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/ambient-cold/20200413.C_bairdi.113.D9.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.113.D9.uninfected.cold.megan_R2.fq -o cold_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/ambient-cold/20200413.C_bairdi.113.D9.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.113.D9.uninfected.cold.megan_R2.fq } ### [ output ] => { cold_01 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to cold_01/logs [2020-04-26 06:47:10.943] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 06:47:10.943] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 06:47:10.943] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 06:47:10.943] [jointLog] [info] parsing read library format [2020-04-26 06:47:10.943] [jointLog] [info] There is 1 library. [2020-04-26 06:47:10.996] [jointLog] [info] Loading pufferfish index [2020-04-26 06:47:10.996] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.279 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 210.43 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 116.18 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.4273 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.075 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.3993 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 196.28 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.9098 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 273.36 us ----------------------------------------- [2020-04-26 06:47:11.248] [jointLog] [info] done [2020-04-26 06:47:11.248] [jointLog] [info] Index contained 40,435 targets [2020-04-26 06:47:11.260] [jointLog] [info] Number of decoys : 0  processed 500,001 fragments hits: 1,588,264, hits per frag: 3.73 processed 1,000,000 fragments hits: 3,173,182, hits per frag: 3.51263 processed 1,500,000 fragments hits: 4,765,907, hits per frag: 3.36883 processed 2,000,000 fragments hits: 6,347,964, hits per frag: 3.31724 [2020-04-26 06:47:17.939] [jointLog] [info] Computed 72,896 rich equivalence classes for further processing [2020-04-26 06:47:17.939] [jointLog] [info] Counted 2,278,269 total reads in the equivalence classes [2020-04-26 06:47:17.956] [jointLog] [info] Number of mappings discarded because of alignment score : 461,126 [2020-04-26 06:47:17.956] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,736 [2020-04-26 06:47:17.956] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 06:47:17.956] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,352 [2020-04-26 06:47:17.959] [jointLog] [warning] Only 2278269 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 06:47:17.959] [jointLog] [info] Mapping rate = 99.1406% [2020-04-26 06:47:17.959] [jointLog] [info] finished quantifyLibrary() [2020-04-26 06:47:17.961] [jointLog] [info] Starting optimizer [2020-04-26 06:47:17.983] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 06:47:17.988] [jointLog] [info] iteration = 0 | max rel diff. = 5251.8 [2020-04-26 06:47:18.272] [jointLog] [info] iteration = 100 | max rel diff. = 4.04623 [2020-04-26 06:47:18.553] [jointLog] [info] iteration = 200 | max rel diff. = 0.447318 [2020-04-26 06:47:18.831] [jointLog] [info] iteration = 300 | max rel diff. = 0.569988 [2020-04-26 06:47:19.112] [jointLog] [info] iteration = 400 | max rel diff. = 0.168167 [2020-04-26 06:47:19.387] [jointLog] [info] iteration = 500 | max rel diff. = 19.2218 [2020-04-26 06:47:19.671] [jointLog] [info] iteration = 600 | max rel diff. = 0.201265 [2020-04-26 06:47:19.942] [jointLog] [info] iteration = 700 | max rel diff. = 0.0526721 [2020-04-26 06:47:20.217] [jointLog] [info] iteration = 800 | max rel diff. = 0.11362 [2020-04-26 06:47:20.307] [jointLog] [info] iteration = 833 | max rel diff. = 0.00428601 [2020-04-26 06:47:20.309] [jointLog] [info] Finished optimizer [2020-04-26 06:47:20.309] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl cold_01/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > cold_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/ambient-cold/20200413.C_bairdi.118.D9.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.118.D9.infected.ambient.megan_R2.fq -o ambient_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/ambient-cold/20200413.C_bairdi.118.D9.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.118.D9.infected.ambient.megan_R2.fq } ### [ output ] => { ambient_01 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to ambient_01/logs [2020-04-26 06:55:50.884] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 06:55:50.884] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 06:55:50.884] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 06:55:50.884] [jointLog] [info] parsing read library format [2020-04-26 06:55:50.884] [jointLog] [info] There is 1 library. [2020-04-26 06:55:50.944] [jointLog] [info] Loading pufferfish index [2020-04-26 06:55:50.944] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.368 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 215.4 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 123.46 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.4584 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.271 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.7151 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 129.27 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.3482 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 217.54 us ----------------------------------------- [2020-04-26 06:55:51.129] [jointLog] [info] done [2020-04-26 06:55:51.129] [jointLog] [info] Index contained 40,435 targets [2020-04-26 06:55:51.143] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,774,255, hits per frag: 6.78438 processed 1,000,001 fragments hits: 5,561,756, hits per frag: 6.26978 [2020-04-26 06:55:57.048] [jointLog] [info] Computed 68,078 rich equivalence classes for further processing [2020-04-26 06:55:57.048] [jointLog] [info] Counted 1,441,032 total reads in the equivalence classes [2020-04-26 06:55:57.077] [jointLog] [info] Number of mappings discarded because of alignment score : 600,987 [2020-04-26 06:55:57.077] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 15,865 [2020-04-26 06:55:57.077] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 06:55:57.077] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,603 [2020-04-26 06:55:57.081] [jointLog] [warning] Only 1441032 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 06:55:57.081] [jointLog] [info] Mapping rate = 98.8786% [2020-04-26 06:55:57.081] [jointLog] [info] finished quantifyLibrary() [2020-04-26 06:55:57.083] [jointLog] [info] Starting optimizer [2020-04-26 06:55:57.114] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 06:55:57.124] [jointLog] [info] iteration = 0 | max rel diff. = 3390.97 [2020-04-26 06:55:57.521] [jointLog] [info] iteration = 100 | max rel diff. = 3.2453 [2020-04-26 06:55:57.912] [jointLog] [info] iteration = 200 | max rel diff. = 5.81034 [2020-04-26 06:55:58.301] [jointLog] [info] iteration = 300 | max rel diff. = 0.0265555 [2020-04-26 06:55:58.690] [jointLog] [info] iteration = 400 | max rel diff. = 0.0447717 [2020-04-26 06:55:59.084] [jointLog] [info] iteration = 500 | max rel diff. = 0.181473 [2020-04-26 06:55:59.480] [jointLog] [info] iteration = 600 | max rel diff. = 0.879968 [2020-04-26 06:55:59.490] [jointLog] [info] iteration = 603 | max rel diff. = 0.00401471 [2020-04-26 06:55:59.494] [jointLog] [info] Finished optimizer [2020-04-26 06:55:59.494] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl ambient_01/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > ambient_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/ambient-cold/20200413.C_bairdi.132.D9.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.132.D9.infected.ambient.megan_R2.fq -o ambient_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/ambient-cold/20200413.C_bairdi.132.D9.