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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 113_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.113.D9.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.113.D9.uninfected.cold.megan_R2.fq } Logs will be written to 113_quant/logs [2020-04-30 07:02:02.167] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:02:02.167] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:02:02.167] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:02:02.167] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:02:02.167] [jointLog] [info] parsing read library format [2020-04-30 07:02:02.168] [jointLog] [info] There is 1 library. [2020-04-30 07:02:02.313] [jointLog] [info] Loading pufferfish index [2020-04-30 07:02:02.325] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:02:02.325] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 197.65 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 27.566 ms ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 40.187 ms ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 173.43 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 114.53 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 69.67 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 202.52 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 109.97 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 22.167 ms ----------------------------------------- [2020-04-30 07:02:03.366] [jointLog] [info] done [2020-04-30 07:02:03.366] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:02:03.394] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:02:04.112] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 891,009, hits per frag: 2.35433 processed 1,000,000 fragments hits: 1,783,881, hits per frag: 1.99829 processed 1,500,001 fragments hits: 2,676,045, hits per frag: 1.88392 processed 2,000,000 fragments hits: 3,567,034, hits per frag: 1.89204 [2020-04-30 07:02:09.845] [jointLog] [info] Computed 29,560 rich equivalence classes for further processing [2020-04-30 07:02:09.845] [jointLog] [info] Counted 2,280,001 total reads in the equivalence classes [2020-04-30 07:02:09.859] [jointLog] [info] Number of mappings discarded because of alignment score : 374,533 [2020-04-30 07:02:09.859] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 17,004 [2020-04-30 07:02:09.859] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:02:09.859] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,693 [2020-04-30 07:02:09.862] [jointLog] [warning] Only 2280001 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:02:09.862] [jointLog] [info] Mapping rate = 99.2159% [2020-04-30 07:02:09.862] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:02:09.862] [jointLog] [info] Starting optimizer [2020-04-30 07:02:09.880] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:02:09.881] [jointLog] [info] iteration = 0 | max rel diff. = 5257.12 [2020-04-30 07:02:09.980] [jointLog] [info] iteration = 100 | max rel diff. = 3.85996 [2020-04-30 07:02:10.064] [jointLog] [info] iteration = 200 | max rel diff. = 0.541331 [2020-04-30 07:02:10.145] [jointLog] [info] iteration = 300 | max rel diff. = 1.43929 [2020-04-30 07:02:10.227] [jointLog] [info] iteration = 400 | max rel diff. = 0.305201 [2020-04-30 07:02:10.308] [jointLog] [info] iteration = 500 | max rel diff. = 0.1238 [2020-04-30 07:02:10.389] [jointLog] [info] iteration = 600 | max rel diff. = 1.16644 [2020-04-30 07:02:10.470] [jointLog] [info] iteration = 700 | max rel diff. = 0.0468106 [2020-04-30 07:02:10.551] [jointLog] [info] iteration = 800 | max rel diff. = 0.05072 [2020-04-30 07:02:10.571] [jointLog] [info] iteration = 826 | max rel diff. = 0.00419771 [2020-04-30 07:02:10.572] [jointLog] [info] Finished optimizer [2020-04-30 07:02:10.572] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 118_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.118.D9.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.118.D9.infected.ambient.megan_R2.fq } Logs will be written to 118_quant/logs [2020-04-30 07:02:12.467] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:02:12.467] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:02:12.467] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:02:12.467] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:02:12.467] [jointLog] [info] parsing read library format [2020-04-30 07:02:12.467] [jointLog] [info] There is 1 library. [2020-04-30 07:02:12.544] [jointLog] [info] Loading pufferfish index [2020-04-30 07:02:12.544] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:02:12.544] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 24.78 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 273.34 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 169.77 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 55.606 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 75.008 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 59.048 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 128.46 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 48.085 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 460.05 us ----------------------------------------- [2020-04-30 07:02:12.937] [jointLog] [info] done [2020-04-30 07:02:12.937] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:02:12.964] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:02:13.915] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 770,597, hits per frag: 2.03102 processed 1,000,000 fragments hits: 1,540,642, hits per frag: 1.56311 [2020-04-30 07:02:19.970] [jointLog] [info] Computed 20,478 rich equivalence classes for further processing [2020-04-30 07:02:19.970] [jointLog] [info] Counted 1,444,344 total reads in the equivalence classes [2020-04-30 07:02:19.984] [jointLog] [info] Number of mappings discarded because of alignment score : 476,424 [2020-04-30 07:02:19.984] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 12,553 [2020-04-30 07:02:19.984] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:02:19.984] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,556 [2020-04-30 07:02:19.988] [jointLog] [warning] Only 1444344 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:02:19.988] [jointLog] [info] Mapping rate = 99.1059% [2020-04-30 07:02:19.988] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:02:19.989] [jointLog] [info] Starting optimizer [2020-04-30 07:02:20.007] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:02:20.010] [jointLog] [info] iteration = 0 | max rel diff. = 3436.25 [2020-04-30 07:02:20.107] [jointLog] [info] iteration = 100 | max rel diff. = 5.38666 [2020-04-30 07:02:20.192] [jointLog] [info] iteration = 200 | max rel diff. = 4.42195 [2020-04-30 07:02:20.273] [jointLog] [info] iteration = 300 | max rel diff. = 0.0190746 [2020-04-30 07:02:20.354] [jointLog] [info] iteration = 400 | max rel diff. = 0.0379255 [2020-04-30 07:02:20.428] [jointLog] [info] iteration = 500 | max rel diff. = 0.0367448 [2020-04-30 07:02:20.502] [jointLog] [info] iteration = 600 | max rel diff. = 0.0283916 [2020-04-30 07:02:20.529] [jointLog] [info] iteration = 637 | max rel diff. = 0.0082443 [2020-04-30 07:02:20.529] [jointLog] [info] Finished optimizer [2020-04-30 07:02:20.529] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 127_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.127.D9.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.127.D9.infected.warm.megan_R2.fq } Logs will be written to 127_quant/logs [2020-04-30 07:02:22.257] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:02:22.257] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:02:22.257] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:02:22.257] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:02:22.257] [jointLog] [info] parsing read library format [2020-04-30 07:02:22.258] [jointLog] [info] There is 1 library. [2020-04-30 07:02:22.322] [jointLog] [info] Loading pufferfish index [2020-04-30 07:02:22.322] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:02:22.322] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 20.802 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 285.32 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 188.6 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 7.8638 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 50.209 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.9229 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 24.432 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.1332 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 288.59 us ----------------------------------------- [2020-04-30 07:02:22.434] [jointLog] [info] done [2020-04-30 07:02:22.434] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:02:22.450] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:02:23.039] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 879,015, hits per frag: 2.08326 processed 1,000,000 fragments hits: 1,756,831, hits per frag: 1.88178 processed 1,500,000 fragments hits: 2,637,139, hits per frag: 1.82777 processed 2,000,001 fragments hits: 3,515,658, hits per frag: 1.81752 [2020-04-30 07:02:28.994] [jointLog] [info] Computed 30,255 rich equivalence classes for further processing [2020-04-30 07:02:28.994] [jointLog] [info] Counted 2,320,962 total reads in the equivalence classes [2020-04-30 07:02:29.006] [jointLog] [info] Number of mappings discarded because of alignment score : 439,216 [2020-04-30 07:02:29.006] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 16,284 [2020-04-30 07:02:29.006] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:02:29.006] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,506 [2020-04-30 07:02:29.009] [jointLog] [warning] Only 2320962 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:02:29.009] [jointLog] [info] Mapping rate = 99.2551% [2020-04-30 07:02:29.009] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:02:29.011] [jointLog] [info] Starting optimizer [2020-04-30 07:02:29.027] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:02:29.029] [jointLog] [info] iteration = 0 | max rel diff. = 4876.02 [2020-04-30 07:02:29.153] [jointLog] [info] iteration = 100 | max rel diff. = 15.1856 [2020-04-30 07:02:29.238] [jointLog] [info] iteration = 200 | max rel diff. = 2.09506 [2020-04-30 07:02:29.319] [jointLog] [info] iteration = 300 | max rel diff. = 0.631201 [2020-04-30 07:02:29.401] [jointLog] [info] iteration = 400 | max rel diff. = 0.0474015 [2020-04-30 07:02:29.482] [jointLog] [info] iteration = 500 | max rel diff. = 0.208421 [2020-04-30 07:02:29.564] [jointLog] [info] iteration = 600 | max rel diff. = 0.693294 [2020-04-30 07:02:29.645] [jointLog] [info] iteration = 700 | max rel diff. = 0.812229 [2020-04-30 07:02:29.727] [jointLog] [info] iteration = 800 | max rel diff. = 0.0262918 [2020-04-30 07:02:29.803] [jointLog] [info] iteration = 894 | max rel diff. = 0.00757559 [2020-04-30 07:02:29.804] [jointLog] [info] Finished optimizer [2020-04-30 07:02:29.804] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 132_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.132.D9.