classes [2020-04-26 00:44:50.417] [jointLog] [info] Number of mappings discarded because of alignment score : 1,110,009 [2020-04-26 00:44:50.417] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,705 [2020-04-26 00:44:50.417] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 00:44:50.417] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,808 [2020-04-26 00:44:50.422] [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. [2020-04-26 00:44:50.422] [jointLog] [info] Mapping rate = 99.1136% [2020-04-26 00:44:50.422] [jointLog] [info] finished quantifyLibrary() [2020-04-26 00:44:50.423] [jointLog] [info] Starting optimizer [2020-04-26 00:44:50.446] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 00:44:50.455] [jointLog] [info] iteration = 0 | max rel diff. = 6035.87 [2020-04-26 00:44:50.864] [jointLog] [info] iteration = 100 | max rel diff. = 7.40856 [2020-04-26 00:44:51.267] [jointLog] [info] iteration = 200 | max rel diff. = 5.82293 [2020-04-26 00:44:51.672] [jointLog] [info] iteration = 300 | max rel diff. = 0.216888 [2020-04-26 00:44:51.971] [jointLog] [info] iteration = 375 | max rel diff. = 0.00745998 [2020-04-26 00:44:51.972] [jointLog] [info] Finished optimizer [2020-04-26 00:44:51.972] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D12_01/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D12_01/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.222.D12.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.222.D12.uninfected.cold.megan_R2.fq -o D12_02 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.222.D12.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.222.D12.uninfected.cold.megan_R2.fq } ### [ output ] => { D12_02 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D12_02/logs [2020-04-26 00:53:23.043] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 00:53:23.043] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 00:53:23.043] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 00:53:23.043] [jointLog] [info] parsing read library format [2020-04-26 00:53:23.043] [jointLog] [info] There is 1 library. [2020-04-26 00:53:23.101] [jointLog] [info] Loading pufferfish index [2020-04-26 00:53:23.101] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.387 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 196 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 108.34 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.6124 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.965 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.345 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 68.215 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.4888 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 195.37 us ----------------------------------------- [2020-04-26 00:53:23.223] [jointLog] [info] done [2020-04-26 00:53:23.223] [jointLog] [info] Index contained 40,435 targets [2020-04-26 00:53:23.237] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,586,488, hits per frag: 3.8137 processed 1,000,000 fragments hits: 3,171,945, hits per frag: 3.40693 [2020-04-26 00:53:27.164] [jointLog] [info] Computed 59,979 rich equivalence classes for further processing [2020-04-26 00:53:27.164] [jointLog] [info] Counted 1,344,958 total reads in the equivalence classes [2020-04-26 00:53:27.181] [jointLog] [info] Number of mappings discarded because of alignment score : 339,452 [2020-04-26 00:53:27.181] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 14,114 [2020-04-26 00:53:27.181] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 00:53:27.181] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,729 [2020-04-26 00:53:27.184] [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. [2020-04-26 00:53:27.184] [jointLog] [info] Mapping rate = 98.8393% [2020-04-26 00:53:27.184] [jointLog] [info] finished quantifyLibrary() [2020-04-26 00:53:27.187] [jointLog] [info] Starting optimizer [2020-04-26 00:53:27.212] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 00:53:27.218] [jointLog] [info] iteration = 0 | max rel diff. = 3200.66 [2020-04-26 00:53:27.461] [jointLog] [info] iteration = 100 | max rel diff. = 15.9748 [2020-04-26 00:53:27.694] [jointLog] [info] iteration = 200 | max rel diff. = 0.375802 [2020-04-26 00:53:27.934] [jointLog] [info] iteration = 300 | max rel diff. = 0.0429109 [2020-04-26 00:53:28.169] [jointLog] [info] iteration = 400 | max rel diff. = 0.0190115 [2020-04-26 00:53:28.405] [jointLog] [info] iteration = 500 | max rel diff. = 0.0215478 [2020-04-26 00:53:28.643] [jointLog] [info] iteration = 600 | max rel diff. = 0.0152558 [2020-04-26 00:53:28.878] [jointLog] [info] iteration = 700 | max rel diff. = 0.396061 [2020-04-26 00:53:29.027] [jointLog] [info] iteration = 762 | max rel diff. = 0.0029772 [2020-04-26 00:53:29.028] [jointLog] [info] Finished optimizer [2020-04-26 00:53:29.028] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D12_02/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D12_02/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.254.D12.infected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.254.D12.infected.cold.megan_R2.fq -o D12_03 