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.132.D9.infected.ambient.megan_R2.fq } ### [ output ] => { ambient_02 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to ambient_02/logs [2020-04-26 07:04:30.047] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 07:04:30.047] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 07:04:30.047] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 07:04:30.047] [jointLog] [info] parsing read library format [2020-04-26 07:04:30.047] [jointLog] [info] There is 1 library. [2020-04-26 07:04:30.102] [jointLog] [info] Loading pufferfish index [2020-04-26 07:04:30.103] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 16.342 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 202.96 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 129.22 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.4379 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.209 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.7451 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 66.406 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.9197 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 219.09 us ----------------------------------------- [2020-04-26 07:04:30.229] [jointLog] [info] done [2020-04-26 07:04:30.229] [jointLog] [info] Index contained 40,435 targets [2020-04-26 07:04:30.240] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,222,313, hits per frag: 4.76185 processed 1,000,000 fragments hits: 4,444,814, hits per frag: 4.97276 processed 1,500,000 fragments hits: 6,667,014, hits per frag: 4.76534 [2020-04-26 07:04:36.130] [jointLog] [info] Computed 81,779 rich equivalence classes for further processing [2020-04-26 07:04:36.130] [jointLog] [info] Counted 1,745,454 total reads in the equivalence classes [2020-04-26 07:04:36.151] [jointLog] [info] Number of mappings discarded because of alignment score : 733,446 [2020-04-26 07:04:36.151] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,154 [2020-04-26 07:04:36.151] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 07:04:36.151] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,582 [2020-04-26 07:04:36.154] [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 07:04:36.154] [jointLog] [info] Mapping rate = 98.6937% [2020-04-26 07:04:36.154] [jointLog] [info] finished quantifyLibrary() [2020-04-26 07:04:36.156] [jointLog] [info] Starting optimizer [2020-04-26 07:04:36.183] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 07:04:36.189] [jointLog] [info] iteration = 0 | max rel diff. = 3747.29 [2020-04-26 07:04:36.519] [jointLog] [info] iteration = 100 | max rel diff. = 4.26197 [2020-04-26 07:04:36.857] [jointLog] [info] iteration = 200 | max rel diff. = 2.41322 [2020-04-26 07:04:37.197] [jointLog] [info] iteration = 300 | max rel diff. = 1.03586 [2020-04-26 07:04:37.545] [jointLog] [info] iteration = 400 | max rel diff. = 0.0529547 [2020-04-26 07:04:37.893] [jointLog] [info] iteration = 500 | max rel diff. = 0.0102767 [2020-04-26 07:04:38.247] [jointLog] [info] iteration = 600 | max rel diff. = 0.290856 [2020-04-26 07:04:38.265] [jointLog] [info] iteration = 606 | max rel diff. = 0.00617136 [2020-04-26 07:04:38.266] [jointLog] [info] Finished optimizer [2020-04-26 07:04:38.266] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl ambient_02/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > ambient_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/ambient-cold/20200413.C_bairdi.151.D9.infected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.151.D9.infected.cold.megan_R2.fq -o cold_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/ambient-cold/20200413.C_bairdi.151.D9.infected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.151.D9.infected.cold.megan_R2.fq } ### [ output ] => { cold_02 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to cold_02/logs [2020-04-26 07:13:08.714] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 07:13:08.714] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 07:13:08.714] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 07:13:08.714] [jointLog] [info] parsing read library format [2020-04-26 07:13:08.714] [jointLog] [info] There is 1 library. ----------------------------------------- | Loading contig table | Time = 17.186 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 213.44 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 73.103 us ----------------------------------------- [2020-04-26 07:13:08.776] [jointLog] [info] Loading pufferfish index [2020-04-26 07:13:08.777] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading mphf table | Time = 6.3181 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.055 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.7324 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 69.205 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.3844 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 112.89 us ----------------------------------------- [2020-04-26 07:13:08.907] [jointLog] [info] done [2020-04-26 07:13:08.907] [jointLog] [info] Index contained 40,435 targets [2020-04-26 07:13:08.921] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,686,046, hits per frag: 4.27778 processed 1,000,000 fragments hits: 3,373,914, hits per frag: 3.85516 processed 1,500,000 fragments hits: 5,055,037, hits per frag: 3.46157 processed 2,000,001 fragments hits: 6,745,527, hits per frag: 3.53077 processed 2,500,000 fragments hits: 8,435,614, hits per frag: 3.58648 processed 3,000,000 fragments hits: 10,121,283, hits per frag: 3.40259 processed 3,500,000 fragments hits: 11,816,124, hits per frag: 3.52947 processed 4,000,000 fragments hits: 13,500,655, hits per frag: 3.44599 [2020-04-26 07:13:20.160] [jointLog] [info] Computed 99,602 rich equivalence classes for further processing [2020-04-26 07:13:20.160] [jointLog] [info] Counted 4,278,214 total reads in the equivalence classes [2020-04-26 07:13:20.179] [jointLog] [info] Number of mappings discarded because of alignment score : 1,083,051 [2020-04-26 07:13:20.179] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 31,025 [2020-04-26 07:13:20.179] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 07:13:20.179] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,877 [2020-04-26 07:13:20.183] [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 07:13:20.183] [jointLog] [info] Mapping rate = 99.2386% [2020-04-26 07:13:20.183] [jointLog] [info] finished quantifyLibrary() [2020-04-26 07:13:20.184] [jointLog] [info] Starting optimizer [2020-04-26 07:13:20.208] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 07:13:20.220] [jointLog] [info] iteration = 0 | max rel diff. = 9617.12 [2020-04-26 07:13:20.737] [jointLog] [info] iteration = 100 | max rel diff. = 8.28216 [2020-04-26 07:13:21.254] [jointLog] [info] iteration = 200 | max rel diff. = 5.66174 [2020-04-26 07:13:21.771] [jointLog] [info] iteration = 300 | max rel diff. = 0.322196 [2020-04-26 07:13:22.287] [jointLog] [info] iteration = 400 | max rel diff. = 0.597547 [2020-04-26 07:13:22.812] [jointLog] [info] iteration = 500 | max rel diff. = 0.165034 [2020-04-26 07:13:23.331] [jointLog] [info] iteration = 600 | max rel diff. = 0.224161 [2020-04-26 07:13:23.850] [jointLog] [info] iteration = 700 | max rel diff. = 0.0609157 [2020-04-26 07:13:24.368] [jointLog] [info] iteration = 800 | max rel diff. = 0.0650154 [2020-04-26 07:13:24.684] [jointLog] [info] iteration = 862 | max rel diff. = 0.00325945 [2020-04-26 07:13:24.687] [jointLog] [info] Finished optimizer [2020-04-26 07:13:24.687] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl cold_02/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > cold_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/ambient-cold/20200413.C_bairdi.178.D9.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.178.D9.infected.ambient.megan_R2.fq -o ambient_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/ambient-cold/20200413.C_bairdi.178.D9.