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.132.D9.infected.ambient.megan_R2.fq } Logs will be written to 132_quant/logs [2020-04-30 07:02:31.546] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:02:31.546] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:02:31.546] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:02:31.546] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:02:31.546] [jointLog] [info] parsing read library format [2020-04-30 07:02:31.546] [jointLog] [info] There is 1 library. [2020-04-30 07:02:31.614] [jointLog] [info] Loading pufferfish index [2020-04-30 07:02:31.614] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:02:31.614] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 27.752 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 300.98 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 185.78 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 8.2613 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 55.204 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 78.159 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 397.8 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 160.39 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 562.23 us ----------------------------------------- [2020-04-30 07:02:32.344] [jointLog] [info] done [2020-04-30 07:02:32.344] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:02:32.373] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:02:33.096] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 803,856, hits per frag: 2.11548 processed 1,000,000 fragments hits: 1,606,912, hits per frag: 1.67368 processed 1,500,000 fragments hits: 2,409,358, hits per frag: 1.63202 [2020-04-30 07:02:38.756] [jointLog] [info] Computed 23,977 rich equivalence classes for further processing [2020-04-30 07:02:38.756] [jointLog] [info] Counted 1,748,058 total reads in the equivalence classes [2020-04-30 07:02:38.768] [jointLog] [info] Number of mappings discarded because of alignment score : 527,438 [2020-04-30 07:02:38.768] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,550 [2020-04-30 07:02:38.768] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:02:38.768] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,439 [2020-04-30 07:02:38.771] [jointLog] [warning] Only 1748058 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:02:38.771] [jointLog] [info] Mapping rate = 98.841% [2020-04-30 07:02:38.771] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:02:38.772] [jointLog] [info] Starting optimizer [2020-04-30 07:02:38.790] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:02:38.792] [jointLog] [info] iteration = 0 | max rel diff. = 3792.63 [2020-04-30 07:02:38.907] [jointLog] [info] iteration = 100 | max rel diff. = 18.3887 [2020-04-30 07:02:38.986] [jointLog] [info] iteration = 200 | max rel diff. = 0.501756 [2020-04-30 07:02:39.064] [jointLog] [info] iteration = 300 | max rel diff. = 1.48997 [2020-04-30 07:02:39.141] [jointLog] [info] iteration = 400 | max rel diff. = 0.22212 [2020-04-30 07:02:39.219] [jointLog] [info] iteration = 500 | max rel diff. = 0.0265549 [2020-04-30 07:02:39.296] [jointLog] [info] iteration = 600 | max rel diff. = 0.101989 [2020-04-30 07:02:39.304] [jointLog] [info] iteration = 612 | max rel diff. = 0.00444295 [2020-04-30 07:02:39.305] [jointLog] [info] Finished optimizer [2020-04-30 07:02:39.305] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 151_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.151.D9.infected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.151.D9.infected.cold.megan_R2.fq } Logs will be written to 151_quant/logs [2020-04-30 07:02:40.893] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:02:40.893] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:02:40.893] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:02:40.893] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:02:40.893] [jointLog] [info] parsing read library format [2020-04-30 07:02:40.893] [jointLog] [info] There is 1 library. [2020-04-30 07:02:40.945] [jointLog] [info] Loading pufferfish index [2020-04-30 07:02:40.945] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:02:40.945] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 22.33 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 274 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 168.86 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 7.2031 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 51.862 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.95 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 24.299 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.0989 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 297.28 us ----------------------------------------- [2020-04-30 07:02:41.059] [jointLog] [info] done [2020-04-30 07:02:41.059] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:02:41.075] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:02:41.932] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 855,824, hits per frag: 2.01361 processed 1,000,000 fragments hits: 1,711,634, hits per frag: 1.85641 processed 1,500,000 fragments hits: 2,565,668, hits per frag: 1.84268 processed 2,000,000 fragments hits: 3,423,129, hits per frag: 1.75361 processed 2,500,000 fragments hits: 4,280,597, hits per frag: 1.72154 processed 3,000,001 fragments hits: 5,136,558, hits per frag: 1.71637 processed 3,500,000 fragments hits: 5,994,486, hits per frag: 1.75807 processed 4,000,000 fragments hits: 6,851,090, hits per frag: 1.72758 [2020-04-30 07:02:53.428] [jointLog] [info] Computed 34,832 rich equivalence classes for further processing [2020-04-30 07:02:53.428] [jointLog] [info] Counted 4,281,878 total reads in the equivalence classes [2020-04-30 07:02:53.440] [jointLog] [info] Number of mappings discarded because of alignment score : 900,934 [2020-04-30 07:02:53.440] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 27,361 [2020-04-30 07:02:53.440] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:02:53.440] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,757 [2020-04-30 07:02:53.443] [jointLog] [warning] Only 4281878 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:02:53.443] [jointLog] [info] Mapping rate = 99.3236% [2020-04-30 07:02:53.443] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:02:53.444] [jointLog] [info] Starting optimizer [2020-04-30 07:02:53.460] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:02:53.461] [jointLog] [info] iteration = 0 | max rel diff. = 9627.48 [2020-04-30 07:02:53.567] [jointLog] [info] iteration = 100 | max rel diff. = 10.5111 [2020-04-30 07:02:53.658] [jointLog] [info] iteration = 200 | max rel diff. = 11.0011 [2020-04-30 07:02:53.746] [jointLog] [info] iteration = 300 | max rel diff. = 0.306574 [2020-04-30 07:02:53.834] [jointLog] [info] iteration = 400 | max rel diff. = 3.82001 [2020-04-30 07:02:53.921] [jointLog] [info] iteration = 500 | max rel diff. = 18.5265 [2020-04-30 07:02:54.008] [jointLog] [info] iteration = 600 | max rel diff. = 0.179279 [2020-04-30 07:02:54.096] [jointLog] [info] iteration = 700 | max rel diff. = 0.0595298 [2020-04-30 07:02:54.183] [jointLog] [info] iteration = 800 | max rel diff. = 0.507489 [2020-04-30 07:02:54.243] [jointLog] [info] iteration = 871 | max rel diff. = 0.00340919 [2020-04-30 07:02:54.244] [jointLog] [info] Finished optimizer [2020-04-30 07:02:54.244] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 173_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.173.D9.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.173.D9.infected.warm.megan_R2.fq } Logs will be written to 173_quant/logs [2020-04-30 07:02:56.193] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:02:56.193] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:02:56.193] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:02:56.193] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:02:56.193] [jointLog] [info] parsing read library format [2020-04-30 07:02:56.193] [jointLog] [info] There is 1 library. [2020-04-30 07:02:56.281] [jointLog] [info] Loading pufferfish index [2020-04-30 07:02:56.281] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:02:56.281] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 19.76 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 315.38 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 202.03 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 8.9155 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 49.52 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.7925 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 25.476 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.3054 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 297.11 us ----------------------------------------- [2020-04-30 07:02:56.393] [jointLog] [info] done [2020-04-30 07:02:56.393] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:02:56.410] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:02:57.084] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 845,625, hits per frag: 1.86244 processed 1,000,001 fragments hits: 1,690,327, hits per frag: 1.90336 [2020-04-30 07:03:01.464] [jointLog] [info] Computed 13,995 rich equivalence classes for further processing [2020-04-30 07:03:01.464] [jointLog] [info] Counted 1,455,183 total reads in the equivalence classes [2020-04-30 07:03:01.476] [jointLog] [info] Number of mappings discarded because of alignment score : 418,254 [2020-04-30 07:03:01.476] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 17,284 [2020-04-30 07:03:01.476] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:03:01.476] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,337 [2020-04-30 07:03:01.479] [jointLog] [warning] Only 1455183 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:03:01.479] [jointLog] [info] Mapping rate = 98.7505% [2020-04-30 07:03:01.479] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:03:01.480] [jointLog] [info] Starting optimizer [2020-04-30 07:03:01.492] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:03:01.495] [jointLog] [info] iteration = 0 | max rel diff. = 3460.05 [2020-04-30 07:03:01.589] [jointLog] [info] iteration = 100 | max rel diff. = 3.73156 [2020-04-30 07:03:01.657] [jointLog] [info] iteration = 200 | max rel diff. = 0.676305 [2020-04-30 07:03:01.718] [jointLog] [info] iteration = 300 | max rel diff. = 0.0691932 [2020-04-30 07:03:01.779] [jointLog] [info] iteration = 400 | max rel diff. = 0.0638414 [2020-04-30 07:03:01.831] [jointLog] [info] iteration = 487 | max rel diff. = 0.00441576 [2020-04-30 07:03:01.832] [jointLog] [info] Finished optimizer [2020-04-30 07:03:01.832] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 178_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.178.D9.