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.254.D12.infected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.254.D12.infected.cold.megan_R2.fq } ### [ output ] => { D12_03 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D12_03/logs [2020-04-26 01:01:59.263] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 01:01:59.263] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 01:01:59.263] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 01:01:59.263] [jointLog] [info] parsing read library format [2020-04-26 01:01:59.264] [jointLog] [info] There is 1 library. [2020-04-26 01:01:59.316] [jointLog] [info] Loading pufferfish index [2020-04-26 01:01:59.316] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 10.983 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 200.41 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 118.02 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.3848 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.91 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.5178 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 147.14 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.0457 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 233.24 us ----------------------------------------- [2020-04-26 01:01:59.517] [jointLog] [info] done [2020-04-26 01:01:59.517] [jointLog] [info] Index contained 40,435 targets [2020-04-26 01:01:59.529] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,790,667, hits per frag: 4.04231 processed 1,000,000 fragments hits: 3,579,732, hits per frag: 3.91012 processed 1,500,000 fragments hits: 5,369,755, hits per frag: 3.67083 [2020-04-26 01:02:05.750] [jointLog] [info] Computed 64,990 rich equivalence classes for further processing [2020-04-26 01:02:05.750] [jointLog] [info] Counted 1,951,686 total reads in the equivalence classes [2020-04-26 01:02:05.767] [jointLog] [info] Number of mappings discarded because of alignment score : 660,574 [2020-04-26 01:02:05.767] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 21,117 [2020-04-26 01:02:05.767] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 01:02:05.767] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,559 [2020-04-26 01:02:05.771] [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. [2020-04-26 01:02:05.771] [jointLog] [info] Mapping rate = 98.8965% [2020-04-26 01:02:05.771] [jointLog] [info] finished quantifyLibrary() [2020-04-26 01:02:05.772] [jointLog] [info] Starting optimizer [2020-04-26 01:02:05.806] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 01:02:05.814] [jointLog] [info] iteration = 0 | max rel diff. = 4105.55 [2020-04-26 01:02:06.228] [jointLog] [info] iteration = 100 | max rel diff. = 0.699333 [2020-04-26 01:02:06.636] [jointLog] [info] iteration = 200 | max rel diff. = 2.52957 [2020-04-26 01:02:07.045] [jointLog] [info] iteration = 300 | max rel diff. = 0.302864 [2020-04-26 01:02:07.461] [jointLog] [info] iteration = 400 | max rel diff. = 0.341243 [2020-04-26 01:02:07.478] [jointLog] [info] iteration = 405 | max rel diff. = 0.00790166 [2020-04-26 01:02:07.479] [jointLog] [info] Finished optimizer [2020-04-26 01:02:07.479] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D12_03/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D12_03/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.272.D12.infected.warm.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.272.D12.infected.warm.megan_R2.fq -o D12_04 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.272.D12.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.272.D12.infected.warm.megan_R2.fq } ### [ output ] => { D12_04 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D12_04/logs [2020-04-26 01:10:37.407] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 01:10:37.407] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 01:10:37.407] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 01:10:37.407] [jointLog] [info] parsing read library format [2020-04-26 01:10:37.407] [jointLog] [info] There is 1 library. [2020-04-26 01:10:37.465] [jointLog] [info] Loading pufferfish index [2020-04-26 01:10:37.465] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.369 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 201.73 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 119.49 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.5998 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 = 2.4744 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 100.65 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.4072 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 223.63 us ----------------------------------------- [2020-04-26 01:10:37.622] [jointLog] [info] done [2020-04-26 01:10:37.622] [jointLog] [info] Index contained 40,435 targets [2020-04-26 01:10:37.636] [jointLog] [info] Number of decoys : 0 [2020-04-26 01:10:39.604] [jointLog] [info] Computed 34,296 rich equivalence classes for further processing [2020-04-26 01:10:39.604] [jointLog] [info] Counted 379,958 total reads in the equivalence classes [2020-04-26 01:10:39.638] [jointLog] [info] Number of mappings discarded because of alignment score : 250,107 [2020-04-26 01:10:39.638] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,667 [2020-04-26 01:10:39.638] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 01:10:39.638] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 899 [2020-04-26 01:10:39.642] [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. [2020-04-26 01:10:39.642] [jointLog] [info] Mapping rate = 94.4906% [2020-04-26 01:10:39.642] [jointLog] [info] finished quantifyLibrary() [2020-04-26 01:10:39.644] [jointLog] [info] Starting optimizer [2020-04-26 01:10:39.665] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 01:10:39.669] [jointLog] [info] iteration = 0 | max rel diff. = 901.762 [2020-04-26 01:10:39.863] [jointLog] [info] iteration = 100 | max rel diff. = 8.01469 [2020-04-26 01:10:40.051] [jointLog] [info] iteration = 200 | max rel diff. = 0.0667104 [2020-04-26 01:10:40.248] [jointLog] [info] iteration = 300 | max rel diff. = 0.78548 [2020-04-26 01:10:40.440] [jointLog] [info] iteration = 400 | max rel diff. = 0.0839953 [2020-04-26 01:10:40.640] [jointLog] [info] iteration = 500 | max rel diff. = 1.0362 [2020-04-26 01:10:40.669] [jointLog] [info] iteration = 516 | max rel diff. = 0.000648412 [2020-04-26 01:10:40.670] [jointLog] [info] Finished optimizer [2020-04-26 01:10:40.670] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D12_04/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D12_04/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.280.D12.infected.warm.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.280.D12.infected.warm.megan_R2.fq -o D12_05 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.280.D12.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.280.D12.infected.warm.megan_R2.fq } ### [ output ] => { D12_05 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D12_05/logs [2020-04-26 01:19:11.334] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 01:19:11.334] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 01:19:11.334] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 01:19:11.334] [jointLog] [info] parsing read library format [2020-04-26 01:19:11.334] [jointLog] [info] There is 1 library. [2020-04-26 01:19:11.402] [jointLog] [info] Loading pufferfish index [2020-04-26 01:19:11.402] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 18.573 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 213.68 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 126.25 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.8339 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.117 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4383 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 146.15 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.017 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 221.79 us ----------------------------------------- [2020-04-26 01:19:11.610] [jointLog] [info] done [2020-04-26 01:19:11.610] [jointLog] [info] Index contained 40,435 targets [2020-04-26 01:19:11.624] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,858,792, hits per frag: 4.93245 [2020-04-26 01:19:14.388] [jointLog] [info] Computed 61,135 rich equivalence classes for further processing [2020-04-26 01:19:14.388] [jointLog] [info] Counted 792,535 total reads in the equivalence classes [2020-04-26 01:19:14.406] [jointLog] [info] Number of mappings discarded because of alignment score : 329,161 [2020-04-26 01:19:14.406] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,416 [2020-04-26 01:19:14.406] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 01:19:14.406] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,914 [2020-04-26 01:19:14.410] [jointLog] [warning] Only 792535 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 01:19:14.410] [jointLog] [info] Mapping rate = 97.217% [2020-04-26 01:19:14.410] [jointLog] [info] finished quantifyLibrary() [2020-04-26 01:19:14.412] [jointLog] [info] Starting optimizer [2020-04-26 01:19:14.432] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 01:19:14.437] [jointLog] [info] iteration = 0 | max rel diff. = 1898.84 [2020-04-26 01:19:14.660] [jointLog] [info] iteration = 100 | max rel diff. = 0.878653 [2020-04-26 01:19:14.878] [jointLog] [info] iteration = 200 | max rel diff. = 19.6534 [2020-04-26 01:19:15.090] [jointLog] [info] iteration = 300 | max rel diff. = 0.0151188 [2020-04-26 01:19:15.306] [jointLog] [info] iteration = 399 | max rel diff. = 0.00554938 [2020-04-26 01:19:15.307] [jointLog] [info] Finished optimizer [2020-04-26 01:19:15.307] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D12_05/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D12_05/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.294.D12.infected.warm.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.294.D12.infected.warm.megan_R2.fq -o D12_06 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.294.D12.