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.178.D9.infected.ambient.megan_R2.fq } ### [ output ] => { ambient_03 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to ambient_03/logs [2020-04-26 07:21:55.313] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 07:21:55.313] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 07:21:55.313] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 07:21:55.313] [jointLog] [info] parsing read library format [2020-04-26 07:21:55.313] [jointLog] [info] There is 1 library. [2020-04-26 07:21:55.371] [jointLog] [info] Loading pufferfish index [2020-04-26 07:21:55.371] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 10.835 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 186.84 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 111.62 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.6798 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.795 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.3069 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 68.581 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.0165 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 213.14 us ----------------------------------------- [2020-04-26 07:21:55.493] [jointLog] [info] done [2020-04-26 07:21:55.493] [jointLog] [info] Index contained 40,435 targets [2020-04-26 07:21:55.507] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,306,529, hits per frag: 6.41322 processed 1,000,001 fragments hits: 4,614,057, hits per frag: 4.75595 processed 1,500,000 fragments hits: 6,928,905, hits per frag: 5.01693 processed 2,000,000 fragments hits: 9,243,120, hits per frag: 4.85883 processed 2,500,000 fragments hits: 11,556,289, hits per frag: 4.68554 processed 3,000,000 fragments hits: 13,862,301, hits per frag: 4.81521 [2020-04-26 07:22:05.110] [jointLog] [info] Computed 93,527 rich equivalence classes for further processing [2020-04-26 07:22:05.110] [jointLog] [info] Counted 3,186,382 total reads in the equivalence classes [2020-04-26 07:22:05.131] [jointLog] [info] Number of mappings discarded because of alignment score : 1,265,421 [2020-04-26 07:22:05.131] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 26,413 [2020-04-26 07:22:05.131] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 07:22:05.131] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 5,312 [2020-04-26 07:22:05.135] [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 07:22:05.135] [jointLog] [info] Mapping rate = 99.1442% [2020-04-26 07:22:05.135] [jointLog] [info] finished quantifyLibrary() [2020-04-26 07:22:05.137] [jointLog] [info] Starting optimizer [2020-04-26 07:22:05.169] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 07:22:05.179] [jointLog] [info] iteration = 0 | max rel diff. = 7295.8 [2020-04-26 07:22:05.629] [jointLog] [info] iteration = 100 | max rel diff. = 13.4681 [2020-04-26 07:22:06.084] [jointLog] [info] iteration = 200 | max rel diff. = 2.82041 [2020-04-26 07:22:06.534] [jointLog] [info] iteration = 300 | max rel diff. = 0.315199 [2020-04-26 07:22:06.987] [jointLog] [info] iteration = 400 | max rel diff. = 0.244708 [2020-04-26 07:22:07.439] [jointLog] [info] iteration = 500 | max rel diff. = 0.0934327 [2020-04-26 07:22:07.612] [jointLog] [info] iteration = 539 | max rel diff. = 0.00664314 [2020-04-26 07:22:07.614] [jointLog] [info] Finished optimizer [2020-04-26 07:22:07.614] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl ambient_03/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > ambient_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/ambient-cold/20200413.C_bairdi.221.D12.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.221.D12.uninfected.cold.megan_R2.fq -o cold_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/ambient-cold/20200413.C_bairdi.221.D12.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.221.D12.uninfected.cold.megan_R2.fq } ### [ output ] => { cold_03 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to cold_03/logs [2020-04-26 07:30:38.052] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 07:30:38.052] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 07:30:38.052] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 07:30:38.052] [jointLog] [info] parsing read library format [2020-04-26 07:30:38.052] [jointLog] [info] There is 1 library. [2020-04-26 07:30:38.107] [jointLog] [info] Loading pufferfish index [2020-04-26 07:30:38.107] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.093 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 204.92 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 116.61 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.3522 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.269 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.6664 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 64.154 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.7099 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 228.61 us ----------------------------------------- [2020-04-26 07:30:38.225] [jointLog] [info] done [2020-04-26 07:30:38.225] [jointLog] [info] Index contained 40,435 targets [2020-04-26 07:30:38.236] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,242,748, hits per frag: 4.69381 processed 1,000,001 fragments hits: 4,488,140, hits per frag: 4.68006 processed 1,500,000 fragments hits: 6,734,909, hits per frag: 4.77169 processed 2,000,000 fragments hits: 8,977,667, hits per frag: 4.71624 processed 2,500,000 fragments hits: 11,219,582, hits per frag: 4.73239 [2020-04-26 07:30:46.585] [jointLog] [info] Computed 79,760 rich equivalence classes for further processing [2020-04-26 07:30:46.585] [jointLog] [info] Counted 2,609,007 total reads in the equivalence classes [2020-04-26 07:30:46.606] [jointLog] [info] Number of mappings discarded because of alignment score : 1,110,006 [2020-04-26 07:30:46.606] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,705 [2020-04-26 07:30:46.606] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 07:30:46.606] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,808 [2020-04-26 07:30:46.609] [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 07:30:46.609] [jointLog] [info] Mapping rate = 99.1136% [2020-04-26 07:30:46.609] [jointLog] [info] finished quantifyLibrary() [2020-04-26 07:30:46.610] [jointLog] [info] Starting optimizer [2020-04-26 07:30:46.632] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 07:30:46.641] [jointLog] [info] iteration = 0 | max rel diff. = 6035.68 [2020-04-26 07:30:47.039] [jointLog] [info] iteration = 100 | max rel diff. = 6.73724 [2020-04-26 07:30:47.426] [jointLog] [info] iteration = 200 | max rel diff. = 9.10024 [2020-04-26 07:30:47.816] [jointLog] [info] iteration = 300 | max rel diff. = 0.222748 [2020-04-26 07:30:48.101] [jointLog] [info] iteration = 375 | max rel diff. = 0.00742665 [2020-04-26 07:30:48.102] [jointLog] [info] Finished optimizer [2020-04-26 07:30:48.102] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl cold_03/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > cold_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/ambient-cold/20200413.C_bairdi.222.D12.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.222.D12.uninfected.cold.megan_R2.fq -o cold_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/ambient-cold/20200413.C_bairdi.222.D12.