CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l ISR -1 /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329774_reads_1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329774_reads_2.fq -o 329774_01  -p 28 --validateMappings 
Version Info: Could not resolve upgrade information in the alotted time.
Check for upgrades manually at https://combine-lab.github.io/salmon
### salmon (mapping-based) v1.1.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329774_reads_1.fq }
### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329774_reads_2.fq }
### [ output ] => { 329774_01 }
### [ threads ] => { 28 }
### [ validateMappings ] => { }
Logs will be written to 329774_01/logs
[2020-04-16 21:37:32.894] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-16 21:37:32.894] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-16 21:37:32.894] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-16 21:37:32.894] [jointLog] [info] parsing read library format
[2020-04-16 21:37:32.894] [jointLog] [info] There is 1 library.
[2020-04-16 21:37:32.960] [jointLog] [info] Loading pufferfish index
[2020-04-16 21:37:32.960] [jointLog] [info] Loading dense pufferfish index.
-----------------------------------------
| Loading contig table | Time = 20.897 ms
-----------------------------------------
size = 98890
-----------------------------------------
| Loading contig offsets | Time = 307.23 us
-----------------------------------------
-----------------------------------------
| Loading reference lengths | Time = 189.65 us
-----------------------------------------
-----------------------------------------
| Loading mphf table | Time = 8.6467 ms
-----------------------------------------
size = 21703191
Number of ones: 98889
Number of ones per inventory item: 512
Inventory entries filled: 194
-----------------------------------------
| Loading contig boundaries | Time = 49.136 ms
-----------------------------------------
size = 21703191
-----------------------------------------
| Loading sequence | Time = 3.4051 ms
-----------------------------------------
size = 18736521
-----------------------------------------
| Loading positions | Time = 205.8 ms
-----------------------------------------
size = 33327850
-----------------------------------------
| Loading reference sequence | Time = 6.8554 ms
-----------------------------------------
-----------------------------------------
| Loading reference accumulative lengths | Time = 504.83 us
-----------------------------------------




[2020-04-16 21:37:33.256] [jointLog] [info] done
[2020-04-16 21:37:33.256] [jointLog] [info] Index contained 40,435 targets
[2020-04-16 21:37:33.282] [jointLog] [info] Number of decoys : 0