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.178.D9.infected.ambient.megan_R2.fq } Logs will be written to 178_quant/logs [2020-04-30 07:03:03.475] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:03:03.475] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:03:03.475] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:03:03.475] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:03:03.475] [jointLog] [info] parsing read library format [2020-04-30 07:03:03.475] [jointLog] [info] There is 1 library. [2020-04-30 07:03:03.543] [jointLog] [info] Loading pufferfish index [2020-04-30 07:03:03.544] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:03:03.544] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 20.811 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 294.45 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 180.38 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 8.0409 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 50.028 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 3.2496 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 25.109 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.1844 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 298.22 us ----------------------------------------- [2020-04-30 07:03:03.656] [jointLog] [info] done [2020-04-30 07:03:03.656] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:03:03.673] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:03:04.368] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 829,925, hits per frag: 1.73861 processed 1,000,000 fragments hits: 1,662,022, hits per frag: 1.84047 processed 1,500,000 fragments hits: 2,494,707, hits per frag: 1.7612 processed 2,000,000 fragments hits: 3,327,231, hits per frag: 1.67317 processed 2,500,000 fragments hits: 4,161,750, hits per frag: 1.70609 processed 3,000,000 fragments hits: 4,993,946, hits per frag: 1.72318 [2020-04-30 07:03:14.268] [jointLog] [info] Computed 26,039 rich equivalence classes for further processing [2020-04-30 07:03:14.268] [jointLog] [info] Counted 3,189,366 total reads in the equivalence classes [2020-04-30 07:03:14.280] [jointLog] [info] Number of mappings discarded because of alignment score : 981,336 [2020-04-30 07:03:14.280] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 23,429 [2020-04-30 07:03:14.280] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:03:14.280] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,120 [2020-04-30 07:03:14.283] [jointLog] [warning] Only 3189366 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:03:14.283] [jointLog] [info] Mapping rate = 99.2371% [2020-04-30 07:03:14.283] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:03:14.284] [jointLog] [info] Starting optimizer [2020-04-30 07:03:14.299] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:03:14.301] [jointLog] [info] iteration = 0 | max rel diff. = 7375.34 [2020-04-30 07:03:14.399] [jointLog] [info] iteration = 100 | max rel diff. = 14.9726 [2020-04-30 07:03:14.483] [jointLog] [info] iteration = 200 | max rel diff. = 0.237581 [2020-04-30 07:03:14.562] [jointLog] [info] iteration = 300 | max rel diff. = 0.312664 [2020-04-30 07:03:14.641] [jointLog] [info] iteration = 400 | max rel diff. = 0.177105 [2020-04-30 07:03:14.720] [jointLog] [info] iteration = 500 | max rel diff. = 0.0780449 [2020-04-30 07:03:14.773] [jointLog] [info] iteration = 568 | max rel diff. = 0.0086786 [2020-04-30 07:03:14.774] [jointLog] [info] Finished optimizer [2020-04-30 07:03:14.774] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 221_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.221.D12.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.221.D12.uninfected.cold.megan_R2.fq } Logs will be written to 221_quant/logs [2020-04-30 07:03:16.762] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:03:16.762] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:03:16.762] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:03:16.762] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:03:16.762] [jointLog] [info] parsing read library format [2020-04-30 07:03:16.762] [jointLog] [info] There is 1 library. [2020-04-30 07:03:16.854] [jointLog] [info] Loading pufferfish index [2020-04-30 07:03:16.854] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:03:16.854] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 32.163 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 377.75 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 250.47 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 9.4647 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 63.665 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 3.4004 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 28.687 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.6154 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 310.99 us ----------------------------------------- [2020-04-30 07:03:16.998] [jointLog] [info] done [2020-04-30 07:03:16.998] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:03:17.014] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:03:17.821] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 789,007, hits per frag: 1.90644 processed 1,500,000 fragments hits: 2,365,709, hits per frag: 1.68559 processed 2,000,000 fragments hits: 3,152,903, hits per frag: 1.63172 processed 2,500,000 fragments hits: 3,942,906, hits per frag: 1.65505 [2020-04-30 07:03:26.045] [jointLog] [info] Computed 14,142 rich equivalence classes for further processing [2020-04-30 07:03:26.045] [jointLog] [info] Counted 2,610,801 total reads in the equivalence classes [2020-04-30 07:03:26.057] [jointLog] [info] Number of mappings discarded because of alignment score : 828,701 [2020-04-30 07:03:26.057] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 20,911 [2020-04-30 07:03:26.057] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:03:26.057] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,619 [2020-04-30 07:03:26.060] [jointLog] [warning] Only 2610801 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:03:26.060] [jointLog] [info] Mapping rate = 99.1818% [2020-04-30 07:03:26.060] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:03:26.061] [jointLog] [info] Starting optimizer [2020-04-30 07:03:26.075] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:03:26.078] [jointLog] [info] iteration = 0 | max rel diff. = 5797.17 [2020-04-30 07:03:26.156] [jointLog] [info] iteration = 100 | max rel diff. = 11.9299 [2020-04-30 07:03:26.223] [jointLog] [info] iteration = 200 | max rel diff. = 3.52464 [2020-04-30 07:03:26.284] [jointLog] [info] iteration = 300 | max rel diff. = 2.25293 [2020-04-30 07:03:26.345] [jointLog] [info] iteration = 400 | max rel diff. = 0.033746 [2020-04-30 07:03:26.379] [jointLog] [info] iteration = 456 | max rel diff. = 0.00325304 [2020-04-30 07:03:26.380] [jointLog] [info] Finished optimizer [2020-04-30 07:03:26.380] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 222_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.222.D12.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.222.D12.uninfected.cold.megan_R2.fq } Logs will be written to 222_quant/logs [2020-04-30 07:03:28.060] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:03:28.060] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:03:28.060] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:03:28.060] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:03:28.060] [jointLog] [info] parsing read library format [2020-04-30 07:03:28.060] [jointLog] [info] There is 1 library. [2020-04-30 07:03:28.127] [jointLog] [info] Loading pufferfish index [2020-04-30 07:03:28.127] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:03:28.127] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 33.06 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 492.28 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 268.37 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 11.028 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 65.759 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 3.5455 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 28.487 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.4884 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 299.51 us ----------------------------------------- [2020-04-30 07:03:28.276] [jointLog] [info] done [2020-04-30 07:03:28.276] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:03:28.292] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:03:28.835] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 842,411, hits per frag: 1.77597 processed 1,000,000 fragments hits: 1,684,441, hits per frag: 1.84917 [2020-04-30 07:03:32.122] [jointLog] [info] Computed 25,813 rich equivalence classes for further processing [2020-04-30 07:03:32.122] [jointLog] [info] Counted 1,346,110 total reads in the equivalence classes [2020-04-30 07:03:32.135] [jointLog] [info] Number of mappings discarded because of alignment score : 272,233 [2020-04-30 07:03:32.135] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 12,962 [2020-04-30 07:03:32.135] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:03:32.135] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,352 [2020-04-30 07:03:32.138] [jointLog] [warning] Only 1346110 