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.222.D12.uninfected.cold.megan_R2.fq } ### [ output ] => { cold_04 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to cold_04/logs [2020-04-26 07:39:18.879] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 07:39:18.879] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 07:39:18.879] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 07:39:18.879] [jointLog] [info] parsing read library format [2020-04-26 07:39:18.879] [jointLog] [info] There is 1 library. [2020-04-26 07:39:18.932] [jointLog] [info] Loading pufferfish index [2020-04-26 07:39:18.932] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.171 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 223.28 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 123.33 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.4332 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.812 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.5269 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 87.556 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.7061 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 213.12 us ----------------------------------------- [2020-04-26 07:39:19.074] [jointLog] [info] done [2020-04-26 07:39:19.074] [jointLog] [info] Index contained 40,435 targets [2020-04-26 07:39:19.085] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,585,448, hits per frag: 3.84219 processed 1,000,001 fragments hits: 3,172,093, hits per frag: 3.4096 [2020-04-26 07:39:23.006] [jointLog] [info] Computed 60,028 rich equivalence classes for further processing [2020-04-26 07:39:23.006] [jointLog] [info] Counted 1,344,957 total reads in the equivalence classes [2020-04-26 07:39:23.021] [jointLog] [info] Number of mappings discarded because of alignment score : 339,477 [2020-04-26 07:39:23.021] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 14,115 [2020-04-26 07:39:23.021] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 07:39:23.021] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,729 [2020-04-26 07:39:23.024] [jointLog] [warning] Only 1344957 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 07:39:23.024] [jointLog] [info] Mapping rate = 98.8392% [2020-04-26 07:39:23.024] [jointLog] [info] finished quantifyLibrary() [2020-04-26 07:39:23.026] [jointLog] [info] Starting optimizer [2020-04-26 07:39:23.053] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 07:39:23.058] [jointLog] [info] iteration = 0 | max rel diff. = 3213.81 [2020-04-26 07:39:23.305] [jointLog] [info] iteration = 100 | max rel diff. = 16.3108 [2020-04-26 07:39:23.552] [jointLog] [info] iteration = 200 | max rel diff. = 0.397798 [2020-04-26 07:39:23.795] [jointLog] [info] iteration = 300 | max rel diff. = 0.0811915 [2020-04-26 07:39:24.036] [jointLog] [info] iteration = 400 | max rel diff. = 0.0183414 [2020-04-26 07:39:24.274] [jointLog] [info] iteration = 500 | max rel diff. = 0.0213546 [2020-04-26 07:39:24.487] [jointLog] [info] iteration = 591 | max rel diff. = 0.00447786 [2020-04-26 07:39:24.488] [jointLog] [info] Finished optimizer [2020-04-26 07:39:24.488] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl cold_04/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > cold_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/ambient-cold/20200413.C_bairdi.254.D12.infected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.254.D12.infected.cold.megan_R2.fq -o cold_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/ambient-cold/20200413.C_bairdi.254.D12.infected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.254.D12.infected.cold.megan_R2.fq } ### [ output ] => { cold_05 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to cold_05/logs [2020-04-26 07:47:54.597] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 07:47:54.598] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 07:47:54.598] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 07:47:54.598] [jointLog] [info] parsing read library format [2020-04-26 07:47:54.598] [jointLog] [info] There is 1 library. [2020-04-26 07:47:54.649] [jointLog] [info] Loading pufferfish index [2020-04-26 07:47:54.649] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.28 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 205.96 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 115.22 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.4541 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.087 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.6232 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 208.94 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.6218 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 261.95 us ----------------------------------------- [2020-04-26 07:47:54.913] [jointLog] [info] done [2020-04-26 07:47:54.913] [jointLog] [info] Index contained 40,435 targets [2020-04-26 07:47:54.925] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,790,331, hits per frag: 3.96701 processed 1,000,000 fragments hits: 3,579,658, hits per frag: 3.64184 processed 1,500,000 fragments hits: 5,369,735, hits per frag: 3.79002 [2020-04-26 07:48:01.033] [jointLog] [info] Computed 65,053 rich equivalence classes for further processing [2020-04-26 07:48:01.033] [jointLog] [info] Counted 1,951,686 total reads in the equivalence classes [2020-04-26 07:48:01.050] [jointLog] [info] Number of mappings discarded because of alignment score : 660,574 [2020-04-26 07:48:01.050] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 21,117 [2020-04-26 07:48:01.050] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 07:48:01.050] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,559 [2020-04-26 07:48:01.054] [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 07:48:01.054] [jointLog] [info] Mapping rate = 98.8965% [2020-04-26 07:48:01.054] [jointLog] [info] finished quantifyLibrary() [2020-04-26 07:48:01.055] [jointLog] [info] Starting optimizer [2020-04-26 07:48:01.076] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 07:48:01.087] [jointLog] [info] iteration = 0 | max rel diff. = 4259.61 [2020-04-26 07:48:01.497] [jointLog] [info] iteration = 100 | max rel diff. = 1.25246 [2020-04-26 07:48:01.908] [jointLog] [info] iteration = 200 | max rel diff. = 4.92837 [2020-04-26 07:48:02.317] [jointLog] [info] iteration = 300 | max rel diff. = 0.11667 [2020-04-26 07:48:02.724] [jointLog] [info] iteration = 400 | max rel diff. = 0.0200521 [2020-04-26 07:48:03.123] [jointLog] [info] iteration = 500 | max rel diff. = 0.0363908 [2020-04-26 07:48:03.515] [jointLog] [info] iteration = 600 | max rel diff. = 0.245749 [2020-04-26 07:48:03.535] [jointLog] [info] iteration = 606 | max rel diff. = 0.00626976 [2020-04-26 07:48:03.537] [jointLog] [info] Finished optimizer [2020-04-26 07:48:03.537] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl cold_05/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > cold_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/ambient-cold/20200413.C_bairdi.334.D12.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.334.D12.infected.ambient.megan_R2.fq -o ambient_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/ambient-cold/20200413.C_bairdi.334.D12.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.334.D12.infected.ambient.megan_R2.fq } ### [ output ] => { ambient_04 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to ambient_04/logs [2020-04-26 07:56:33.762] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 07:56:33.762] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 07:56:33.762] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 07:56:33.762] [jointLog] [info] parsing read library format [2020-04-26 07:56:33.762] [jointLog] [info] There is 1 library. [2020-04-26 07:56:33.815] [jointLog] [info] Loading pufferfish index [2020-04-26 07:56:33.815] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.147 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 206.57 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 120.76 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.4983 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.158 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.7409 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 225.16 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.8362 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 263.73 us ----------------------------------------- [2020-04-26 07:56:34.095] [jointLog] [info] done [2020-04-26 07:56:34.095] [jointLog] [info] Index contained 40,435 targets [2020-04-26 07:56:34.107] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,645,402, hits per frag: 5.54064 processed 1,000,001 fragments hits: 5,296,286, hits per frag: 6.06564 [2020-04-26 07:56:38.699] [jointLog] [info] Computed 60,248 rich equivalence classes for further processing [2020-04-26 07:56:38.699] [jointLog] [info] Counted 1,107,447 total reads in the equivalence classes [2020-04-26 07:56:38.718] [jointLog] [info] Number of mappings discarded because of alignment score : 485,232 [2020-04-26 07:56:38.718] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 12,165 [2020-04-26 07:56:38.718] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 07:56:38.718] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,777 [2020-04-26 07:56:38.721] [jointLog] [warning] Only 1107447 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 07:56:38.721] [jointLog] [info] Mapping rate = 98.8793% [2020-04-26 07:56:38.721] [jointLog] [info] finished quantifyLibrary() [2020-04-26 07:56:38.722] [jointLog] [info] Starting optimizer [2020-04-26 07:56:38.742] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 07:56:38.747] [jointLog] [info] iteration = 0 | max rel diff. = 2448.04 [2020-04-26 07:56:39.065] [jointLog] [info] iteration = 100 | max rel diff. = 1.12463 [2020-04-26 07:56:39.375] [jointLog] [info] iteration = 200 | max rel diff. = 0.834168 [2020-04-26 07:56:39.682] [jointLog] [info] iteration = 300 | max rel diff. = 0.498739 [2020-04-26 07:56:39.990] [jointLog] [info] iteration = 400 | max rel diff. = 0.0727068 [2020-04-26 07:56:40.132] [jointLog] [info] iteration = 447 | max rel diff. = 0.00226002 [2020-04-26 07:56:40.133] [jointLog] [info] Finished optimizer [2020-04-26 07:56:40.133] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl ambient_04/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > ambient_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/ambient-cold/20200413.C_bairdi.349.D12.