processed 500,000 fragments
hits: 735,728, hits per frag:  2.00507

processed 1,000,000 fragments
hits: 1,472,918, hits per frag:  1.60226

processed 1,500,000 fragments
hits: 2,210,441, hits per frag:  1.54428

processed 2,000,000 fragments
hits: 2,947,003, hits per frag:  1.496

processed 2,500,000 fragments
hits: 3,682,135, hits per frag:  1.52866

processed 3,000,000 fragments
hits: 4,417,206, hits per frag:  1.51259

processed 3,500,000 fragments
hits: 5,153,911, hits per frag:  1.51035

processed 4,000,000 fragments
hits: 5,899,048, hits per frag:  1.50541

processed 4,500,000 fragments
hits: 6,628,693, hits per frag:  1.48476

processed 5,000,000 fragments
hits: 7,367,724, hits per frag:  1.47438

processed 5,000,014 fragments
hits: 7,367,733, hits per frag:  1.49912

processed 5,500,000 fragments
hits: 8,111,907, hits per frag:  1.49748

processed 6,000,000 fragments
hits: 8,852,549, hits per frag:  1.48644

processed 6,500,000 fragments
hits: 9,589,586, hits per frag:  1.50025

processed 7,000,000 fragments
hits: 10,324,028, hits per frag:  1.49775

processed 7,500,000 fragments
hits: 11,058,967, hits per frag:  1.4954

processed 8,000,000 fragments
hits: 11,793,081, hits per frag:  1.49535

processed 8,500,001 fragments
hits: 12,530,305, hits per frag:  1.49159

processed 9,000,000 fragments
hits: 13,262,781, hits per frag:  1.4857

processed 9,500,000 fragments
hits: 13,998,477, hits per frag:  1.47817

processed 10,000,000 fragments
hits: 14,743,838, hits per frag:  1.49136

processed 10,500,000 fragments
hits: 15,492,453, hits per frag:  1.48323

processed 11,000,000 fragments
hits: 16,240,297, hits per frag:  1.48395

processed 11,500,000 fragments
hits: 16,988,967, hits per frag:  1.48918

processed 12,000,000 fragments
hits: 17,734,550, hits per frag:  1.49125

processed 12,500,000 fragments
hits: 18,480,589, hits per frag:  1.49178

processed 13,000,000 fragments
hits: 19,229,273, hits per frag:  1.49151

processed 13,500,000 fragments
hits: 19,978,751, hits per frag:  1.48942

processed 14,000,000 fragments
hits: 20,726,132, hits per frag:  1.48344

processed 14,500,000 fragments
hits: 21,477,306, hits per frag:  1.49495

processed 15,000,000 fragments
hits: 22,225,283, hits per frag:  1.49017

processed 15,500,000 fragments
hits: 22,970,694, hits per frag:  1.48868

processed 16,000,000 fragments
hits: 23,718,514, hits per frag:  1.49398

processed 16,500,000 fragments
hits: 24,464,400, hits per frag:  1.4952

processed 17,000,000 fragments
hits: 25,219,677, hits per frag:  1.48447

processed 17,500,000 fragments
hits: 25,965,685, hits per frag:  1.48406

processed 18,000,000 fragments
hits: 26,702,890, hits per frag:  1.48626

processed 18,500,000 fragments
hits: 27,442,360, hits per frag:  1.48571

processed 19,000,000 fragments
hits: 28,160,815, hits per frag:  1.49564

processed 19,500,000 fragments
hits: 28,879,132, hits per frag:  1.4853

processed 20,000,000 fragments
hits: 29,622,667, hits per frag:  1.48583

processed 20,500,000 fragments
hits: 30,365,876, hits per frag:  1.48244

processed 21,000,000 fragments
hits: 31,107,722, hits per frag:  1.48375

processed 21,500,000 fragments
hits: 31,836,537, hits per frag:  1.48855

processed 22,000,000 fragments
hits: 32,579,295, hits per frag:  1.48709

processed 22,500,000 fragments
hits: 33,328,498, hits per frag:  1.48636

processed 23,000,000 fragments
hits: 34,074,122, hits per frag:  1.48618

processed 23,500,000 fragments
hits: 34,816,881, hits per frag:  1.48839

processed 24,000,000 fragments
hits: 35,556,690, hits per frag:  1.48344

processed 24,500,000 fragments
hits: 36,297,280, hits per frag:  1.48176

processed 25,000,001 fragments
hits: 37,032,112, hits per frag:  1.48438

processed 25,500,001 fragments
hits: 37,768,209, hits per frag:  1.4872

processed 26,000,000 fragments
hits: 38,504,482, hits per frag:  1.48436

processed 26,500,000 fragments
hits: 39,242,389, hits per frag:  1.48666

processed 27,000,000 fragments
hits: 39,977,852, hits per frag:  1.48648

processed 27,500,000 fragments
hits: 40,713,971, hits per frag:  1.48208

processed 28,000,001 fragments
hits: 41,449,319, hits per frag:  1.48183

processed 28,500,000 fragments
hits: 42,183,023, hits per frag:  1.4805

processed 29,000,000 fragments
hits: 42,917,537, hits per frag:  1.48702

processed 29,500,000 fragments
hits: 43,652,405, hits per frag:  1.482

processed 30,000,001 fragments
hits: 44,385,181, hits per frag:  1.48097

processed 30,500,002 fragments
hits: 45,120,267, hits per frag:  1.48074

processed 31,000,000 fragments
hits: 45,855,461, hits per frag:  1.48333

processed 31,500,000 fragments
hits: 46,588,904, hits per frag:  1.47928

processed 32,000,000 fragments
hits: 47,330,727, hits per frag:  1.48769

processed 32,500,000 fragments
hits: 48,057,817, hits per frag:  1.48376

processed 33,000,000 fragments
hits: 48,791,903, hits per frag:  1.48086

processed 33,500,000 fragments
hits: 49,529,060, hits per frag:  1.48531

processed 34,000,000 fragments
hits: 50,272,777, hits per frag:  1.48069

processed 34,500,001 fragments
hits: 51,014,484, hits per frag:  1.48486

processed 35,000,000 fragments
hits: 51,762,700, hits per frag:  1.48228

processed 35,500,000 fragments
hits: 52,507,919, hits per frag:  1.48406

processed 36,000,000 fragments
hits: 53,251,931, hits per frag:  1.48621

processed 36,500,000 fragments
hits: 53,996,598, hits per frag:  1.47994

processed 37,000,000 fragments
hits: 54,744,474, hits per frag:  1.48424

processed 37,500,001 fragments
hits: 55,487,597, hits per frag:  1.48024

processed 38,000,000 fragments
hits: 56,232,968, hits per frag:  1.48241

processed 38,500,000 fragments
hits: 56,978,520, hits per frag:  1.48319

processed 39,000,000 fragments
hits: 57,723,096, hits per frag:  1.48147

processed 39,500,000 fragments
hits: 58,465,855, hits per frag:  1.48027

processed 40,000,000 fragments
hits: 59,208,277, hits per frag:  1.48229

processed 40,500,002 fragments
hits: 59,952,506, hits per frag:  1.48366

processed 41,000,000 fragments
hits: 60,698,441, hits per frag:  1.4832

processed 41,500,000 fragments
hits: 61,420,120, hits per frag:  1.48162

processed 42,000,000 fragments
hits: 62,154,772, hits per frag:  1.48003

processed 42,500,000 fragments
hits: 62,895,367, hits per frag:  1.48192

processed 43,000,001 fragments
hits: 63,623,992, hits per frag:  1.48374

processed 43,500,000 fragments
hits: 64,321,145, hits per frag:  1.48322

processed 44,000,000 fragments
hits: 65,050,137, hits per frag:  1.48061

processed 44,500,001 fragments
hits: 65,785,204, hits per frag:  1.48153

processed 45,000,001 fragments
hits: 66,510,232, hits per frag:  1.47968

processed 45,500,000 fragments
hits: 67,243,469, hits per frag:  1.48095[2020-04-16 21:39:27.168] [jointLog] [info] Thread saw mini-batch with a maximum of 39.50% zero probability fragments
[2020-04-16 21:39:27.193] [jointLog] [info] Thread saw mini-batch with a maximum of 38.56% zero probability fragments
[2020-04-16 21:39:27.200] [jointLog] [info] Thread saw mini-batch with a maximum of 39.16% zero probability fragments
[2020-04-16 21:39:27.244] [jointLog] [info] Thread saw mini-batch with a maximum of 38.70% zero probability fragments
[2020-04-16 21:39:27.279] [jointLog] [info] Thread saw mini-batch with a maximum of 38.50% zero probability fragments
[2020-04-16 21:39:27.285] [jointLog] [info] Thread saw mini-batch with a maximum of 38.96% zero probability fragments
[2020-04-16 21:39:27.295] [jointLog] [info] Thread saw mini-batch with a maximum of 38.42% zero probability fragments
[2020-04-16 21:39:27.307] [jointLog] [info] Thread saw mini-batch with a maximum of 39.24% zero probability fragments
[2020-04-16 21:39:27.315] [jointLog] [info] Thread saw mini-batch with a maximum of 38.88% zero probability fragments
[2020-04-16 21:39:27.316] [jointLog] [info] Thread saw mini-batch with a maximum of 38.42% zero probability fragments
[2020-04-16 21:39:27.335] [jointLog] [info] Thread saw mini-batch with a maximum of 38.68% zero probability fragments
[2020-04-16 21:39:27.341] [jointLog] [info] Thread saw mini-batch with a maximum of 39.16% zero probability fragments
[2020-04-16 21:39:27.342] [jointLog] [info] Thread saw mini-batch with a maximum of 38.52% zero probability fragments
[2020-04-16 21:39:27.355] [jointLog] [info] Thread saw mini-batch with a maximum of 38.52% zero probability fragments
[2020-04-16 21:39:27.374] [jointLog] [info] Thread saw mini-batch with a maximum of 38.42% zero probability fragments
[2020-04-16 21:39:27.384] [jointLog] [info] Thread saw mini-batch with a maximum of 38.74% zero probability fragments
[2020-04-16 21:39:27.387] [jointLog] [info] Thread saw mini-batch with a maximum of 39.10% zero probability fragments
[2020-04-16 21:39:27.403] [jointLog] [info] Thread saw mini-batch with a maximum of 38.18% zero probability fragments
[2020-04-16 21:39:27.428] [jointLog] [info] Thread saw mini-batch with a maximum of 39.36% zero probability fragments
[2020-04-16 21:39:27.428] [jointLog] [info] Thread saw mini-batch with a maximum of 38.78% zero probability fragments
[2020-04-16 21:39:27.441] [jointLog] [info] Thread saw mini-batch with a maximum of 39.44% zero probability fragments
[2020-04-16 21:39:27.448] [jointLog] [info] Thread saw mini-batch with a maximum of 38.58% zero probability fragments
[2020-04-16 21:39:27.459] [jointLog] [info] Thread saw mini-batch with a maximum of 38.66% zero probability fragments
[2020-04-16 21:39:27.469] [jointLog] [info] Thread saw mini-batch with a maximum of 39.36% zero probability fragments
[2020-04-16 21:39:27.490] [jointLog] [info] Thread saw mini-batch with a maximum of 38.52% zero probability fragments
[2020-04-16 21:39:27.491] [jointLog] [info] Thread saw mini-batch with a maximum of 39.12% zero probability fragments
[2020-04-16 21:39:27.509] [jointLog] [info] Thread saw mini-batch with a maximum of 38.72% zero probability fragments
[2020-04-16 21:39:27.509] [jointLog] [info] Thread saw mini-batch with a maximum of 39.08% zero probability fragments




[2020-04-16 21:39:27.701] [jointLog] [info] Computed 98,842 rich equivalence classes for further processing
[2020-04-16 21:39:27.701] [jointLog] [info] Counted 10,131,977 total reads in the equivalence classes 






[2020-04-16 21:39:27.718] [jointLog] [warning] 1.3183e-05% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 17.