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:03:32.138] [jointLog] [info] Mapping rate = 98.924% [2020-04-30 07:03:32.138] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:03:32.139] [jointLog] [info] Starting optimizer [2020-04-30 07:03:32.152] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:03:32.154] [jointLog] [info] iteration = 0 | max rel diff. = 2858.26 [2020-04-30 07:03:32.248] [jointLog] [info] iteration = 100 | max rel diff. = 7.30647 [2020-04-30 07:03:32.330] [jointLog] [info] iteration = 200 | max rel diff. = 1.05557 [2020-04-30 07:03:32.408] [jointLog] [info] iteration = 300 | max rel diff. = 0.0419766 [2020-04-30 07:03:32.485] [jointLog] [info] iteration = 400 | max rel diff. = 0.71107 [2020-04-30 07:03:32.563] [jointLog] [info] iteration = 500 | max rel diff. = 0.026917 [2020-04-30 07:03:32.631] [jointLog] [info] iteration = 589 | max rel diff. = 0.00445131 [2020-04-30 07:03:32.632] [jointLog] [info] Finished optimizer [2020-04-30 07:03:32.632] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 254_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.254.D12.infected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.254.D12.infected.cold.megan_R2.fq } Logs will be written to 254_quant/logs [2020-04-30 07:03:34.337] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:03:34.337] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:03:34.337] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:03:34.337] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:03:34.337] [jointLog] [info] parsing read library format [2020-04-30 07:03:34.337] [jointLog] [info] There is 1 library. [2020-04-30 07:03:34.388] [jointLog] [info] Loading pufferfish index [2020-04-30 07:03:34.388] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:03:34.388] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 21.712 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 293.25 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 95.911 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.9788 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 51.885 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 3.3126 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 27.355 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.4432 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 161.92 us ----------------------------------------- [2020-04-30 07:03:34.505] [jointLog] [info] done [2020-04-30 07:03:34.505] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:03:34.521] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:03:35.197] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 804,931, hits per frag: 1.78381 processed 1,000,000 fragments hits: 1,609,693, hits per frag: 1.69607 processed 1,500,000 fragments hits: 2,413,744, hits per frag: 1.72176 [2020-04-30 07:03:41.045] [jointLog] [info] Computed 23,317 rich equivalence classes for further processing [2020-04-30 07:03:41.045] [jointLog] [info] Counted 1,954,258 total reads in the equivalence classes [2020-04-30 07:03:41.057] [jointLog] [info] Number of mappings discarded because of alignment score : 528,963 [2020-04-30 07:03:41.057] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,545 [2020-04-30 07:03:41.057] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:03:41.057] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,874 [2020-04-30 07:03:41.060] [jointLog] [warning] Only 1954258 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:03:41.060] [jointLog] [info] Mapping rate = 99.0268% [2020-04-30 07:03:41.060] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:03:41.061] [jointLog] [info] Starting optimizer [2020-04-30 07:03:41.077] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:03:41.079] [jointLog] [info] iteration = 0 | max rel diff. = 4641.55 [2020-04-30 07:03:41.169] [jointLog] [info] iteration = 100 | max rel diff. = 10.9424 [2020-04-30 07:03:41.249] [jointLog] [info] iteration = 200 | max rel diff. = 1.17574 [2020-04-30 07:03:41.325] [jointLog] [info] iteration = 300 | max rel diff. = 0.150236 [2020-04-30 07:03:41.369] [jointLog] [info] iteration = 359 | max rel diff. = 0.00536461 [2020-04-30 07:03:41.370] [jointLog] [info] Finished optimizer [2020-04-30 07:03:41.370] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 272_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.272.D12.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.272.D12.infected.warm.megan_R2.fq } Logs will be written to 272_quant/logs [2020-04-30 07:03:43.125] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:03:43.125] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:03:43.125] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:03:43.125] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:03:43.125] [jointLog] [info] parsing read library format [2020-04-30 07:03:43.125] [jointLog] [info] There is 1 library. [2020-04-30 07:03:43.201] [jointLog] [info] Loading pufferfish index [2020-04-30 07:03:43.201] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:03:43.201] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 24.358 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 335.9 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 210.24 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 9.4783 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 53.676 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 4.0354 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 29.421 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.6952 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 314.92 us ----------------------------------------- [2020-04-30 07:03:43.328] [jointLog] [info] done [2020-04-30 07:03:43.328] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:03:43.344] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:03:44.126] [jointLog] [info] Automatically detected most likely library type as IU [2020-04-30 07:03:45.472] [jointLog] [info] Computed 14,093 rich equivalence classes for further processing [2020-04-30 07:03:45.472] [jointLog] [info] Counted 380,273 total reads in the equivalence classes [2020-04-30 07:03:45.484] [jointLog] [info] Number of mappings discarded because of alignment score : 211,758 [2020-04-30 07:03:45.484] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 19,352 [2020-04-30 07:03:45.484] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:03:45.484] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 589 [2020-04-30 07:03:45.487] [jointLog] [warning] Only 380273 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:03:45.487] [jointLog] [info] Mapping rate = 94.5689% [2020-04-30 07:03:45.487] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:03:45.489] [jointLog] [info] Starting optimizer [2020-04-30 07:03:45.504] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:03:45.505] [jointLog] [info] iteration = 0 | max rel diff. = 905.932 [2020-04-30 07:03:45.583] [jointLog] [info] iteration = 100 | max rel diff. = 15.2479 [2020-04-30 07:03:45.651] [jointLog] [info] iteration = 200 | max rel diff. = 0.0667936 [2020-04-30 07:03:45.714] [jointLog] [info] iteration = 300 | max rel diff. = 0.16758 [2020-04-30 07:03:45.753] [jointLog] [info] iteration = 364 | max rel diff. = 0.00776935 [2020-04-30 07:03:45.754] [jointLog] [info] Finished optimizer [2020-04-30 07:03:45.754] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 280_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.280.D12.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.280.D12.infected.warm.megan_R2.fq } Logs will be written to 280_quant/logs [2020-04-30 07:03:47.390] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:03:47.390] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:03:47.390] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:03:47.390] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:03:47.390] [jointLog] [info] parsing read library format [2020-04-30 07:03:47.390] [jointLog] [info] There is 1 library. [2020-04-30 07:03:47.457] [jointLog] [info] Loading pufferfish index [2020-04-30 07:03:47.457] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:03:47.457] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 21.07 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 316.56 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 187.45 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 8.6114 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 49.775 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 3.0872 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 28.614 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.6125 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 310.93 us ----------------------------------------- [2020-04-30 07:03:47.574] [jointLog] [info] done [2020-04-30 07:03:47.574] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:03:47.590] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:03:48.263] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 820,550, hits per frag: 1.69332 [2020-04-30 07:03:50.672] [jointLog] [info] Computed 28,476 rich equivalence classes for further processing [2020-04-30 07:03:50.672] [jointLog] [info] Counted 793,397 total reads in the equivalence classes [2020-04-30 07:03:50.684] [jointLog] [info] Number of mappings discarded because of alignment score : 276,234 [2020-04-30 07:03:50.684] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 17,554 [2020-04-30 07:03:50.684] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:03:50.684] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,573 [2020-04-30 07:03:50.687] [jointLog] [warning] Only 793397 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:03:50.687] [jointLog] [info] Mapping rate = 97.3227% [2020-04-30 07:03:50.687] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:03:50.688] [jointLog] [info] Starting optimizer [2020-04-30 07:03:50.702] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:03:50.704] [jointLog] [info] iteration = 0 | max rel diff. = 1901.91 [2020-04-30 07:03:50.804] [jointLog] [info] iteration = 100 | max rel diff. = 1.31233 [2020-04-30 07:03:50.892] [jointLog] [info] iteration = 200 | max rel diff. = 0.211411 [2020-04-30 07:03:50.974] [jointLog] [info] iteration = 300 | max rel diff. = 0.0504288 [2020-04-30 07:03:51.056] [jointLog] [info] iteration = 400 | max rel diff. = 7.6828 [2020-04-30 07:03:51.057] [jointLog] [info] iteration = 402 | max rel diff. = 0.00621768 [2020-04-30 07:03:51.058] [jointLog] [info] Finished optimizer [2020-04-30 07:03:51.058] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 294_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.294.D12.