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.349.D12.infected.ambient.megan_R2.fq -o ambient_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/ambient-cold/20200413.C_bairdi.349.D12.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.349.D12.infected.ambient.megan_R2.fq } ### [ output ] => { ambient_05 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to ambient_05/logs [2020-04-26 08:05:10.754] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 08:05:10.754] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 08:05:10.754] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 08:05:10.754] [jointLog] [info] parsing read library format [2020-04-26 08:05:10.754] [jointLog] [info] There is 1 library. ----------------------------------------- | Loading contig table | Time = 11.583 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 214.25 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 117.31 us ----------------------------------------- [2020-04-26 08:05:10.820] [jointLog] [info] Loading pufferfish index [2020-04-26 08:05:10.820] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading mphf table | Time = 6.3713 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.154 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.6721 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 132.19 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 5.5409 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 229.4 us ----------------------------------------- [2020-04-26 08:05:11.008] [jointLog] [info] done [2020-04-26 08:05:11.008] [jointLog] [info] Index contained 40,435 targets [2020-04-26 08:05:11.022] [jointLog] [info] Number of decoys : 0 [2020-04-26 08:05:11.708] [jointLog] [info] Computed 21,387 rich equivalence classes for further processing [2020-04-26 08:05:11.708] [jointLog] [info] Counted 79,375 total reads in the equivalence classes [2020-04-26 08:05:11.734] [jointLog] [info] Number of mappings discarded because of alignment score : 85,737 [2020-04-26 08:05:11.734] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 8,609 [2020-04-26 08:05:11.734] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 08:05:11.734] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 338 [2020-04-26 08:05:11.738] [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 08:05:11.738] [jointLog] [info] Mapping rate = 86.6407% [2020-04-26 08:05:11.738] [jointLog] [info] finished quantifyLibrary() [2020-04-26 08:05:11.739] [jointLog] [info] Starting optimizer [2020-04-26 08:05:11.753] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 08:05:11.755] [jointLog] [info] iteration = 0 | max rel diff. = 190.232 [2020-04-26 08:05:11.860] [jointLog] [info] iteration = 100 | max rel diff. = 0.35742 [2020-04-26 08:05:11.935] [jointLog] [info] iteration = 176 | max rel diff. = 0.00397233 [2020-04-26 08:05:11.936] [jointLog] [info] Finished optimizer [2020-04-26 08:05:11.936] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl ambient_05/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > ambient_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/ambient-cold/20200413.C_bairdi.359.D12.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.359.D12.infected.ambient.megan_R2.fq -o ambient_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/ambient-cold/20200413.C_bairdi.359.D12.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.359.D12.infected.ambient.megan_R2.fq } ### [ output ] => { ambient_06 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to ambient_06/logs [2020-04-26 08:13:43.013] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 08:13:43.013] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 08:13:43.013] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 08:13:43.013] [jointLog] [info] parsing read library format [2020-04-26 08:13:43.013] [jointLog] [info] There is 1 library. ----------------------------------------- | Loading contig table | Time = 10.897 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 186.39 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 51.212 us ----------------------------------------- [2020-04-26 08:13:43.082] [jointLog] [info] Loading pufferfish index [2020-04-26 08:13:43.082] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading mphf table | Time = 5.8615 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.868 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.8323 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 65.331 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.3851 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 93.73 us ----------------------------------------- [2020-04-26 08:13:43.201] [jointLog] [info] done [2020-04-26 08:13:43.201] [jointLog] [info] Index contained 40,435 targets [2020-04-26 08:13:43.214] [jointLog] [info] Number of decoys : 0  processed 500,001 fragments hits: 2,087,239, hits per frag: 4.94273 processed 1,000,000 fragments hits: 4,175,322, hits per frag: 4.31113 processed 1,500,000 fragments hits: 6,263,916, hits per frag: 4.40539 processed 2,000,000 fragments hits: 8,361,300, hits per frag: 4.41892 processed 2,500,000 fragments hits: 10,451,612, hits per frag: 4.22295 processed 3,000,000 fragments hits: 12,535,152, hits per frag: 4.33533 [2020-04-26 08:13:52.372] [jointLog] [info] Computed 95,533 rich equivalence classes for further processing [2020-04-26 08:13:52.372] [jointLog] [info] Counted 3,196,425 total reads in the equivalence classes [2020-04-26 08:13:52.392] [jointLog] [info] Number of mappings discarded because of alignment score : 1,080,611 [2020-04-26 08:13:52.392] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 24,486 [2020-04-26 08:13:52.392] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 08:13:52.392] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,462 [2020-04-26 08:13:52.396] [jointLog] [warning] Only 3196425 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 08:13:52.396] [jointLog] [info] Mapping rate = 99.2016% [2020-04-26 08:13:52.396] [jointLog] [info] finished quantifyLibrary() [2020-04-26 08:13:52.398] [jointLog] [info] Starting optimizer [2020-04-26 08:13:52.424] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 08:13:52.433] [jointLog] [info] iteration = 0 | max rel diff. = 7373.04 [2020-04-26 08:13:52.812] [jointLog] [info] iteration = 100 | max rel diff. = 14.7581 [2020-04-26 08:13:53.191] [jointLog] [info] iteration = 200 | max rel diff. = 7.33361 [2020-04-26 08:13:53.573] [jointLog] [info] iteration = 300 | max rel diff. = 1.83114 [2020-04-26 08:13:53.954] [jointLog] [info] iteration = 400 | max rel diff. = 0.279964 [2020-04-26 08:13:54.336] [jointLog] [info] iteration = 500 | max rel diff. = 0.151216 [2020-04-26 08:13:54.722] [jointLog] [info] iteration = 600 | max rel diff. = 0.0835096 [2020-04-26 08:13:55.105] [jointLog] [info] iteration = 700 | max rel diff. = 0.0311626 [2020-04-26 08:13:55.484] [jointLog] [info] iteration = 800 | max rel diff. = 0.030291 [2020-04-26 08:13:55.607] [jointLog] [info] iteration = 833 | max rel diff. = 0.00668361 [2020-04-26 08:13:55.611] [jointLog] [info] Finished optimizer [2020-04-26 08:13:55.611] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl ambient_06/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > ambient_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/ambient-cold/20200413.C_bairdi.425.D26.