[2020-04-16 21:39:27.718] [jointLog] [info] Number of mappings discarded because of alignment score : 346,351,652
[2020-04-16 21:39:27.718] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,521,101
[2020-04-16 21:39:27.718] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-16 21:39:27.718] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 224,049
[2020-04-16 21:39:27.718] [jointLog] [info] Mapping rate = 22.2616%

[2020-04-16 21:39:27.718] [jointLog] [info] finished quantifyLibrary()
[2020-04-16 21:39:27.720] [jointLog] [info] Starting optimizer
[2020-04-16 21:39:27.747] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-16 21:39:27.751] [jointLog] [info] iteration = 0 | max rel diff. = 19848
[2020-04-16 21:39:28.023] [jointLog] [info] iteration = 100 | max rel diff. = 4.09158
[2020-04-16 21:39:28.265] [jointLog] [info] iteration = 200 | max rel diff. = 0.641741
[2020-04-16 21:39:28.506] [jointLog] [info] iteration = 300 | max rel diff. = 0.115438
[2020-04-16 21:39:28.747] [jointLog] [info] iteration = 400 | max rel diff. = 5.54545
[2020-04-16 21:39:28.987] [jointLog] [info] iteration = 500 | max rel diff. = 0.0476926
[2020-04-16 21:39:29.228] [jointLog] [info] iteration = 600 | max rel diff. = 0.0858241
[2020-04-16 21:39:29.467] [jointLog] [info] iteration = 700 | max rel diff. = 0.0844504
[2020-04-16 21:39:29.707] [jointLog] [info] iteration = 800 | max rel diff. = 0.00492056
[2020-04-16 21:39:29.707] [jointLog] [info] iteration = 801 | max rel diff. = 0.00492056
[2020-04-16 21:39:29.708] [jointLog] [info] Finished optimizer
[2020-04-16 21:39:29.708] [jointLog] [info] writing output 

CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl 329774_01/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > 329774_01/quant.sf.genes
CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l ISR -1 /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329775_reads_1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329775_reads_2.fq -o 329775_01  -p 28 --validateMappings 
Version Info: Could not resolve upgrade information in the alotted time.
Check for upgrades manually at https://combine-lab.github.io/salmon
### salmon (mapping-based) v1.1.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329775_reads_1.fq }
### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329775_reads_2.fq }
### [ output ] => { 329775_01 }
### [ threads ] => { 28 }
### [ validateMappings ] => { }
Logs will be written to 329775_01/logs
[2020-04-16 21:48:00.345] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-16 21:48:00.345] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-16 21:48:00.345] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-16 21:48:00.345] [jointLog] [info] parsing read library format
[2020-04-16 21:48:00.345] [jointLog] [info] There is 1 library.
[2020-04-16 21:48:00.411] [jointLog] [info] Loading pufferfish index
[2020-04-16 21:48:00.411] [jointLog] [info] Loading dense pufferfish index.
-----------------------------------------
| Loading contig table | Time = 21.589 ms
-----------------------------------------
size = 98890
-----------------------------------------
| Loading contig offsets | Time = 308.22 us
-----------------------------------------
-----------------------------------------
| Loading reference lengths | Time = 199.66 us
-----------------------------------------
-----------------------------------------
| Loading mphf table | Time = 8.9959 ms
-----------------------------------------
size = 21703191
Number of ones: 98889
Number of ones per inventory item: 512
Inventory entries filled: 194
-----------------------------------------
| Loading contig boundaries | Time = 48.771 ms
-----------------------------------------
size = 21703191
-----------------------------------------
| Loading sequence | Time = 3.3367 ms
-----------------------------------------
size = 18736521
-----------------------------------------
| Loading positions | Time = 326.71 ms
-----------------------------------------
size = 33327850
-----------------------------------------
| Loading reference sequence | Time = 6.6981 ms
-----------------------------------------
-----------------------------------------
| Loading reference accumulative lengths | Time = 450.08 us
-----------------------------------------




[2020-04-16 21:48:00.829] [jointLog] [info] done
[2020-04-16 21:48:00.829] [jointLog] [info] Index contained 40,435 targets
[2020-04-16 21:48:00.853] [jointLog] [info] Number of decoys : 0