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.294.D12.infected.warm.megan_R2.fq } ### [ output ] => { D12_06 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D12_06/logs [2020-04-26 01:27:45.503] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 01:27:45.503] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 01:27:45.503] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 01:27:45.503] [jointLog] [info] parsing read library format [2020-04-26 01:27:45.503] [jointLog] [info] There is 1 library. [2020-04-26 01:27:45.555] [jointLog] [info] Loading pufferfish index [2020-04-26 01:27:45.555] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.057 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 205.12 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 114.38 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.4079 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.073 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4604 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 112.62 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 6.4091 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 321.55 us ----------------------------------------- [2020-04-26 01:27:45.724] [jointLog] [info] done [2020-04-26 01:27:45.724] [jointLog] [info] Index contained 40,435 targets [2020-04-26 01:27:45.740] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,736,971, hits per frag: 4.29731 processed 1,000,000 fragments hits: 3,474,249, hits per frag: 4.00783 processed 1,500,000 fragments hits: 5,217,876, hits per frag: 3.66142 processed 2,000,000 fragments hits: 6,965,139, hits per frag: 3.64068 processed 2,500,000 fragments hits: 8,705,642, hits per frag: 3.66523 processed 3,000,000 fragments hits: 10,449,809, hits per frag: 3.54996 [2020-04-26 01:27:54.456] [jointLog] [info] Computed 81,531 rich equivalence classes for further processing [2020-04-26 01:27:54.456] [jointLog] [info] Counted 3,165,463 total reads in the equivalence classes [2020-04-26 01:27:54.474] [jointLog] [info] Number of mappings discarded because of alignment score : 937,197 [2020-04-26 01:27:54.474] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 23,634 [2020-04-26 01:27:54.474] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 01:27:54.474] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,170 [2020-04-26 01:27:54.477] [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. [2020-04-26 01:27:54.477] [jointLog] [info] Mapping rate = 99.2286% [2020-04-26 01:27:54.477] [jointLog] [info] finished quantifyLibrary() [2020-04-26 01:27:54.478] [jointLog] [info] Starting optimizer [2020-04-26 01:27:54.503] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 01:27:54.512] [jointLog] [info] iteration = 0 | max rel diff. = 7006.3 [2020-04-26 01:27:54.967] [jointLog] [info] iteration = 100 | max rel diff. = 14.0406 [2020-04-26 01:27:55.420] [jointLog] [info] iteration = 200 | max rel diff. = 1.15886 [2020-04-26 01:27:55.874] [jointLog] [info] iteration = 300 | max rel diff. = 0.0870837 [2020-04-26 01:27:56.323] [jointLog] [info] iteration = 400 | max rel diff. = 0.171369 [2020-04-26 01:27:56.754] [jointLog] [info] iteration = 500 | max rel diff. = 0.0918939 [2020-04-26 01:27:57.180] [jointLog] [info] iteration = 600 | max rel diff. = 0.0217714 [2020-04-26 01:27:57.337] [jointLog] [info] iteration = 637 | max rel diff. = 0.00370413 [2020-04-26 01:27:57.339] [jointLog] [info] Finished optimizer [2020-04-26 01:27:57.339] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D12_06/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D12_06/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.334.D12.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.334.D12.infected.ambient.megan_R2.fq -o D12_07 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.334.D12.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.334.D12.infected.ambient.megan_R2.fq } ### [ output ] => { D12_07 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D12_07/logs [2020-04-26 01:36:27.745] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 01:36:27.745] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 01:36:27.745] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 01:36:27.745] [jointLog] [info] parsing read library format [2020-04-26 01:36:27.746] [jointLog] [info] There is 1 library. [2020-04-26 01:36:27.797] [jointLog] [info] Loading pufferfish index [2020-04-26 01:36:27.797] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 10.919 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 201.21 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 116.81 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.8886 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.933 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.5002 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 138.67 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.0864 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 118.47 us ----------------------------------------- [2020-04-26 01:36:27.989] [jointLog] [info] done [2020-04-26 01:36:27.989] [jointLog] [info] Index contained 40,435 targets [2020-04-26 01:36:28.001] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,645,545, hits per frag: 6.10157 processed 1,000,000 fragments hits: 5,294,763, hits per frag: 5.56911 [2020-04-26 01:36:32.648] [jointLog] [info] Computed 60,278 rich equivalence classes for further processing [2020-04-26 