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.425.D26.uninfected.cold.megan_R2.fq -o cold_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/ambient-cold/20200413.C_bairdi.425.D26.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.425.D26.uninfected.cold.megan_R2.fq } ### [ output ] => { cold_06 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to cold_06/logs [2020-04-26 08:22:26.152] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 08:22:26.152] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 08:22:26.152] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 08:22:26.152] [jointLog] [info] parsing read library format [2020-04-26 08:22:26.152] [jointLog] [info] There is 1 library. [2020-04-26 08:22:26.227] [jointLog] [info] Loading pufferfish index [2020-04-26 08:22:26.228] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.068 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 180.83 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 104.22 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.6402 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.821 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.79 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 92.681 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.5813 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 198.3 us ----------------------------------------- [2020-04-26 08:22:26.375] [jointLog] [info] done [2020-04-26 08:22:26.375] [jointLog] [info] Index contained 40,435 targets [2020-04-26 08:22:26.388] [jointLog] [info] Number of decoys : 0 [2020-04-26 08:22:27.125] [jointLog] [info] Computed 12,683 rich equivalence classes for further processing [2020-04-26 08:22:27.125] [jointLog] [info] Counted 75,333 total reads in the equivalence classes [2020-04-26 08:22:27.158] [jointLog] [info] Number of mappings discarded because of alignment score : 63,773 [2020-04-26 08:22:27.158] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,953 [2020-04-26 08:22:27.158] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 08:22:27.158] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 724 [2020-04-26 08:22:27.161] [jointLog] [warning] Only 75333 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 08:22:27.161] [jointLog] [info] Mapping rate = 95.7059% [2020-04-26 08:22:27.161] [jointLog] [info] finished quantifyLibrary() [2020-04-26 08:22:27.163] [jointLog] [info] Starting optimizer [2020-04-26 08:22:27.176] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 08:22:27.178] [jointLog] [info] iteration = 0 | max rel diff. = 158.412 [2020-04-26 08:22:27.269] [jointLog] [info] iteration = 100 | max rel diff. = 0.0748582 [2020-04-26 08:22:27.320] [jointLog] [info] iteration = 160 | max rel diff. = 0.00269421 [2020-04-26 08:22:27.321] [jointLog] [info] Finished optimizer [2020-04-26 08:22:27.321] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl cold_06/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > cold_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/ambient-cold/20200413.C_bairdi.427.D26.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.427.D26.uninfected.cold.megan_R2.fq -o cold_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/ambient-cold/20200413.C_bairdi.427.D26.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.427.D26.uninfected.cold.megan_R2.fq } ### [ output ] => { cold_07 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to cold_07/logs [2020-04-26 08:30:58.143] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 08:30:58.143] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 08:30:58.143] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 08:30:58.143] [jointLog] [info] parsing read library format [2020-04-26 08:30:58.143] [jointLog] [info] There is 1 library. [2020-04-26 08:30:58.202] [jointLog] [info] Loading pufferfish index [2020-04-26 08:30:58.202] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.103 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 185.93 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 106.03 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.5922 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.647 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.1971 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 30.302 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.4347 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 194.48 us ----------------------------------------- [2020-04-26 08:30:58.285] [jointLog] [info] done [2020-04-26 08:30:58.285] [jointLog] [info] Index contained 40,435 targets [2020-04-26 08:30:58.298] [jointLog] [info] Number of decoys : 0 [2020-04-26 08:30:59.052] [jointLog] [info] Computed 8,627 rich equivalence classes for further processing [2020-04-26 08:30:59.052] [jointLog] [info] Counted 49,503 total reads in the equivalence classes [2020-04-26 08:30:59.085] [jointLog] [info] Number of mappings discarded because of alignment score : 49,151 [2020-04-26 08:30:59.085] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,787 [2020-04-26 08:30:59.085] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 08:30:59.085] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 268 [2020-04-26 08:30:59.088] [jointLog] [warning] Only 49503 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 08:30:59.088] [jointLog] [info] Mapping rate = 87.3115% [2020-04-26 08:30:59.088] [jointLog] [info] finished quantifyLibrary() [2020-04-26 08:30:59.090] [jointLog] [info] Starting optimizer [2020-04-26 08:30:59.099] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 08:30:59.102] [jointLog] [info] iteration = 0 | max rel diff. = 119.445 [2020-04-26 08:30:59.174] [jointLog] [info] iteration = 100 | max rel diff. = 13.0895 [2020-04-26 08:30:59.243] [jointLog] [info] iteration = 200 | max rel diff. = 0.274983 [2020-04-26 08:30:59.249] [jointLog] [info] iteration = 210 | max rel diff. = 0.0094877 [2020-04-26 08:30:59.250] [jointLog] [info] Finished optimizer [2020-04-26 08:30:59.250] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl cold_07/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > cold_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/ambient-cold/20200413.C_bairdi.445.D26.infected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.445.D26.infected.cold.megan_R2.fq -o cold_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/ambient-cold/20200413.C_bairdi.445.D26.infected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.445.D26.infected.cold.megan_R2.fq } ### [ output ] => { cold_08 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to cold_08/logs [2020-04-26 08:39:29.377] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 08:39:29.377] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 08:39:29.377] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 08:39:29.377] [jointLog] [info] parsing read library format [2020-04-26 08:39:29.377] [jointLog] [info] There is 1 library. [2020-04-26 08:39:29.435] [jointLog] [info] Loading pufferfish index [2020-04-26 08:39:29.435] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.204 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 196.9 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 106.96 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.5299 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.651 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.1609 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 28.981 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.4157 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 195.26 us ----------------------------------------- [2020-04-26 08:39:29.517] [jointLog] [info] done [2020-04-26 08:39:29.517] [jointLog] [info] Index contained 40,435 targets [2020-04-26 