processed 500,000 fragments
hits: 986,889, hits per frag:  2.77571

processed 1,000,000 fragments
hits: 1,970,239, hits per frag:  2.19799

processed 1,500,000 fragments
hits: 2,947,037, hits per frag:  2.04503

processed 2,000,000 fragments
hits: 3,929,322, hits per frag:  1.98962

processed 2,500,000 fragments
hits: 4,905,260, hits per frag:  2.07168

processed 3,000,000 fragments
hits: 5,880,556, hits per frag:  1.98088

processed 3,500,000 fragments
hits: 6,855,818, hits per frag:  2.01618

processed 4,000,000 fragments
hits: 7,833,928, hits per frag:  2.00023

processed 4,500,001 fragments
hits: 8,820,717, hits per frag:  1.98656

processed 5,000,000 fragments
hits: 9,805,456, hits per frag:  1.96631

processed 5,500,000 fragments
hits: 10,783,401, hits per frag:  1.99823

processed 6,000,000 fragments
hits: 11,760,808, hits per frag:  1.98907

processed 6,500,000 fragments
hits: 12,737,629, hits per frag:  1.98352

processed 7,000,000 fragments
hits: 13,710,015, hits per frag:  1.97381

processed 7,500,000 fragments
hits: 14,682,125, hits per frag:  1.99232

processed 8,000,000 fragments
hits: 15,663,911, hits per frag:  1.96349

processed 8,500,000 fragments
hits: 16,663,329, hits per frag:  1.97638

processed 9,000,000 fragments
hits: 17,663,503, hits per frag:  1.98205

processed 9,500,001 fragments
hits: 18,662,289, hits per frag:  1.98413

processed 10,000,000 fragments
hits: 19,665,938, hits per frag:  1.99428

processed 10,500,000 fragments
hits: 20,663,017, hits per frag:  1.96845

processed 11,000,000 fragments
hits: 21,663,769, hits per frag:  1.98508

processed 11,500,000 fragments
hits: 22,665,600, hits per frag:  1.97841

processed 12,000,000 fragments
hits: 23,661,975, hits per frag:  1.9843

processed 12,500,000 fragments
hits: 24,656,666, hits per frag:  1.97842

processed 13,000,000 fragments
hits: 25,658,155, hits per frag:  1.97538

processed 13,500,000 fragments
hits: 26,656,493, hits per frag:  1.9784

processed 14,000,000 fragments
hits: 27,656,124, hits per frag:  1.97832

processed 14,500,000 fragments
hits: 28,659,275, hits per frag:  1.99887

processed 15,000,000 fragments
hits: 29,654,104, hits per frag:  1.98261

processed 15,500,000 fragments
hits: 30,628,956, hits per frag:  1.98346

processed 16,000,000 fragments
hits: 31,593,169, hits per frag:  1.98747

processed 16,500,001 fragments
hits: 32,546,549, hits per frag:  1.97939

processed 17,000,000 fragments
hits: 33,529,741, hits per frag:  1.97791

processed 17,500,000 fragments
hits: 34,524,345, hits per frag:  1.98094

processed 18,000,000 fragments
hits: 35,510,626, hits per frag:  1.99079

processed 18,500,000 fragments
hits: 36,489,075, hits per frag:  1.97484

processed 19,000,000 fragments
hits: 37,476,809, hits per frag:  1.98472

processed 19,500,000 fragments
hits: 38,473,593, hits per frag:  1.98599

processed 20,000,000 fragments
hits: 39,467,632, hits per frag:  1.985

processed 20,500,000 fragments
hits: 40,461,904, hits per frag:  1.97955

processed 21,000,000 fragments
hits: 41,439,252, hits per frag:  1.98237

processed 21,500,000 fragments
hits: 42,416,966, hits per frag:  1.97461

processed 22,000,000 fragments
hits: 43,395,284, hits per frag:  1.98307

processed 22,500,000 fragments
hits: 44,369,571, hits per frag:  1.97804

processed 23,000,000 fragments
hits: 45,343,966, hits per frag:  1.97921

processed 23,500,000 fragments
hits: 46,322,928, hits per frag:  1.98746

processed 24,000,000 fragments
hits: 47,296,502, hits per frag:  1.97413

processed 24,500,000 fragments
hits: 48,272,541, hits per frag:  1.97835

processed 25,000,000 fragments
hits: 49,246,024, hits per frag:  1.97002

processed 25,500,000 fragments
hits: 50,222,106, hits per frag:  1.97576

processed 26,000,000 fragments
hits: 51,195,520, hits per frag:  1.98136

processed 26,500,000 fragments
hits: 52,173,477, hits per frag:  1.97445

processed 27,000,000 fragments
hits: 53,145,721, hits per frag:  1.97354

processed 27,500,000 fragments
hits: 54,118,681, hits per frag:  1.97695

processed 28,000,000 fragments
hits: 55,095,191, hits per frag:  1.97661

processed 28,500,000 fragments
hits: 56,080,425, hits per frag:  1.97512

processed 29,000,000 fragments
hits: 57,080,047, hits per frag:  1.97148

processed 29,500,000 fragments
hits: 58,073,684, hits per frag:  1.96931

processed 30,000,001 fragments
hits: 59,072,845, hits per frag:  1.96929

processed 30,500,000 fragments
hits: 60,062,751, hits per frag:  1.96984

processed 31,000,000 fragments
hits: 61,060,100, hits per frag:  1.97793

processed 31,500,000 fragments
hits: 62,052,143, hits per frag:  1.97111

processed 32,000,000 fragments
hits: 63,042,183, hits per frag:  1.97042

processed 32,500,000 fragments
hits: 64,036,415, hits per frag:  1.97512

processed 33,000,001 fragments
hits: 65,030,853, hits per frag:  1.98038

processed 33,500,000 fragments
hits: 66,018,263, hits per frag:  1.97081

processed 34,000,000 fragments
hits: 67,009,222, hits per frag:  1.97764

processed 34,500,000 fragments
hits: 67,999,458, hits per frag:  1.9787

processed 35,000,000 fragments
hits: 68,985,737, hits per frag:  1.97386

processed 35,500,001 fragments
hits: 69,946,123, hits per frag:  1.97374

processed 36,000,000 fragments
hits: 70,922,015, hits per frag:  1.97519

processed 36,500,000 fragments
hits: 71,890,108, hits per frag:  1.97304

processed 37,000,000 fragments
hits: 72,811,402, hits per frag:  1.97047

processed 37,500,000 fragments
hits: 73,773,377, hits per frag:  1.96932

processed 38,000,000 fragments
hits: 74,743,831, hits per frag:  1.97129

processed 38,500,001 fragments
hits: 75,703,649, hits per frag:  1.97241[2020-04-16 21:49:29.345] [jointLog] [info] Thread saw mini-batch with a maximum of 49.52% zero probability fragments
[2020-04-16 21:49:29.345] [jointLog] [info] Thread saw mini-batch with a maximum of 48.86% zero probability fragments
[2020-04-16 21:49:29.346] [jointLog] [info] Thread saw mini-batch with a maximum of 49.24% zero probability fragments
[2020-04-16 21:49:29.361] [jointLog] [info] Thread saw mini-batch with a maximum of 48.10% zero probability fragments
[2020-04-16 21:49:29.396] [jointLog] [info] Thread saw mini-batch with a maximum of 49.16% zero probability fragments
[2020-04-16 21:49:29.406] [jointLog] [info] Thread saw mini-batch with a maximum of 48.50% zero probability fragments
[2020-04-16 21:49:29.419] [jointLog] [info] Thread saw mini-batch with a maximum of 48.20% zero probability fragments
[2020-04-16 21:49:29.435] [jointLog] [info] Thread saw mini-batch with a maximum of 49.48% zero probability fragments
[2020-04-16 21:49:29.446] [jointLog] [info] Thread saw mini-batch with a maximum of 48.34% zero probability fragments
[2020-04-16 21:49:29.446] [jointLog] [info] Thread saw mini-batch with a maximum of 48.50% zero probability fragments
[2020-04-16 21:49:29.485] [jointLog] [info] Thread saw mini-batch with a maximum of 49.56% zero probability fragments
[2020-04-16 21:49:29.487] [jointLog] [info] Thread saw mini-batch with a maximum of 48.70% zero probability fragments
[2020-04-16 21:49:29.487] [jointLog] [info] Thread saw mini-batch with a maximum of 48.38% zero probability fragments
[2020-04-16 21:49:29.509] [jointLog] [info] Thread saw mini-batch with a maximum of 48.24% zero probability fragments
[2020-04-16 21:49:29.514] [jointLog] [info] Thread saw mini-batch with a maximum of 48.48% zero probability fragments
[2020-04-16 21:49:29.520] [jointLog] [info] Thread saw mini-batch with a maximum of 49.32% zero probability fragments
[2020-04-16 21:49:29.522] [jointLog] [info] Thread saw mini-batch with a maximum of 47.60% zero probability fragments
[2020-04-16 21:49:29.530] [jointLog] [info] Thread saw mini-batch with a maximum of 49.24% zero probability fragments
[2020-04-16 21:49:29.541] [jointLog] [info] Thread saw mini-batch with a maximum of 48.52% zero probability fragments
[2020-04-16 21:49:29.555] [jointLog] [info] Thread saw mini-batch with a maximum of 48.30% zero probability fragments
[2020-04-16 21:49:29.565] [jointLog] [info] Thread saw mini-batch with a maximum of 48.72% zero probability fragments
[2020-04-16 21:49:29.573] [jointLog] [info] Thread saw mini-batch with a maximum of 48.24% zero probability fragments
[2020-04-16 21:49:29.602] [jointLog] [info] Thread saw mini-batch with a maximum of 49.50% zero probability fragments
[2020-04-16 21:49:29.602] [jointLog] [info] Thread saw mini-batch with a maximum of 47.56% zero probability fragments
[2020-04-16 21:49:29.606] [jointLog] [info] Thread saw mini-batch with a maximum of 48.64% zero probability fragments
[2020-04-16 21:49:29.609] [jointLog] [info] Thread saw mini-batch with a maximum of 49.10% zero probability fragments
[2020-04-16 21:49:29.626] [jointLog] [info] Thread saw mini-batch with a maximum of 48.04% zero probability fragments
[2020-04-16 21:49:29.667] [jointLog] [info] Thread saw mini-batch with a maximum of 49.20% zero probability fragments




[2020-04-16 21:49:29.858] [jointLog] [info] Computed 83,741 rich equivalence classes for further processing
[2020-04-16 21:49:29.858] [jointLog] [info] Counted 12,258,577 total reads in the equivalence classes 






[2020-04-16 21:49:29.875] [jointLog] [warning] 1.03228e-05% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 16.