01:36:32.648] [jointLog] [info] Counted 1,107,450 total reads in the equivalence classes [2020-04-26 01:36:32.667] [jointLog] [info] Number of mappings discarded because of alignment score : 485,230 [2020-04-26 01:36:32.667] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 12,162 [2020-04-26 01:36:32.667] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 01:36:32.667] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,777 [2020-04-26 01:36:32.671] [jointLog] [warning] Only 1107450 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 01:36:32.671] [jointLog] [info] Mapping rate = 98.8796% [2020-04-26 01:36:32.671] [jointLog] [info] finished quantifyLibrary() [2020-04-26 01:36:32.673] [jointLog] [info] Starting optimizer [2020-04-26 01:36:32.693] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 01:36:32.700] [jointLog] [info] iteration = 0 | max rel diff. = 2447.76 [2020-04-26 01:36:33.003] [jointLog] [info] iteration = 100 | max rel diff. = 0.432227 [2020-04-26 01:36:33.310] [jointLog] [info] iteration = 200 | max rel diff. = 0.877732 [2020-04-26 01:36:33.607] [jointLog] [info] iteration = 300 | max rel diff. = 0.505082 [2020-04-26 01:36:33.895] [jointLog] [info] iteration = 400 | max rel diff. = 0.517791 [2020-04-26 01:36:34.031] [jointLog] [info] iteration = 449 | max rel diff. = 0.00321503 [2020-04-26 01:36:34.033] [jointLog] [info] Finished optimizer [2020-04-26 01:36:34.033] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D12_07/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D12_07/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.349.D12.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.349.D12.infected.ambient.megan_R2.fq -o D12_08 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.349.D12.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.349.D12.infected.ambient.megan_R2.fq } ### [ output ] => { D12_08 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D12_08/logs [2020-04-26 01:45:04.614] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 01:45:04.614] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 01:45:04.614] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 01:45:04.614] [jointLog] [info] parsing read library format [2020-04-26 01:45:04.614] [jointLog] [info] There is 1 library. ----------------------------------------- | Loading contig table | Time = 11.242 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 201.75 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 116.31 us ----------------------------------------- [2020-04-26 01:45:04.677] [jointLog] [info] Loading pufferfish index [2020-04-26 01:45:04.677] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading mphf table | Time = 6.5108 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.762 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4461 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 101.42 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.2847 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 216.26 us ----------------------------------------- [2020-04-26 01:45:04.834] [jointLog] [info] done [2020-04-26 01:45:04.834] [jointLog] [info] Index contained 40,435 targets [2020-04-26 01:45:04.848] [jointLog] [info] Number of decoys : 0 [2020-04-26 01:45:05.689] [jointLog] [info] Computed 21,295 rich equivalence classes for further processing [2020-04-26 01:45:05.689] [jointLog] [info] Counted 79,375 total reads in the equivalence classes [2020-04-26 01:45:05.716] [jointLog] [info] Number of mappings discarded because of alignment score : 85,737 [2020-04-26 01:45:05.716] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 8,609 [2020-04-26 01:45:05.716] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 01:45:05.716] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 338 [2020-04-26 01:45:05.719] [jointLog] [warning] Only 79375 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 01:45:05.719] [jointLog] [info] Mapping rate = 86.6407% [2020-04-26 01:45:05.719] [jointLog] [info] finished quantifyLibrary() [2020-04-26 01:45:05.721] [jointLog] [info] Starting optimizer [2020-04-26 01:45:05.733] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 01:45:05.735] [jointLog] [info] iteration = 0 | max rel diff. = 190.219 [2020-04-26 01:45:05.840] [jointLog] [info] iteration = 100 | max rel diff. = 0.221464 [2020-04-26 01:45:05.910] [jointLog] [info] iteration = 175 | max rel diff. = 0.00828657 [2020-04-26 01:45:05.911] [jointLog] [info] Finished optimizer [2020-04-26 01:45:05.911] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D12_08/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D12_08/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.359.D12.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.359.D12.infected.ambient.megan_R2.fq -o D12_09 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.359.D12.