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.294.D12.infected.warm.megan_R2.fq } Logs will be written to 294_quant/logs [2020-04-30 07:03:52.664] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:03:52.664] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:03:52.664] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:03:52.664] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:03:52.664] [jointLog] [info] parsing read library format [2020-04-30 07:03:52.664] [jointLog] [info] There is 1 library. [2020-04-30 07:03:52.733] [jointLog] [info] Loading pufferfish index [2020-04-30 07:03:52.733] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:03:52.733] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 24.439 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 314.06 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 208.76 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 8.6117 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 54.616 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 3.4889 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 28.284 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.643 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 310.7 us ----------------------------------------- [2020-04-30 07:03:52.858] [jointLog] [info] done [2020-04-30 07:03:52.858] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:03:52.875] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:03:53.505] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 798,074, hits per frag: 1.7341 processed 1,000,001 fragments hits: 1,595,454, hits per frag: 1.75801 processed 1,500,000 fragments hits: 2,393,548, hits per frag: 1.65399 processed 2,000,001 fragments hits: 3,189,937, hits per frag: 1.66886 processed 2,500,000 fragments hits: 3,986,134, hits per frag: 1.66491 processed 3,000,001 fragments hits: 4,782,196, hits per frag: 1.61931 [2020-04-30 07:04:01.774] [jointLog] [info] Computed 24,349 rich equivalence classes for further processing [2020-04-30 07:04:01.774] [jointLog] [info] Counted 3,167,685 total reads in the equivalence classes [2020-04-30 07:04:01.786] [jointLog] [info] Number of mappings discarded because of alignment score : 719,234 [2020-04-30 07:04:01.786] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 21,412 [2020-04-30 07:04:01.786] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:04:01.786] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,235 [2020-04-30 07:04:01.789] [jointLog] [warning] Only 3167685 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:04:01.789] [jointLog] [info] Mapping rate = 99.2983% [2020-04-30 07:04:01.789] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:04:01.790] [jointLog] [info] Starting optimizer [2020-04-30 07:04:01.806] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:04:01.807] [jointLog] [info] iteration = 0 | max rel diff. = 6601.82 [2020-04-30 07:04:01.899] [jointLog] [info] iteration = 100 | max rel diff. = 9.58813 [2020-04-30 07:04:01.978] [jointLog] [info] iteration = 200 | max rel diff. = 3.33627 [2020-04-30 07:04:02.053] [jointLog] [info] iteration = 300 | max rel diff. = 0.302549 [2020-04-30 07:04:02.127] [jointLog] [info] iteration = 400 | max rel diff. = 2.87797 [2020-04-30 07:04:02.200] [jointLog] [info] iteration = 500 | max rel diff. = 0.357354 [2020-04-30 07:04:02.270] [jointLog] [info] iteration = 596 | max rel diff. = 0.0028829 [2020-04-30 07:04:02.271] [jointLog] [info] Finished optimizer [2020-04-30 07:04:02.271] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 334_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.334.D12.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.334.D12.infected.ambient.megan_R2.fq } Logs will be written to 334_quant/logs [2020-04-30 07:04:03.955] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:04:03.955] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:04:03.955] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:04:03.955] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:04:03.955] [jointLog] [info] parsing read library format [2020-04-30 07:04:03.955] [jointLog] [info] There is 1 library. [2020-04-30 07:04:04.040] [jointLog] [info] Loading pufferfish index [2020-04-30 07:04:04.041] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:04:04.041] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 20.702 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 316.18 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 194.4 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 8.8135 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 50.1 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 3.2065 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 29.045 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.6357 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 306.63 us ----------------------------------------- [2020-04-30 07:04:04.159] [jointLog] [info] done [2020-04-30 07:04:04.159] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:04:04.175] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:04:05.019] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 748,834, hits per frag: 1.71904 processed 1,000,000 fragments hits: 1,498,761, hits per frag: 1.58117 [2020-04-30 07:04:09.346] [jointLog] [info] Computed 15,856 rich equivalence classes for further processing [2020-04-30 07:04:09.346] [jointLog] [info] Counted 1,108,997 total reads in the equivalence classes [2020-04-30 07:04:09.358] [jointLog] [info] Number of mappings discarded because of alignment score : 362,640 [2020-04-30 07:04:09.358] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 10,615 [2020-04-30 07:04:09.358] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:04:09.358] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,854 [2020-04-30 07:04:09.362] [jointLog] [warning] Only 1108997 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:04:09.362] [jointLog] [info] Mapping rate = 99.0177% [2020-04-30 07:04:09.362] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:04:09.363] [jointLog] [info] Starting optimizer [2020-04-30 07:04:09.378] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:04:09.380] [jointLog] [info] iteration = 0 | max rel diff. = 2470.87 [2020-04-30 07:04:09.487] [jointLog] [info] iteration = 100 | max rel diff. = 0.279124 [2020-04-30 07:04:09.567] [jointLog] [info] iteration = 200 | max rel diff. = 0.824234 [2020-04-30 07:04:09.642] [jointLog] [info] iteration = 300 | max rel diff. = 0.488518 [2020-04-30 07:04:09.717] [jointLog] [info] iteration = 400 | max rel diff. = 0.0322291 [2020-04-30 07:04:09.753] [jointLog] [info] iteration = 449 | max rel diff. = 0.00615236 [2020-04-30 07:04:09.754] [jointLog] [info] Finished optimizer [2020-04-30 07:04:09.754] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 349_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.349.D12.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.349.D12.infected.ambient.megan_R2.fq } Logs will be written to 349_quant/logs [2020-04-30 07:04:11.735] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:04:11.735] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:04:11.735] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:04:11.735] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:04:11.735] [jointLog] [info] parsing read library format [2020-04-30 07:04:11.735] [jointLog] [info] There is 1 library. [2020-04-30 07:04:11.809] [jointLog] [info] Loading pufferfish index [2020-04-30 07:04:11.809] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:04:11.809] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 20.639 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 308.11 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 200.16 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 8.6769 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 50.364 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 3.5002 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 28.705 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.6202 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 318.89 us ----------------------------------------- [2020-04-30 07:04:11.927] [jointLog] [info] done [2020-04-30 07:04:11.927] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:04:11.943] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:04:12.629] [jointLog] [info] Automatically detected most likely library type as IU [2020-04-30 07:04:12.907] [jointLog] [info] Computed 12,887 rich equivalence classes for further processing [2020-04-30 07:04:12.907] [jointLog] [info] Counted 79,579 total reads in the equivalence classes [2020-04-30 07:04:12.940] [jointLog] [info] Number of mappings discarded because of alignment score : 76,381 [2020-04-30 07:04:12.940] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 8,405 [2020-04-30 07:04:12.940] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:04:12.940] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 250 [2020-04-30 07:04:12.944] [jointLog] [warning] Only 79579 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:04:12.944] [jointLog] [info] Mapping rate = 86.8634% [2020-04-30 07:04:12.944] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:04:12.945] [jointLog] [info] Starting optimizer [2020-04-30 07:04:12.959] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:04:12.962] [jointLog] [info] iteration = 0 | max rel diff. = 190.712 [2020-04-30 07:04:13.044] [jointLog] [info] iteration = 100 | max rel diff. = 0.298364 [2020-04-30 07:04:13.115] [jointLog] [info] iteration = 200 | max rel diff. = 0.16591 [2020-04-30 07:04:13.147] [jointLog] [info] iteration = 248 | max rel diff. = 0.00949298 [2020-04-30 07:04:13.148] [jointLog] [info] Finished optimizer [2020-04-30 07:04:13.148] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 359_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.359.D12.