[2020-04-16 21:49:29.875] [jointLog] [info] Number of mappings discarded because of alignment score : 308,851,365
[2020-04-16 21:49:29.875] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,468,837
[2020-04-16 21:49:29.875] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-16 21:49:29.875] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 246,007
[2020-04-16 21:49:29.875] [jointLog] [info] Mapping rate = 31.6358%

[2020-04-16 21:49:29.875] [jointLog] [info] finished quantifyLibrary()
[2020-04-16 21:49:29.877] [jointLog] [info] Starting optimizer
[2020-04-16 21:49:29.903] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-16 21:49:29.907] [jointLog] [info] iteration = 0 | max rel diff. = 22691.2
[2020-04-16 21:49:30.186] [jointLog] [info] iteration = 100 | max rel diff. = 19.6926
[2020-04-16 21:49:30.437] [jointLog] [info] iteration = 200 | max rel diff. = 0.16521
[2020-04-16 21:49:30.685] [jointLog] [info] iteration = 300 | max rel diff. = 0.683127
[2020-04-16 21:49:30.930] [jointLog] [info] iteration = 400 | max rel diff. = 0.0950398
[2020-04-16 21:49:31.176] [jointLog] [info] iteration = 500 | max rel diff. = 1.41531
[2020-04-16 21:49:31.422] [jointLog] [info] iteration = 600 | max rel diff. = 0.0672739
[2020-04-16 21:49:31.668] [jointLog] [info] iteration = 700 | max rel diff. = 0.032643
[2020-04-16 21:49:31.914] [jointLog] [info] iteration = 800 | max rel diff. = 0.0295341
[2020-04-16 21:49:32.160] [jointLog] [info] iteration = 900 | max rel diff. = 0.108655
[2020-04-16 21:49:32.253] [jointLog] [info] iteration = 939 | max rel diff. = 0.00369978
[2020-04-16 21:49:32.256] [jointLog] [info] Finished optimizer
[2020-04-16 21:49:32.256] [jointLog] [info] writing output 

CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl 329775_01/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > 329775_01/quant.sf.genes
CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l ISR -1 /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329776_reads_1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329776_reads_2.fq -o 329776_01  -p 28 --validateMappings 
Version Info: Could not resolve upgrade information in the alotted time.
Check for upgrades manually at https://combine-lab.github.io/salmon
### salmon (mapping-based) v1.1.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329776_reads_1.fq }
### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329776_reads_2.fq }
### [ output ] => { 329776_01 }
### [ threads ] => { 28 }
### [ validateMappings ] => { }
Logs will be written to 329776_01/logs
[2020-04-16 21:58:02.984] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-16 21:58:02.984] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-16 21:58:02.984] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-16 21:58:02.984] [jointLog] [info] parsing read library format
[2020-04-16 21:58:02.985] [jointLog] [info] There is 1 library.
[2020-04-16 21:58:03.048] [jointLog] [info] Loading pufferfish index
[2020-04-16 21:58:03.049] [jointLog] [info] Loading dense pufferfish index.
-----------------------------------------
| Loading contig table | Time = 19.847 ms
-----------------------------------------
size = 98890
-----------------------------------------
| Loading contig offsets | Time = 320.62 us
-----------------------------------------
-----------------------------------------
| Loading reference lengths | Time = 197.98 us
-----------------------------------------
-----------------------------------------
| Loading mphf table | Time = 9.5632 ms
-----------------------------------------
size = 21703191
Number of ones: 98889
Number of ones per inventory item: 512
Inventory entries filled: 194
-----------------------------------------
| Loading contig boundaries | Time = 48.44 ms
-----------------------------------------
size = 21703191
-----------------------------------------
| Loading sequence | Time = 3.2047 ms
-----------------------------------------
size = 18736521
-----------------------------------------
| Loading positions | Time = 168.67 ms
-----------------------------------------
size = 33327850
-----------------------------------------
| Loading reference sequence | Time = 6.9234 ms
-----------------------------------------
-----------------------------------------
| Loading reference accumulative lengths | Time = 493.43 us
-----------------------------------------




[2020-04-16 21:58:03.307] [jointLog] [info] done
[2020-04-16 21:58:03.307] [jointLog] [info] Index contained 40,435 targets
[2020-04-16 21:58:03.332] [jointLog] [info] Number of decoys : 0