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.359.D12.infected.ambient.megan_R2.fq } ### [ output ] => { D12_09 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D12_09/logs [2020-04-26 01:53:36.352] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 01:53:36.352] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 01:53:36.352] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 01:53:36.352] [jointLog] [info] parsing read library format [2020-04-26 01:53:36.352] [jointLog] [info] There is 1 library. [2020-04-26 01:53:36.404] [jointLog] [info] Loading pufferfish index [2020-04-26 01:53:36.404] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.391 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 204.41 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 114.22 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.4691 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.92 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.4387 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 22.48 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.5975 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 214.54 us ----------------------------------------- [2020-04-26 01:53:36.480] [jointLog] [info] done [2020-04-26 01:53:36.480] [jointLog] [info] Index contained 40,435 targets [2020-04-26 01:53:36.492] [jointLog] [info] Number of decoys : 0  processed 500,001 fragments hits: 2,086,838, hits per frag: 5.74564 processed 1,000,000 fragments hits: 4,174,589, hits per frag: 4.55398 processed 1,500,000 fragments hits: 6,263,821, hits per frag: 4.40568 processed 2,000,000 fragments hits: 8,361,549, hits per frag: 4.38907 processed 2,500,000 fragments hits: 10,451,669, hits per frag: 4.25726 processed 3,000,000 fragments hits: 12,534,801, hits per frag: 4.32948 [2020-04-26 01:53:45.861] [jointLog] [info] Computed 95,566 rich equivalence classes for further processing [2020-04-26 01:53:45.861] [jointLog] [info] Counted 3,196,427 total reads in the equivalence classes [2020-04-26 01:53:45.881] [jointLog] [info] Number of mappings discarded because of alignment score : 1,080,607 [2020-04-26 01:53:45.881] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 24,484 [2020-04-26 01:53:45.881] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 01:53:45.881] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,462 [2020-04-26 01:53:45.884] [jointLog] [warning] Only 3196427 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 01:53:45.884] [jointLog] [info] Mapping rate = 99.2017% [2020-04-26 01:53:45.884] [jointLog] [info] finished quantifyLibrary() [2020-04-26 01:53:45.885] [jointLog] [info] Starting optimizer [2020-04-26 01:53:45.910] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 01:53:45.917] [jointLog] [info] iteration = 0 | max rel diff. = 7372.2 [2020-04-26 01:53:46.322] [jointLog] [info] iteration = 100 | max rel diff. = 16.4913 [2020-04-26 01:53:46.723] [jointLog] [info] iteration = 200 | max rel diff. = 11.3941 [2020-04-26 01:53:47.118] [jointLog] [info] iteration = 300 | max rel diff. = 0.735245 [2020-04-26 01:53:47.515] [jointLog] [info] iteration = 400 | max rel diff. = 0.351225 [2020-04-26 01:53:47.908] [jointLog] [info] iteration = 500 | max rel diff. = 0.154959 [2020-04-26 01:53:48.309] [jointLog] [info] iteration = 600 | max rel diff. = 0.0119094 [2020-04-26 01:53:48.702] [jointLog] [info] iteration = 700 | max rel diff. = 0.0420495 [2020-04-26 01:53:49.093] [jointLog] [info] iteration = 800 | max rel diff. = 0.0424652 [2020-04-26 01:53:49.257] [jointLog] [info] iteration = 843 | max rel diff. = 0.00706082 [2020-04-26 01:53:49.259] [jointLog] [info] Finished optimizer [2020-04-26 01:53:49.259] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D12_09/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D12_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/D9-D12/20200413.C_bairdi.72.D9.infected.warm.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.72.D9.infected.warm.megan_R2.fq -o D9_08 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.72.D9.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.72.D9.infected.warm.megan_R2.fq } ### [ output ] => { D9_08 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_08/logs [2020-04-26 02:02:19.872] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 02:02:19.872] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 02:02:19.872] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 02:02:19.872] [jointLog] [info] parsing read library format [2020-04-26 02:02:19.872] [jointLog] [info] There is 1 library. [2020-04-26 02:02:19.932] [jointLog] [info] Loading pufferfish index [2020-04-26 02:02:19.932] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.256 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 200.75 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 118.46 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.5783 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.251 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.7769 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 169.31 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.9414 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 253.68 us ----------------------------------------- [2020-04-26 02:02:20.158] [jointLog] [info] done [2020-04-26 02:02:20.158] [jointLog] [info] Index contained 40,435 targets [2020-04-26 02:02:20.173] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,671,463, hits