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.359.D12.infected.ambient.megan_R2.fq } Logs will be written to 359_quant/logs [2020-04-30 07:04:14.979] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:04:14.979] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:04:14.979] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:04:14.979] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:04:14.979] [jointLog] [info] parsing read library format [2020-04-30 07:04:14.979] [jointLog] [info] There is 1 library. [2020-04-30 07:04:15.047] [jointLog] [info] Loading pufferfish index [2020-04-30 07:04:15.047] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:04:15.047] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 21.102 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 316.24 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 186.18 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 8.4784 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 50.434 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 3.0912 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 26.751 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.3451 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 302.39 us ----------------------------------------- [2020-04-30 07:04:15.162] [jointLog] [info] done [2020-04-30 07:04:15.162] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:04:15.179] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:04:15.866] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 844,458, hits per frag: 2.09818 processed 1,000,000 fragments hits: 1,687,983, hits per frag: 1.85319 processed 1,500,000 fragments hits: 2,534,405, hits per frag: 1.74651 processed 2,000,000 fragments hits: 3,381,136, hits per frag: 1.78766 processed 2,500,000 fragments hits: 4,227,968, hits per frag: 1.70398 processed 3,000,000 fragments hits: 5,071,456, hits per frag: 1.71818 [2020-04-30 07:04:24.811] [jointLog] [info] Computed 29,239 rich equivalence classes for further processing [2020-04-30 07:04:24.811] [jointLog] [info] Counted 3,198,705 total reads in the equivalence classes [2020-04-30 07:04:24.823] [jointLog] [info] Number of mappings discarded because of alignment score : 863,773 [2020-04-30 07:04:24.823] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 22,206 [2020-04-30 07:04:24.823] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:04:24.823] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 3,541 [2020-04-30 07:04:24.826] [jointLog] [warning] Only 3198705 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:04:24.826] [jointLog] [info] Mapping rate = 99.2723% [2020-04-30 07:04:24.826] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:04:24.827] [jointLog] [info] Starting optimizer [2020-04-30 07:04:24.845] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:04:24.847] [jointLog] [info] iteration = 0 | max rel diff. = 7222.41 [2020-04-30 07:04:24.969] [jointLog] [info] iteration = 100 | max rel diff. = 15.3561 [2020-04-30 07:04:25.060] [jointLog] [info] iteration = 200 | max rel diff. = 10.0546 [2020-04-30 07:04:25.150] [jointLog] [info] iteration = 300 | max rel diff. = 0.044478 [2020-04-30 07:04:25.240] [jointLog] [info] iteration = 400 | max rel diff. = 0.39081 [2020-04-30 07:04:25.329] [jointLog] [info] iteration = 500 | max rel diff. = 0.122808 [2020-04-30 07:04:25.419] [jointLog] [info] iteration = 600 | max rel diff. = 0.543473 [2020-04-30 07:04:25.506] [jointLog] [info] iteration = 700 | max rel diff. = 0.0530419 [2020-04-30 07:04:25.587] [jointLog] [info] iteration = 800 | max rel diff. = 0.0262999 [2020-04-30 07:04:25.618] [jointLog] [info] iteration = 838 | max rel diff. = 0.00612989 [2020-04-30 07:04:25.618] [jointLog] [info] Finished optimizer [2020-04-30 07:04:25.618] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 425_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.425.D26.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.425.D26.uninfected.cold.megan_R2.fq } Logs will be written to 425_quant/logs [2020-04-30 07:04:27.267] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:04:27.267] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:04:27.267] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:04:27.267] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:04:27.267] [jointLog] [info] parsing read library format [2020-04-30 07:04:27.267] [jointLog] [info] There is 1 library. [2020-04-30 07:04:27.347] [jointLog] [info] Loading pufferfish index [2020-04-30 07:04:27.347] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:04:27.347] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 19.717 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 296.41 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 190.86 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 9.1106 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 49.618 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.857 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 25.967 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.3538 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 296.17 us ----------------------------------------- [2020-04-30 07:04:27.461] [jointLog] [info] done [2020-04-30 07:04:27.461] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:04:27.477] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:04:28.301] [jointLog] [info] Automatically detected most likely library type as IU [2020-04-30 07:04:28.516] [jointLog] [info] Computed 5,798 rich equivalence classes for further processing [2020-04-30 07:04:28.516] [jointLog] [info] Counted 75,532 total reads in the equivalence classes [2020-04-30 07:04:28.550] [jointLog] [info] Number of mappings discarded because of alignment score : 51,320 [2020-04-30 07:04:28.550] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,754 [2020-04-30 07:04:28.550] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:04:28.550] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 331 [2020-04-30 07:04:28.554] [jointLog] [warning] Only 75532 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:04:28.554] [jointLog] [info] Mapping rate = 95.9587% [2020-04-30 07:04:28.554] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:04:28.555] [jointLog] [info] Starting optimizer [2020-04-30 07:04:28.568] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:04:28.571] [jointLog] [info] iteration = 0 | max rel diff. = 153.047 [2020-04-30 07:04:28.640] [jointLog] [info] iteration = 100 | max rel diff. = 0.0554974 [2020-04-30 07:04:28.676] [jointLog] [info] iteration = 161 | max rel diff. = 0.00152478 [2020-04-30 07:04:28.677] [jointLog] [info] Finished optimizer [2020-04-30 07:04:28.677] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 427_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.427.D26.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.427.D26.uninfected.cold.megan_R2.fq } Logs will be written to 427_quant/logs [2020-04-30 07:04:30.518] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:04:30.518] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:04:30.518] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:04:30.518] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:04:30.518] [jointLog] [info] parsing read library format [2020-04-30 07:04:30.519] [jointLog] [info] There is 1 library. [2020-04-30 07:04:30.600] [jointLog] [info] Loading pufferfish index [2020-04-30 07:04:30.600] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:04:30.600] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 20.58 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 300.45 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 189.67 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 8.1227 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 50.026 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 3.1943 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 25.706 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.165 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 300.86 us ----------------------------------------- [2020-04-30 07:04:30.714] [jointLog] [info] done [2020-04-30 07:04:30.714] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:04:30.730] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:04:31.463] [jointLog] [info] Automatically detected most likely library type as IU [2020-04-30 07:04:31.741] [jointLog] [info] Computed 4,673 rich equivalence classes for further processing [2020-04-30 07:04:31.741] [jointLog] [info] Counted 49,677 total reads in the equivalence classes [2020-04-30 07:04:31.790] [jointLog] [info] Number of mappings discarded because of alignment score : 42,895 [2020-04-30 07:04:31.790] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 4,613 [2020-04-30 07:04:31.790] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:04:31.790] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 155 [2020-04-30 07:04:31.794] [jointLog] [warning] Only 49677 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:04:31.794] [jointLog] [info] Mapping rate = 87.6184% [2020-04-30 07:04:31.794] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:04:31.795] [jointLog] [info] Starting optimizer [2020-04-30 07:04:31.807] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:04:31.810] [jointLog] [info] iteration = 0 | max rel diff. = 110.426 [2020-04-30 07:04:31.876] [jointLog] [info] iteration = 100 | max rel diff. = 0.126652 [2020-04-30 07:04:31.899] [jointLog] [info] iteration = 139 | max rel diff. = 0.00959537 [2020-04-30 07:04:31.900] [jointLog] [info] Finished optimizer [2020-04-30 07:04:31.900] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 445_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.445.D26.infected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.445.D26.infected.cold.megan_R2.fq } Logs will be written to 445_quant/logs [2020-04-30 07:04:33.766] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:04:33.766] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:04:33.766] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:04:33.766] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:04:33.766] [jointLog] [info] parsing read library format [2020-04-30 07:04:33.766] [jointLog] [info] There is 1 library. [2020-04-30 07:04:33.833] [jointLog] [info] Loading pufferfish index [2020-04-30 07:04:33.833] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:04:33.833] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 20.192 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 312.82 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 193.68 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 9.4036 