processed 500,000 fragments
hits: 767,830, hits per frag:  1.54469

processed 1,000,000 fragments
hits: 1,534,098, hits per frag:  1.66188

processed 1,500,000 fragments
hits: 2,297,171, hits per frag:  1.56351

processed 2,000,001 fragments
hits: 3,058,232, hits per frag:  1.56954

processed 2,500,000 fragments
hits: 3,824,065, hits per frag:  1.59907

processed 3,000,000 fragments
hits: 4,583,201, hits per frag:  1.53459

processed 3,500,000 fragments
hits: 5,348,158, hits per frag:  1.54263

processed 4,000,001 fragments
hits: 6,108,255, hits per frag:  1.55893

processed 4,500,000 fragments
hits: 6,872,625, hits per frag:  1.53976

processed 5,000,001 fragments
hits: 7,633,371, hits per frag:  1.54643

processed 5,500,000 fragments
hits: 8,396,498, hits per frag:  1.55187

processed 6,000,000 fragments
hits: 9,163,239, hits per frag:  1.5543

processed 6,500,001 fragments
hits: 9,924,424, hits per frag:  1.56056

processed 7,000,000 fragments
hits: 10,684,319, hits per frag:  1.53153

processed 7,500,000 fragments
hits: 11,446,265, hits per frag:  1.53576

processed 8,000,000 fragments
hits: 12,204,450, hits per frag:  1.54018

processed 8,500,000 fragments
hits: 12,962,976, hits per frag:  1.5261

processed 9,000,000 fragments
hits: 13,722,957, hits per frag:  1.54065

processed 9,500,000 fragments
hits: 14,490,261, hits per frag:  1.54306

processed 10,000,000 fragments
hits: 15,266,815, hits per frag:  1.53718

processed 10,500,001 fragments
hits: 16,042,035, hits per frag:  1.54688

processed 11,000,000 fragments
hits: 16,819,093, hits per frag:  1.5363

processed 11,500,000 fragments
hits: 17,594,687, hits per frag:  1.53891

processed 12,000,001 fragments
hits: 18,366,589, hits per frag:  1.54535

processed 12,500,000 fragments
hits: 19,138,885, hits per frag:  1.5382

processed 13,000,000 fragments
hits: 19,913,017, hits per frag:  1.53713

processed 13,500,000 fragments
hits: 20,689,236, hits per frag:  1.53396

processed 14,000,000 fragments
hits: 21,462,984, hits per frag:  1.54377

processed 14,500,000 fragments
hits: 22,235,101, hits per frag:  1.53671

processed 15,000,000 fragments
hits: 23,009,934, hits per frag:  1.54788

processed 15,500,000 fragments
hits: 23,785,051, hits per frag:  1.53613

processed 16,000,001 fragments
hits: 24,560,992, hits per frag:  1.5482

processed 16,500,000 fragments
hits: 25,333,736, hits per frag:  1.54691

processed 17,000,000 fragments
hits: 26,116,360, hits per frag:  1.53873

processed 17,500,000 fragments
hits: 26,885,055, hits per frag:  1.53984

processed 18,000,000 fragments
hits: 27,656,165, hits per frag:  1.5457

processed 18,500,001 fragments
hits: 28,411,619, hits per frag:  1.54259

processed 19,000,000 fragments
hits: 29,171,217, hits per frag:  1.54064

processed 19,500,000 fragments
hits: 29,918,254, hits per frag:  1.53716

processed 20,000,001 fragments
hits: 30,664,070, hits per frag:  1.53493

processed 20,500,000 fragments
hits: 31,437,437, hits per frag:  1.53528

processed 21,000,000 fragments
hits: 32,206,598, hits per frag:  1.54084

processed 21,500,000 fragments
hits: 32,974,197, hits per frag:  1.542

processed 22,000,000 fragments
hits: 33,735,828, hits per frag:  1.53804

processed 22,500,000 fragments
hits: 34,506,810, hits per frag:  1.53607

processed 23,000,000 fragments
hits: 35,277,079, hits per frag:  1.53707

processed 23,500,000 fragments
hits: 36,047,776, hits per frag:  1.53758

processed 24,000,000 fragments
hits: 36,820,482, hits per frag:  1.53589

processed 24,500,000 fragments
hits: 37,593,290, hits per frag:  1.53647

processed 25,000,000 fragments
hits: 38,360,347, hits per frag:  1.53512

processed 25,500,000 fragments
hits: 39,123,288, hits per frag:  1.54007

processed 26,000,000 fragments
hits: 39,881,916, hits per frag:  1.53997

processed 26,500,001 fragments
hits: 40,644,639, hits per frag:  1.54131

processed 27,000,000 fragments
hits: 41,405,729, hits per frag:  1.54304

processed 27,500,000 fragments
hits: 42,164,606, hits per frag:  1.53571

processed 28,000,000 fragments
hits: 42,925,960, hits per frag:  1.53934

processed 28,500,002 fragments
hits: 43,688,525, hits per frag:  1.53448

processed 29,000,000 fragments
hits: 44,452,700, hits per frag:  1.53524

processed 29,500,000 fragments
hits: 45,215,885, hits per frag:  1.53423

processed 30,000,000 fragments
hits: 45,976,255, hits per frag:  1.53597

processed 30,500,000 fragments
hits: 46,735,684, hits per frag:  1.53991

processed 31,000,000 fragments
hits: 47,494,228, hits per frag:  1.53866

processed 31,500,000 fragments
hits: 48,254,246, hits per frag:  1.53314

processed 32,000,000 fragments
hits: 49,016,605, hits per frag:  1.53657

processed 32,500,000 fragments
hits: 49,776,936, hits per frag:  1.53252

processed 33,000,000 fragments
hits: 50,538,325, hits per frag:  1.53815

processed 33,500,000 fragments
hits: 51,299,143, hits per frag:  1.53543

processed 34,000,001 fragments
hits: 52,058,023, hits per frag:  1.53376

processed 34,500,001 fragments
hits: 52,828,422, hits per frag:  1.5357

processed 35,000,000 fragments
hits: 53,597,431, hits per frag:  1.535

processed 35,500,000 fragments
hits: 54,371,209, hits per frag:  1.53695

processed 36,000,002 fragments
hits: 55,145,369, hits per frag:  1.53592

processed 36,500,000 fragments
hits: 55,917,907, hits per frag:  1.53317

processed 37,000,000 fragments
hits: 56,685,877, hits per frag:  1.53487

processed 37,500,000 fragments
hits: 57,461,332, hits per frag:  1.53363

processed 38,000,000 fragments
hits: 58,233,691, hits per frag:  1.53314

processed 38,500,000 fragments
hits: 59,004,460, hits per frag:  1.5354

processed 39,000,001 fragments
hits: 59,778,683, hits per frag:  1.5356

processed 39,500,000 fragments
hits: 60,548,252, hits per frag:  1.53485

processed 40,000,000 fragments
hits: 61,319,610, hits per frag:  1.53667

processed 40,500,000 fragments
hits: 62,088,176, hits per frag:  1.53659

processed 41,000,000 fragments
hits: 62,865,834, hits per frag:  1.53594

processed 41,500,000 fragments
hits: 63,637,563, hits per frag:  1.53665

processed 42,000,000 fragments
hits: 64,408,702, hits per frag:  1.53828

processed 42,500,000 fragments
hits: 65,158,197, hits per frag:  1.53671

processed 43,000,001 fragments
hits: 65,916,913, hits per frag:  1.53594

processed 43,500,000 fragments
hits: 66,686,616, hits per frag:  1.53508

processed 44,000,000 fragments
hits: 67,433,941, hits per frag:  1.53692

processed 44,500,000 fragments
hits: 68,161,054, hits per frag:  1.53242

processed 45,000,000 fragments
hits: 68,914,406, hits per frag:  1.53555

processed 45,500,000 fragments
hits: 69,679,754, hits per frag:  1.53294

processed 46,000,000 fragments
hits: 70,428,231, hits per frag:  1.53606

processed 46,500,000 fragments
hits: 71,187,306, hits per frag:  1.53356[2020-04-16 21:59:42.206] [jointLog] [info] Thread saw mini-batch with a maximum of 43.10% zero probability fragments
[2020-04-16 21:59:42.208] [jointLog] [info] Thread saw mini-batch with a maximum of 43.42% zero probability fragments
[2020-04-16 21:59:42.217] [jointLog] [info] Thread saw mini-batch with a maximum of 42.70% zero probability fragments
[2020-04-16 21:59:42.224] [jointLog] [info] Thread saw mini-batch with a maximum of 42.48% zero probability fragments
[2020-04-16 21:59:42.228] [jointLog] [info] Thread saw mini-batch with a maximum of 43.20% zero probability fragments