08:39:29.530] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,949,541, hits per frag: 5.00595 processed 1,000,000 fragments hits: 3,893,077, hits per frag: 4.20185 processed 1,500,000 fragments hits: 5,841,557, hits per frag: 4.22448 processed 2,000,001 fragments hits: 7,778,925, hits per frag: 4.16274 processed 2,500,001 fragments hits: 9,722,534, hits per frag: 3.9937 [2020-04-26 08:39:36.987] [jointLog] [info] Computed 81,283 rich equivalence classes for further processing [2020-04-26 08:39:36.987] [jointLog] [info] Counted 2,537,570 total reads in the equivalence classes [2020-04-26 08:39:37.011] [jointLog] [info] Number of mappings discarded because of alignment score : 763,753 [2020-04-26 08:39:37.011] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 25,278 [2020-04-26 08:39:37.011] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 08:39:37.011] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 6,111 [2020-04-26 08:39:37.015] [jointLog] [warning] Only 2537570 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 08:39:37.015] [jointLog] [info] Mapping rate = 98.9786% [2020-04-26 08:39:37.015] [jointLog] [info] finished quantifyLibrary() [2020-04-26 08:39:37.017] [jointLog] [info] Starting optimizer [2020-04-26 08:39:37.040] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 08:39:37.046] [jointLog] [info] iteration = 0 | max rel diff. = 5794.47 [2020-04-26 08:39:37.370] [jointLog] [info] iteration = 100 | max rel diff. = 20.9384 [2020-04-26 08:39:37.694] [jointLog] [info] iteration = 200 | max rel diff. = 2.32699 [2020-04-26 08:39:38.013] [jointLog] [info] iteration = 300 | max rel diff. = 14.1017 [2020-04-26 08:39:38.332] [jointLog] [info] iteration = 400 | max rel diff. = 0.074888 [2020-04-26 08:39:38.661] [jointLog] [info] iteration = 500 | max rel diff. = 1.13821 [2020-04-26 08:39:38.968] [jointLog] [info] iteration = 596 | max rel diff. = 0.00983689 [2020-04-26 08:39:38.969] [jointLog] [info] Finished optimizer [2020-04-26 08:39:38.969] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl cold_08/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > cold_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/ambient-cold/20200413.C_bairdi.463.D26.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.463.D26.infected.ambient.megan_R2.fq -o ambient_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/ambient-cold/20200413.C_bairdi.463.D26.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.463.D26.infected.ambient.megan_R2.fq } ### [ output ] => { ambient_07 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to ambient_07/logs [2020-04-26 08:48:09.185] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 08:48:09.185] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 08:48:09.185] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 08:48:09.185] [jointLog] [info] parsing read library format [2020-04-26 08:48:09.185] [jointLog] [info] There is 1 library. ----------------------------------------- | Loading contig table | Time = 11.098 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 183.18 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 109.53 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.5848 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 [2020-04-26 08:48:09.246] [jointLog] [info] Loading pufferfish index [2020-04-26 08:48:09.246] [jointLog] [info] Loading dense pufferfish index. Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.927 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.3135 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 149.82 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.7889 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 205.01 us ----------------------------------------- [2020-04-26 08:48:09.449] [jointLog] [info] done [2020-04-26 08:48:09.449] [jointLog] [info] Index contained 40,435 targets [2020-04-26 08:48:09.463] [jointLog] [info] Number of decoys : 0 [2020-04-26 08:48:11.057] [jointLog] [info] Computed 4,766 rich equivalence classes for further processing [2020-04-26 08:48:11.057] [jointLog] [info] Counted 26,916 total reads in the equivalence classes [2020-04-26 08:48:11.098] [jointLog] [info] Number of mappings discarded because of alignment score : 21,743 [2020-04-26 08:48:11.098] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,769 [2020-04-26 08:48:11.098] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 08:48:11.098] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 79 [2020-04-26 08:48:11.102] [jointLog] [warning] Only 26916 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 08:48:11.102] [jointLog] [info] Mapping rate = 89.1878% [2020-04-26 08:48:11.102] [jointLog] [info] finished quantifyLibrary() [2020-04-26 08:48:11.104] [jointLog] [info] Starting optimizer [2020-04-26 08:48:11.113] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 08:48:11.117] [jointLog] [info] iteration = 0 | max rel diff. = 64.4357 [2020-04-26 08:48:11.185] [jointLog] [info] iteration = 100 | max rel diff. = 0.00287416 [2020-04-26 08:48:11.186] [jointLog] [info] Finished optimizer [2020-04-26 08:48:11.186] [jointLog] [info] writing output [2020-04-26 08:48:11.239] [jointLog] [warning] NOTE: Read Lib [[ /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.463.D26.infected.ambient.megan_R1.fq, /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.463.D26.infected.ambient.megan_R2.fq]] : Detected a *potential* strand bias > 1% in an unstranded protocol check the file: ambient_07/lib_format_counts.json for details CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl ambient_07/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > ambient_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/ambient-cold/20200413.C_bairdi.481.D26.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.481.D26.infected.ambient.megan_R2.fq -o ambient_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/ambient-cold/20200413.C_bairdi.481.D26.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.481.D26.infected.ambient.megan_R2.fq } ### [ output ] => { ambient_08 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to ambient_08/logs [2020-04-26 08:56:41.570] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 08:56:41.570] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 08:56:41.570] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 08:56:41.570] [jointLog] [info] parsing read library format [2020-04-26 08:56:41.570] [jointLog] [info] There is 1 library. [2020-04-26 08:56:41.629] [jointLog] [info] Loading pufferfish index [2020-04-26 08:56:41.629] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.077 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 191.92 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 105.86 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 5.6967 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.707 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.2323 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 29.275 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.3842 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 195.42 us ----------------------------------------- [2020-04-26 08:56:41.711] [jointLog] [info] done [2020-04-26 08:56:41.711] [jointLog] [info] Index contained 40,435 targets [2020-04-26 08:56:41.725] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 1,629,450, hits per frag: 4.39279 processed 1,000,000 fragments hits: 3,259,624, hits per frag: 3.36359 [2020-04-26 08:56:45.542] [jointLog] [info] Computed 70,119 rich equivalence classes for further processing [2020-04-26 08:56:45.542] [jointLog] [info] Counted 1,295,947 total reads in the equivalence classes [2020-04-26 08:56:45.557] [jointLog] [info] Number of mappings discarded because of alignment score : 406,747 [2020-04-26 08:56:45.557] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,984 [2020-04-26 08:56:45.557] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 08:56:45.557] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,002 [2020-04-26 08:56:45.561] [jointLog] [warning] Only 1295947 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 