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 49.729 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 3.0144 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 28.705 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.6193 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 312.18 us ----------------------------------------- [2020-04-30 07:04:33.950] [jointLog] [info] done [2020-04-30 07:04:33.950] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:04:33.966] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:04:34.635] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 822,451, hits per frag: 1.75899 processed 1,000,000 fragments hits: 1,644,732, hits per frag: 1.7773 processed 1,500,000 fragments hits: 2,463,867, hits per frag: 1.79366 processed 2,000,000 fragments hits: 3,283,817, hits per frag: 1.76127 processed 2,500,000 fragments hits: 4,105,980, hits per frag: 1.6545 [2020-04-30 07:04:41.382] [jointLog] [info] Computed 29,322 rich equivalence classes for further processing [2020-04-30 07:04:41.382] [jointLog] [info] Counted 2,538,058 total reads in the equivalence classes [2020-04-30 07:04:41.393] [jointLog] [info] Number of mappings discarded because of alignment score : 599,504 [2020-04-30 07:04:41.393] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 24,790 [2020-04-30 07:04:41.393] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:04:41.393] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 4,104 [2020-04-30 07:04:41.397] [jointLog] [warning] Only 2538058 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:04:41.397] [jointLog] [info] Mapping rate = 98.9977% [2020-04-30 07:04:41.397] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:04:41.398] [jointLog] [info] Starting optimizer [2020-04-30 07:04:41.413] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:04:41.415] [jointLog] [info] iteration = 0 | max rel diff. = 5952.2 [2020-04-30 07:04:41.515] [jointLog] [info] iteration = 100 | max rel diff. = 8.17616 [2020-04-30 07:04:41.601] [jointLog] [info] iteration = 200 | max rel diff. = 13.7999 [2020-04-30 07:04:41.682] [jointLog] [info] iteration = 300 | max rel diff. = 4.29595 [2020-04-30 07:04:41.763] [jointLog] [info] iteration = 400 | max rel diff. = 0.243642 [2020-04-30 07:04:41.844] [jointLog] [info] iteration = 500 | max rel diff. = 0.0866499 [2020-04-30 07:04:41.925] [jointLog] [info] iteration = 600 | max rel diff. = 0.0802483 [2020-04-30 07:04:42.005] [jointLog] [info] iteration = 700 | max rel diff. = 0.0693964 [2020-04-30 07:04:42.086] [jointLog] [info] iteration = 800 | max rel diff. = 0.884456 [2020-04-30 07:04:42.167] [jointLog] [info] iteration = 900 | max rel diff. = 0.815251 [2020-04-30 07:04:42.247] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.148547 [2020-04-30 07:04:42.328] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.604452 [2020-04-30 07:04:42.396] [jointLog] [info] iteration = 1,186 | max rel diff. = 0.00376349 [2020-04-30 07:04:42.397] [jointLog] [info] Finished optimizer [2020-04-30 07:04:42.397] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 463_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.463.D26.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.463.D26.infected.ambient.megan_R2.fq } Logs will be written to 463_quant/logs [2020-04-30 07:04:44.065] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:04:44.065] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:04:44.066] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:04:44.066] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:04:44.066] [jointLog] [info] parsing read library format [2020-04-30 07:04:44.066] [jointLog] [info] There is 1 library. [2020-04-30 07:04:44.133] [jointLog] [info] Loading pufferfish index [2020-04-30 07:04:44.133] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:04:44.133] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 20.197 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 301.08 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 185.22 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 9.2147 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 49.694 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.8037 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 26.707 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.3592 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 305.17 us ----------------------------------------- [2020-04-30 07:04:44.247] [jointLog] [info] done [2020-04-30 07:04:44.248] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:04:44.264] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:04:46.211] [jointLog] [info] Computed 2,215 rich equivalence classes for further processing [2020-04-30 07:04:46.211] [jointLog] [info] Counted 27,299 total reads in the equivalence classes [2020-04-30 07:04:46.274] [jointLog] [info] Number of mappings discarded because of alignment score : 16,363 [2020-04-30 07:04:46.274] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 1,386 [2020-04-30 07:04:46.274] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:04:46.274] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 46 [2020-04-30 07:04:46.278] [jointLog] [warning] Only 27299 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:04:46.278] [jointLog] [info] Mapping rate = 90.4569% [2020-04-30 07:04:46.278] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:04:46.279] [jointLog] [info] Starting optimizer [2020-04-30 07:04:46.291] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:04:46.294] [jointLog] [info] iteration = 0 | max rel diff. = 59.9571 [2020-04-30 07:04:46.365] [jointLog] [info] iteration = 100 | max rel diff. = 0.000302898 [2020-04-30 07:04:46.365] [jointLog] [info] Finished optimizer [2020-04-30 07:04:46.365] [jointLog] [info] writing output [2020-04-30 07:04:46.443] [jointLog] [warning] NOTE: Read Lib [[ /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.463.D26.infected.ambient.megan_R1.fq, /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.463.D26.infected.ambient.megan_R2.fq]] : Detected a *potential* strand bias > 1% in an unstranded protocol check the file: 463_quant/lib_format_counts.json for details 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 481_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.481.D26.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.481.D26.infected.ambient.megan_R2.fq } Logs will be written to 481_quant/logs [2020-04-30 07:04:48.299] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:04:48.299] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:04:48.299] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:04:48.299] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:04:48.299] [jointLog] [info] parsing read library format [2020-04-30 07:04:48.299] [jointLog] [info] There is 1 library. [2020-04-30 07:04:48.349] [jointLog] [info] Loading pufferfish index [2020-04-30 07:04:48.349] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:04:48.349] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 17.956 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 259.01 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 169.51 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 6.9225 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 49.555 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.8149 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 24.801 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.0999 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 305.47 us ----------------------------------------- [2020-04-30 07:04:48.456] [jointLog] [info] done [2020-04-30 07:04:48.456] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:04:48.472] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:04:49.059] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 810,665, hits per frag: 2.23865 processed 1,000,000 fragments hits: 1,620,737, hits per frag: 1.78762 [2020-04-30 07:04:52.325] [jointLog] [info] Computed 32,026 rich equivalence classes for further processing [2020-04-30 07:04:52.325] [jointLog] [info] Counted 1,297,181 total reads in the equivalence classes [2020-04-30 07:04:52.337] [jointLog] [info] Number of mappings discarded because of alignment score : 334,174 [2020-04-30 07:04:52.337] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 18,750 [2020-04-30 07:04:52.337] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:04:52.337] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 1,625 [2020-04-30 07:04:52.340] [jointLog] [warning] Only 1297181 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:04:52.340] [jointLog] [info] Mapping rate = 98.2455% [2020-04-30 07:04:52.340] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:04:52.341] [jointLog] [info] Starting optimizer [2020-04-30 07:04:52.354] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:04:52.356] [jointLog] [info] iteration = 0 | max rel diff. = 3070.88 [2020-04-30 07:04:52.462] [jointLog] [info] iteration = 100 | max rel diff. = 5.86972 [2020-04-30 07:04:52.552] [jointLog] [info] iteration = 200 | max rel diff. = 1.88549 [2020-04-30 07:04:52.638] [jointLog] [info] iteration = 300 | max rel diff. = 0.276806 [2020-04-30 07:04:52.724] [jointLog] [info] iteration = 400 | max rel diff. = 0.736597 [2020-04-30 07:04:52.810] [jointLog] [info] iteration = 500 | max rel diff. = 12.4966 [2020-04-30 07:04:52.815] [jointLog] [info] iteration = 506 | max rel diff. = 0.0075709 [2020-04-30 07:04:52.815] [jointLog] [info] Finished optimizer [2020-04-30 07:04:52.815] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 485_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.485.D26.infected.ambient.