[2020-04-16 21:59:42.230] [jointLog] [info] Thread saw mini-batch with a maximum of 43.18% zero probability fragments
[2020-04-16 21:59:42.232] [jointLog] [info] Thread saw mini-batch with a maximum of 43.92% zero probability fragments
[2020-04-16 21:59:42.241] [jointLog] [info] Thread saw mini-batch with a maximum of 42.88% zero probability fragments
[2020-04-16 21:59:42.245] [jointLog] [info] Thread saw mini-batch with a maximum of 42.64% zero probability fragments
[2020-04-16 21:59:42.249] [jointLog] [info] Thread saw mini-batch with a maximum of 42.66% zero probability fragments
[2020-04-16 21:59:42.249] [jointLog] [info] Thread saw mini-batch with a maximum of 43.78% zero probability fragments
[2020-04-16 21:59:42.255] [jointLog] [info] Thread saw mini-batch with a maximum of 42.26% zero probability fragments
[2020-04-16 21:59:42.276] [jointLog] [info] Thread saw mini-batch with a maximum of 42.72% zero probability fragments
[2020-04-16 21:59:42.283] [jointLog] [info] Thread saw mini-batch with a maximum of 43.04% zero probability fragments
[2020-04-16 21:59:42.287] [jointLog] [info] Thread saw mini-batch with a maximum of 43.54% zero probability fragments
[2020-04-16 21:59:42.297] [jointLog] [info] Thread saw mini-batch with a maximum of 42.14% zero probability fragments
[2020-04-16 21:59:42.301] [jointLog] [info] Thread saw mini-batch with a maximum of 42.46% zero probability fragments
[2020-04-16 21:59:42.335] [jointLog] [info] Thread saw mini-batch with a maximum of 43.30% zero probability fragments
[2020-04-16 21:59:42.336] [jointLog] [info] Thread saw mini-batch with a maximum of 42.60% zero probability fragments
[2020-04-16 21:59:42.352] [jointLog] [info] Thread saw mini-batch with a maximum of 42.46% zero probability fragments
[2020-04-16 21:59:42.371] [jointLog] [info] Thread saw mini-batch with a maximum of 42.86% zero probability fragments
[2020-04-16 21:59:42.407] [jointLog] [info] Thread saw mini-batch with a maximum of 42.92% zero probability fragments
[2020-04-16 21:59:42.410] [jointLog] [info] Thread saw mini-batch with a maximum of 43.58% zero probability fragments
[2020-04-16 21:59:42.410] [jointLog] [info] Thread saw mini-batch with a maximum of 42.64% zero probability fragments
[2020-04-16 21:59:42.427] [jointLog] [info] Thread saw mini-batch with a maximum of 43.38% zero probability fragments
[2020-04-16 21:59:42.427] [jointLog] [info] Thread saw mini-batch with a maximum of 42.72% zero probability fragments
[2020-04-16 21:59:42.442] [jointLog] [info] Thread saw mini-batch with a maximum of 42.82% zero probability fragments
[2020-04-16 21:59:42.463] [jointLog] [info] Thread saw mini-batch with a maximum of 43.34% zero probability fragments




[2020-04-16 21:59:42.655] [jointLog] [info] Computed 94,991 rich equivalence classes for further processing
[2020-04-16 21:59:42.655] [jointLog] [info] Counted 10,989,050 total reads in the equivalence classes 






[2020-04-16 21:59:42.672] [jointLog] [warning] 3.21961e-05% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 19.


[2020-04-16 21:59:42.672] [jointLog] [info] Number of mappings discarded because of alignment score : 324,882,706
[2020-04-16 21:59:42.672] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,514,062
[2020-04-16 21:59:42.672] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-16 21:59:42.672] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 218,535
[2020-04-16 21:59:42.672] [jointLog] [info] Mapping rate = 23.587%

[2020-04-16 21:59:42.672] [jointLog] [info] finished quantifyLibrary()
[2020-04-16 21:59:42.674] [jointLog] [info] Starting optimizer
[2020-04-16 21:59:42.705] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-16 21:59:42.710] [jointLog] [info] iteration = 0 | max rel diff. = 20957.7
[2020-04-16 21:59:42.995] [jointLog] [info] iteration = 100 | max rel diff. = 5.56898
[2020-04-16 21:59:43.252] [jointLog] [info] iteration = 200 | max rel diff. = 0.948953
[2020-04-16 21:59:43.503] [jointLog] [info] iteration = 300 | max rel diff. = 1.8391
[2020-04-16 21:59:43.750] [jointLog] [info] iteration = 400 | max rel diff. = 0.0785756
[2020-04-16 21:59:43.997] [jointLog] [info] iteration = 500 | max rel diff. = 0.137425
[2020-04-16 21:59:44.039] [jointLog] [info] iteration = 518 | max rel diff. = 0.00939072
[2020-04-16 21:59:44.040] [jointLog] [info] Finished optimizer
[2020-04-16 21:59:44.040] [jointLog] [info] writing output 

CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl 329776_01/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > 329776_01/quant.sf.genes
CMD: salmon quant -i /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx -l ISR -1 /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329777_reads_1.fq -2 /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329777_reads_2.fq -o 329777_01  -p 28 --validateMappings 
Version Info: Could not resolve upgrade information in the alotted time.
Check for upgrades manually at https://combine-lab.github.io/salmon
### salmon (mapping-based) v1.1.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.salmon.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329777_reads_1.fq }
### [ mates2 ] => { /gscratch/scrubbed/samwhite/outputs/20200415_cbai_salmon_abundance/329777_reads_2.fq }
### [ output ] => { 329777_01 }
### [ threads ] => { 28 }
### [ validateMappings ] => { }
Logs will be written to 329777_01/logs
[2020-04-16 22:08:14.372] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2020-04-16 22:08:14.372] [jointLog] [info] Usage of --validateMappings implies use of minScoreFraction. Since not explicitly specified, it is being set to 0.65
[2020-04-16 22:08:14.372] [jointLog] [info] Usage of --validateMappings implies a default consensus slack of 0.2. Setting consensusSlack to 0.35.
[2020-04-16 22:08:14.372] [jointLog] [info] parsing read library format
[2020-04-16 22:08:14.372] [jointLog] [info] There is 1 library.
[2020-04-16 22:08:14.436] [jointLog] [info] Loading pufferfish index
[2020-04-16 22:08:14.436] [jointLog] [info] Loading dense pufferfish index.
-----------------------------------------
| Loading contig table | Time = 19.167 ms
-----------------------------------------
size = 98890
-----------------------------------------
| Loading contig offsets | Time = 284.51 us
-----------------------------------------
-----------------------------------------
| Loading reference lengths | Time = 97.573 us
-----------------------------------------
-----------------------------------------
| Loading mphf table | Time = 7.2231 ms
-----------------------------------------
size = 21703191
Number of ones: 98889
Number of ones per inventory item: 512
Inventory entries filled: 194
-----------------------------------------
| Loading contig boundaries | Time = 48.751 ms
-----------------------------------------
size = 21703191
-----------------------------------------
| Loading sequence | Time = 3.3063 ms
-----------------------------------------
size = 18736521
-----------------------------------------
| Loading positions | Time = 169.1 ms
-----------------------------------------
size = 33327850
-----------------------------------------
| Loading reference sequence | Time = 7.1865 ms
-----------------------------------------
-----------------------------------------
| Loading reference accumulative lengths | Time = 260.39 us
-----------------------------------------