08:56:45.561] [jointLog] [info] Mapping rate = 98.1521% [2020-04-26 08:56:45.561] [jointLog] [info] finished quantifyLibrary() [2020-04-26 08:56:45.562] [jointLog] [info] Starting optimizer [2020-04-26 08:56:45.585] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 08:56:45.588] [jointLog] [info] iteration = 0 | max rel diff. = 3064.49 [2020-04-26 08:56:45.822] [jointLog] [info] iteration = 100 | max rel diff. = 5.76933 [2020-04-26 08:56:46.046] [jointLog] [info] iteration = 200 | max rel diff. = 0.287623 [2020-04-26 08:56:46.276] [jointLog] [info] iteration = 300 | max rel diff. = 0.135179 [2020-04-26 08:56:46.506] [jointLog] [info] iteration = 400 | max rel diff. = 0.942839 [2020-04-26 08:56:46.731] [jointLog] [info] iteration = 500 | max rel diff. = 0.133679 [2020-04-26 08:56:46.951] [jointLog] [info] iteration = 600 | max rel diff. = 0.794518 [2020-04-26 08:56:47.177] [jointLog] [info] iteration = 700 | max rel diff. = 0.012836 [2020-04-26 08:56:47.335] [jointLog] [info] iteration = 769 | max rel diff. = 0.00982565 [2020-04-26 08:56:47.336] [jointLog] [info] Finished optimizer [2020-04-26 08:56:47.336] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl ambient_08/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > ambient_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/ambient-cold/20200413.C_bairdi.485.D26.infected.ambient.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.485.D26.infected.ambient.megan_R2.fq -o ambient_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/ambient-cold/20200413.C_bairdi.485.D26.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.485.D26.infected.ambient.megan_R2.fq } ### [ output ] => { ambient_09 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to ambient_09/logs [2020-04-26 09:05:18.049] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 09:05:18.049] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 09:05:18.049] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 09:05:18.049] [jointLog] [info] parsing read library format [2020-04-26 09:05:18.049] [jointLog] [info] There is 1 library. [2020-04-26 09:05:18.102] [jointLog] [info] Loading pufferfish index [2020-04-26 09:05:18.102] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.097 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 222.78 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 132.29 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.5672 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 29.978 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.8299 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 61.332 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.7455 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 221.8 us ----------------------------------------- [2020-04-26 09:05:18.218] [jointLog] [info] done [2020-04-26 09:05:18.218] [jointLog] [info] Index contained 40,435 targets [2020-04-26 09:05:18.230] [jointLog] [info] Number of decoys : 0  processed 500,000 fragments hits: 2,018,175, hits per frag: 4.35232 processed 1,000,000 fragments hits: 4,039,274, hits per frag: 4.49498 processed 1,500,000 fragments hits: 6,060,746, hits per frag: 4.19333 [2020-04-26 09:05:23.929] [jointLog] [info] Computed 62,804 rich equivalence classes for further processing [2020-04-26 09:05:23.929] [jointLog] [info] Counted 1,711,628 total reads in the equivalence classes [2020-04-26 09:05:23.948] [jointLog] [info] Number of mappings discarded because of alignment score : 553,510 [2020-04-26 09:05:23.948] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 16,872 [2020-04-26 09:05:23.948] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 09:05:23.948] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,511 [2020-04-26 09:05:23.951] [jointLog] [warning] Only 1711628 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-26 09:05:23.951] [jointLog] [info] Mapping rate = 98.9712% [2020-04-26 09:05:23.951] [jointLog] [info] finished quantifyLibrary() [2020-04-26 09:05:23.952] [jointLog] [info] Starting optimizer [2020-04-26 09:05:23.970] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 09:05:23.975] [jointLog] [info] iteration = 0 | max rel diff. = 4012.37 [2020-04-26 09:05:24.231] [jointLog] [info] iteration = 100 | max rel diff. = 9.24718 [2020-04-26 09:05:24.489] [jointLog] [info] iteration = 200 | max rel diff. = 1.82856 [2020-04-26 09:05:24.753] [jointLog] [info] iteration = 300 | max rel diff. = 0.885471 [2020-04-26 09:05:25.012] [jointLog] [info] iteration = 400 | max rel diff. = 0.0559703 [2020-04-26 09:05:25.271] [jointLog] [info] iteration = 500 | max rel diff. = 0.552296 [2020-04-26 09:05:25.279] [jointLog] [info] iteration = 504 | max rel diff. = 0.00391797 [2020-04-26 09:05:25.280] [jointLog] [info] Finished optimizer [2020-04-26 09:05:25.280] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl ambient_09/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > ambient_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/ambient-cold/20200413.C_bairdi.73.D9.uninfected.cold.megan_R1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.73.D9.uninfected.cold.megan_R2.fq -o cold_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/ambient-cold/20200413.C_bairdi.73.D9.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200422_cbai_DEG_basic_comparisons/ambient-cold/20200413.C_bairdi.73.D9.uninfected.cold.megan_R2.fq } ### [ output ] => { cold_09 } ### [ threads ] => { 28 } ### [ validateMappings ] => { } Logs will be written to cold_09/logs [2020-04-26 09:13:55.807] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-26 09:13:55.807] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-26 09:13:55.807] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-26 09:13:55.807] [jointLog] [info] parsing read library format [2020-04-26 09:13:55.807] [jointLog] [info] There is 1 library. [2020-04-26 09:13:55.859] [jointLog] [info] Loading pufferfish index [2020-04-26 09:13:55.859] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 11.002 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 213.34 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 127.88 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.5419 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 28.672 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.3572 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 106.46 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 3.8575 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 113.41 us ----------------------------------------- [2020-04-26 09:13:56.019] [jointLog] [info] done [2020-04-26 09:13:56.019] [jointLog] [info] Index contained 40,435 targets [2020-04-26 09:13:56.030] [jointLog] [info] Number of decoys : 0 [2020-04-26 09:13:57.188] [jointLog] [info] Computed 8,743 rich equivalence classes for further processing [2020-04-26 09:13:57.188] [jointLog] [info] Counted 91,344 total reads in the equivalence classes [2020-04-26 09:13:57.206] [jointLog] [info] Number of mappings discarded because of alignment score : 98,787 [2020-04-26 09:13:57.206] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 9,280 [2020-04-26 09:13:57.206] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-26 09:13:57.206] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 518 [2020-04-26 09:13:57.209] [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 09:13:57.209] [jointLog] [info] Mapping rate = 89.7518% [2020-04-26 09:13:57.209] [jointLog] [info] finished quantifyLibrary() [2020-04-26 09:13:57.211] [jointLog] [info] Starting optimizer [2020-04-26 09:13:57.224] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-26 09:13:57.227] [jointLog] [info] iteration = 0 | max rel diff. = 223.38 [2020-04-26 09:13:57.319] [jointLog] [info] iteration = 100 | max rel diff. = 0.16251 [2020-04-26 09:13:57.378] [jointLog] [info] iteration = 170 | max rel diff. = 0.007471 [2020-04-26 09:13:57.379] [jointLog] [info] Finished optimizer [2020-04-26 09:13:57.379] [jointLog] [info] writing output CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl cold_09/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > cold_09/quant.sf.genes