per frag: 5.62028 processed 1,000,000 fragments hits: 5,359,029, hits per frag: 6.18121 processed 1,500,000 fragments hits: 8,041,023, hits per frag: 5.72789 [2020-04-26 02:02:25.943] [jointLog] [info] Computed 63,961 rich equivalence classes for further processing [2020-04-26 02:02:25.943] [jointLog] [info] Counted 1,547,156 total reads in the equivalence classes [2020-04-26 02:02:25.965] [jointLog] [info] Number of mappings discarded because of alignment score : 744,608 [2020-04-26 02:02:25.965] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 20,255 [2020-04-26 02:02:25.965] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 02:02:25.965] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,061 [2020-04-26 02:02:25.969] [jointLog] [warning] Only 1547156 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 02:02:25.969] [jointLog] [info] Mapping rate = 98.6772% [2020-04-26 02:02:25.969] [jointLog] [info] finished quantifyLibrary() [2020-04-26 02:02:25.970] [jointLog] [info] Starting optimizer [2020-04-26 02:02:25.989] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 02:02:25.994] [jointLog] [info] iteration = 0 | max rel diff. = 3444.41 [2020-04-26 02:02:26.315] [jointLog] [info] iteration = 100 | max rel diff. = 1.74183 [2020-04-26 02:02:26.631] [jointLog] [info] iteration = 200 | max rel diff. = 0.123649 [2020-04-26 02:02:26.947] [jointLog] [info] iteration = 300 | max rel diff. = 0.132202 [2020-04-26 02:02:27.259] [jointLog] [info] iteration = 400 | max rel diff. = 0.0848587 [2020-04-26 02:02:27.296] [jointLog] [info] iteration = 413 | max rel diff. = 0.00990777 [2020-04-26 02:02:27.297] [jointLog] [info] Finished optimizer [2020-04-26 02:02:27.297] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_08/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_08/quant.sf.genes CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l IU -1 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.73.D9.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.73.D9.uninfected.cold.megan_R2.fq -o D9_09 -p 28 --validateMappings Version Info: Could not resolve upgrade information in the alotted time. Check for upgrades manually at https://combine-lab.github.io/salmon ### salmon (mapping-based) v1.1.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { IU } ### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.73.D9.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/D9-D12/20200413.C_bairdi.73.D9.uninfected.cold.megan_R2.fq } ### [ output ] => { D9_09 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to D9_09/logs [2020-04-26 02:10:57.762] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 02:10:57.762] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 02:10:57.762] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 02:10:57.762] [jointLog] [info] parsing read library format [2020-04-26 02:10:57.762] [jointLog] [info] There is 1 library. [2020-04-26 02:10:57.820] [jointLog] [info] Loading pufferfish index [2020-04-26 02:10:57.820] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.072 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 190.07 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 119.28 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.6863 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 = 2.1277 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 87.084 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.6137 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 197.61 us ----------------------------------------- [2020-04-26 02:10:57.960] [jointLog] [info] done [2020-04-26 02:10:57.960] [jointLog] [info] Index contained 40,435 targets [2020-04-26 02:10:57.974] [jointLog] [info] Number of decoys : 0 [2020-04-26 02:10:59.100] [jointLog] [info] Computed 8,741 rich equivalence classes for further processing [2020-04-26 02:10:59.100] [jointLog] [info] Counted 91,344 total reads in the equivalence classes [2020-04-26 02:10:59.124] [jointLog] [info] Number of mappings discarded because of alignment score : 98,787 [2020-04-26 02:10:59.124] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 9,280 [2020-04-26 02:10:59.124] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 02:10:59.124] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 518 [2020-04-26 02:10:59.127] [jointLog] [warning] Only 91344 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 02:10:59.127] [jointLog] [info] Mapping rate = 89.7518% [2020-04-26 02:10:59.127] [jointLog] [info] finished quantifyLibrary() [2020-04-26 02:10:59.129] [jointLog] [info] Starting optimizer [2020-04-26 02:10:59.142] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 02:10:59.144] [jointLog] [info] iteration = 0 | max rel diff. = 223.367 [2020-04-26 02:10:59.233] [jointLog] [info] iteration = 100 | max rel diff. = 0.163458 [2020-04-26 02:10:59.262] [jointLog] [info] iteration = 136 | max rel diff. = 0.0072367 [2020-04-26 02:10:59.262] [jointLog] [info] Finished optimizer [2020-04-26 02:10:59.262] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl D9_09/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > D9_09/quant.sf.genes