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.485.D26.infected.ambient.megan_R2.fq } Logs will be written to 485_quant/logs [2020-04-30 07:04:54.665] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:04:54.665] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:04:54.665] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:04:54.665] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:04:54.665] [jointLog] [info] parsing read library format [2020-04-30 07:04:54.665] [jointLog] [info] There is 1 library. [2020-04-30 07:04:54.720] [jointLog] [info] Loading pufferfish index [2020-04-30 07:04:54.720] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:04:54.720] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 21.168 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 291.68 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 173.43 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 8.2706 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 50.542 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.7027 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 25.497 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.2323 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 302.22 us ----------------------------------------- [2020-04-30 07:04:54.834] [jointLog] [info] done [2020-04-30 07:04:54.834] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:04:54.850] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:04:55.522] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 786,279, hits per frag: 2.01178 processed 1,000,000 fragments hits: 1,571,290, hits per frag: 1.76284 processed 1,500,000 fragments hits: 2,355,141, hits per frag: 1.60032 [2020-04-30 07:05:01.456] [jointLog] [info] Computed 20,097 rich equivalence classes for further processing [2020-04-30 07:05:01.456] [jointLog] [info] Counted 1,713,501 total reads in the equivalence classes [2020-04-30 07:05:01.468] [jointLog] [info] Number of mappings discarded because of alignment score : 451,979 [2020-04-30 07:05:01.468] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 14,999 [2020-04-30 07:05:01.468] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:05:01.468] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,619 [2020-04-30 07:05:01.472] [jointLog] [warning] Only 1713501 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:05:01.472] [jointLog] [info] Mapping rate = 99.0795% [2020-04-30 07:05:01.472] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:05:01.473] [jointLog] [info] Starting optimizer [2020-04-30 07:05:01.490] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:05:01.491] [jointLog] [info] iteration = 0 | max rel diff. = 4022.53 [2020-04-30 07:05:01.584] [jointLog] [info] iteration = 100 | max rel diff. = 1.10041 [2020-04-30 07:05:01.667] [jointLog] [info] iteration = 200 | max rel diff. = 2.06161 [2020-04-30 07:05:01.747] [jointLog] [info] iteration = 300 | max rel diff. = 1.18506 [2020-04-30 07:05:01.827] [jointLog] [info] iteration = 400 | max rel diff. = 0.0532494 [2020-04-30 07:05:01.904] [jointLog] [info] iteration = 500 | max rel diff. = 0.768103 [2020-04-30 07:05:01.939] [jointLog] [info] iteration = 549 | max rel diff. = 0.00563838 [2020-04-30 07:05:01.939] [jointLog] [info] Finished optimizer [2020-04-30 07:05:01.939] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 72_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.72.D9.infected.warm.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.72.D9.infected.warm.megan_R2.fq } Logs will be written to 72_quant/logs [2020-04-30 07:05:03.953] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:05:03.953] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:05:03.953] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:05:03.953] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:05:03.953] [jointLog] [info] parsing read library format [2020-04-30 07:05:03.953] [jointLog] [info] There is 1 library. [2020-04-30 07:05:04.022] [jointLog] [info] Loading pufferfish index [2020-04-30 07:05:04.022] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:05:04.022] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 20.867 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 301.2 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 183.47 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 8.2048 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 50.365 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 3.0981 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 25.609 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.7187 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 291.11 us ----------------------------------------- [2020-04-30 07:05:04.136] [jointLog] [info] done [2020-04-30 07:05:04.136] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:05:04.152] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:05:04.936] [jointLog] [info] Automatically detected most likely library type as IU  processed 500,000 fragments hits: 766,228, hits per frag: 1.89109 processed 1,000,000 fragments hits: 1,533,280, hits per frag: 1.61634 processed 1,500,000 fragments hits: 2,300,160, hits per frag: 1.57799 [2020-04-30 07:05:10.610] [jointLog] [info] Computed 15,755 rich equivalence classes for further processing [2020-04-30 07:05:10.610] [jointLog] [info] Counted 1,546,941 total reads in the equivalence classes [2020-04-30 07:05:10.621] [jointLog] [info] Number of mappings discarded because of alignment score : 561,816 [2020-04-30 07:05:10.621] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 20,470 [2020-04-30 07:05:10.621] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:05:10.621] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 2,229 [2020-04-30 07:05:10.624] [jointLog] [warning] Only 1546941 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:05:10.624] [jointLog] [info] Mapping rate = 98.6635% [2020-04-30 07:05:10.624] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:05:10.625] [jointLog] [info] Starting optimizer [2020-04-30 07:05:10.641] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:05:10.642] [jointLog] [info] iteration = 0 | max rel diff. = 3610.58 [2020-04-30 07:05:10.744] [jointLog] [info] iteration = 100 | max rel diff. = 2.06392 [2020-04-30 07:05:10.815] [jointLog] [info] iteration = 200 | max rel diff. = 0.213994 [2020-04-30 07:05:10.879] [jointLog] [info] iteration = 300 | max rel diff. = 0.121073 [2020-04-30 07:05:10.944] [jointLog] [info] iteration = 400 | max rel diff. = 0.369173 [2020-04-30 07:05:11.008] [jointLog] [info] iteration = 500 | max rel diff. = 0.0286011 [2020-04-30 07:05:11.037] [jointLog] [info] iteration = 546 | max rel diff. = 0.00203337 [2020-04-30 07:05:11.038] [jointLog] [info] Finished optimizer [2020-04-30 07:05:11.038] [jointLog] [info] writing output 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) v1.2.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx } ### [ libType ] => { A } ### [ validateMappings ] => { } ### [ output ] => { 73_quant } ### [ mates1 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.73.D9.uninfected.cold.megan_R1.fq } ### [ mates2 ] => { /gscratch/srlab/sam/data/C_bairdi/RNAseq/20200413.C_bairdi.73.D9.uninfected.cold.megan_R2.fq } Logs will be written to 73_quant/logs [2020-04-30 07:05:12.730] [jointLog] [info] setting maxHashResizeThreads to 28 [2020-04-30 07:05:12.730] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2020-04-30 07:05:12.730] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65 [2020-04-30 07:05:12.730] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35. [2020-04-30 07:05:12.730] [jointLog] [info] parsing read library format [2020-04-30 07:05:12.730] [jointLog] [info] There is 1 library. [2020-04-30 07:05:12.782] [jointLog] [info] Loading pufferfish index [2020-04-30 07:05:12.783] [jointLog] [warning] The index did not record if the `--keepDuplicates` flag was used. Please consider re-indexing with a newer version of salmon that will propagate this information. [2020-04-30 07:05:12.783] [jointLog] [info] Loading dense pufferfish index. ----------------------------------------- | Loading contig table | Time = 22.269 ms ----------------------------------------- size = 98890 ----------------------------------------- | Loading contig offsets | Time = 295.82 us ----------------------------------------- ----------------------------------------- | Loading reference lengths | Time = 173.27 us ----------------------------------------- ----------------------------------------- | Loading mphf table | Time = 7.4105 ms ----------------------------------------- size = 21703191 Number of ones: 98889 Number of ones per inventory item: 512 Inventory entries filled: 194 ----------------------------------------- | Loading contig boundaries | Time = 51.617 ms ----------------------------------------- size = 21703191 ----------------------------------------- | Loading sequence | Time = 2.8337 ms ----------------------------------------- size = 18736521 ----------------------------------------- | Loading positions | Time = 24.752 ms ----------------------------------------- size = 33327850 ----------------------------------------- | Loading reference sequence | Time = 4.1237 ms ----------------------------------------- ----------------------------------------- | Loading reference accumulative lengths | Time = 291.86 us ----------------------------------------- [2020-04-30 07:05:12.897] [jointLog] [info] done [2020-04-30 07:05:12.897] [jointLog] [info] Index contained 40,435 targets [2020-04-30 07:05:12.913] [jointLog] [info] Number of decoys : 0 [2020-04-30 07:05:13.937] [jointLog] [info] Automatically detected most likely library type as IU [2020-04-30 07:05:14.265] [jointLog] [info] Computed 3,109 rich equivalence classes for further processing [2020-04-30 07:05:14.265] [jointLog] [info] Counted 91,922 total reads in the equivalence classes [2020-04-30 07:05:14.295] [jointLog] [info] Number of mappings discarded because of alignment score : 81,954 [2020-04-30 07:05:14.295] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 8,702 [2020-04-30 07:05:14.295] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0 [2020-04-30 07:05:14.295] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 161 [2020-04-30 07:05:14.298] [jointLog] [warning] Only 91922 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2020-04-30 07:05:14.298] [jointLog] [info] Mapping rate = 90.3197% [2020-04-30 07:05:14.298] [jointLog] [info] finished quantifyLibrary() [2020-04-30 07:05:14.300] [jointLog] [info] Starting optimizer [2020-04-30 07:05:14.311] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2020-04-30 07:05:14.314] [jointLog] [info] iteration = 0 | max rel diff. = 224.624 [2020-04-30 07:05:14.379] [jointLog] [info] iteration = 100 | max rel diff. = 0.396797 [2020-04-30 07:05:14.435] [jointLog] [info] iteration = 200 | max rel diff. = 0.327626 [2020-04-30 07:05:14.458] [jointLog] [info] iteration = 246 | max rel diff. = 0.0063857 [2020-04-30 07:05:14.458] [jointLog] [info] Finished optimizer [2020-04-30 07:05:14.458] [jointLog] [info] writing output