[2020-04-16 22:08:14.691] [jointLog] [info] done
[2020-04-16 22:08:14.692] [jointLog] [info] Index contained 40,435 targets
[2020-04-16 22:08:14.719] [jointLog] [info] Number of decoys : 0


processed 500,000 fragments
hits: 978,430, hits per frag:  2.3396

processed 1,000,000 fragments
hits: 1,954,807, hits per frag:  2.19794

processed 1,500,000 fragments
hits: 2,931,096, hits per frag:  2.07499

processed 2,000,000 fragments
hits: 3,907,136, hits per frag:  1.97129

processed 2,500,000 fragments
hits: 4,883,274, hits per frag:  2.03232

processed 3,000,000 fragments
hits: 5,853,055, hits per frag:  1.99686

processed 3,500,000 fragments
hits: 6,825,176, hits per frag:  1.95996

processed 4,000,000 fragments
hits: 7,797,607, hits per frag:  2.01998

processed 4,500,000 fragments
hits: 8,770,077, hits per frag:  1.96665

processed 5,000,000 fragments
hits: 9,741,665, hits per frag:  1.9654

processed 5,500,000 fragments
hits: 10,714,612, hits per frag:  1.97806

processed 6,000,000 fragments
hits: 11,693,286, hits per frag:  1.96088

processed 6,500,000 fragments
hits: 12,668,781, hits per frag:  1.97714

processed 7,000,000 fragments
hits: 13,642,300, hits per frag:  1.97431

processed 7,500,000 fragments
hits: 14,611,876, hits per frag:  1.95377

processed 8,000,000 fragments
hits: 15,581,103, hits per frag:  1.97315

processed 8,500,000 fragments
hits: 16,551,652, hits per frag:  1.94845

processed 9,000,000 fragments
hits: 17,520,518, hits per frag:  1.94839

processed 9,500,001 fragments
hits: 18,488,622, hits per frag:  1.96386

processed 10,000,000 fragments
hits: 19,459,999, hits per frag:  1.96695

processed 10,500,000 fragments
hits: 20,430,927, hits per frag:  1.95118

processed 11,000,000 fragments
hits: 21,414,806, hits per frag:  1.96271

processed 11,500,000 fragments
hits: 22,400,783, hits per frag:  1.97686

processed 12,000,000 fragments
hits: 23,386,152, hits per frag:  1.96967

processed 12,500,000 fragments
hits: 24,372,225, hits per frag:  1.9532

processed 13,000,000 fragments
hits: 25,357,042, hits per frag:  1.95319

processed 13,500,000 fragments
hits: 26,342,547, hits per frag:  1.96341

processed 14,000,000 fragments
hits: 27,326,553, hits per frag:  1.95892

processed 14,500,000 fragments
hits: 28,313,578, hits per frag:  1.95635

processed 15,000,000 fragments
hits: 29,294,921, hits per frag:  1.95614

processed 15,500,000 fragments
hits: 30,279,517, hits per frag:  1.96996

processed 16,000,000 fragments
hits: 31,266,485, hits per frag:  1.95805

processed 16,500,000 fragments
hits: 32,251,467, hits per frag:  1.95907

processed 17,000,000 fragments
hits: 33,245,640, hits per frag:  1.95682

processed 17,500,000 fragments
hits: 34,226,704, hits per frag:  1.95958

processed 18,000,000 fragments
hits: 35,206,986, hits per frag:  1.96338

processed 18,500,000 fragments
hits: 36,174,722, hits per frag:  1.9583

processed 19,000,000 fragments
hits: 37,129,728, hits per frag:  1.95677

processed 19,500,000 fragments
hits: 38,081,683, hits per frag:  1.9584

processed 20,000,000 fragments
hits: 39,059,642, hits per frag:  1.9608

processed 20,500,000 fragments
hits: 40,041,182, hits per frag:  1.95498

processed 21,000,000 fragments
hits: 41,017,524, hits per frag:  1.96393

processed 21,500,000 fragments
hits: 41,986,791, hits per frag:  1.95593

processed 22,000,000 fragments
hits: 42,964,977, hits per frag:  1.95329

processed 22,500,000 fragments
hits: 43,948,262, hits per frag:  1.95454

processed 23,000,000 fragments
hits: 44,928,420, hits per frag:  1.95904

processed 23,500,000 fragments
hits: 45,913,128, hits per frag:  1.96252

processed 24,000,000 fragments
hits: 46,889,484, hits per frag:  1.95903

processed 24,500,000 fragments
hits: 47,861,572, hits per frag:  1.95372

processed 25,000,000 fragments
hits: 48,832,842, hits per frag:  1.95916

processed 25,500,000 fragments
hits: 49,804,725, hits per frag:  1.95359

processed 26,000,000 fragments
hits: 50,775,524, hits per frag:  1.95859

processed 26,500,001 fragments
hits: 51,751,337, hits per frag:  1.95836

processed 27,000,000 fragments
hits: 52,725,919, hits per frag:  1.95734

processed 27,500,000 fragments
hits: 53,697,090, hits per frag:  1.96077

processed 28,000,000 fragments
hits: 54,666,239, hits per frag:  1.96165

processed 28,500,000 fragments
hits: 55,639,185, hits per frag:  1.95733

processed 29,000,000 fragments
hits: 56,611,682, hits per frag:  1.96157

processed 29,500,001 fragments
hits: 57,581,885, hits per frag:  1.95454

processed 30,000,001 fragments
hits: 58,551,283, hits per frag:  1.95669

processed 30,500,000 fragments
hits: 59,520,650, hits per frag:  1.95911

processed 31,000,000 fragments
hits: 60,490,334, hits per frag:  1.95386

processed 31,500,000 fragments
hits: 61,462,816, hits per frag:  1.95293

processed 32,000,000 fragments
hits: 62,432,361, hits per frag:  1.95458

processed 32,500,000 fragments
hits: 63,405,594, hits per frag:  1.9561

processed 33,000,000 fragments
hits: 64,380,831, hits per frag:  1.95679

processed 33,500,000 fragments
hits: 65,354,341, hits per frag:  1.95357

processed 34,000,001 fragments
hits: 66,325,820, hits per frag:  1.95789

processed 34,500,000 fragments
hits: 67,305,562, hits per frag:  1.95126

processed 35,000,001 fragments
hits: 68,285,138, hits per frag:  1.95708

processed 35,500,000 fragments
hits: 69,271,776, hits per frag:  1.9559

processed 36,000,000 fragments
hits: 70,262,810, hits per frag:  1.9539

processed 36,500,000 fragments
hits: 71,242,366, hits per frag:  1.95199

processed 37,000,000 fragments
hits: 72,224,205, hits per frag:  1.95557

processed 37,500,000 fragments
hits: 73,206,693, hits per frag:  1.95569

processed 38,000,000 fragments
hits: 74,188,114, hits per frag:  1.95487

processed 38,500,000 fragments
hits: 75,174,550, hits per frag:  1.9551

processed 39,000,000 fragments
hits: 76,154,118, hits per frag:  1.96185

processed 39,500,000 fragments
hits: 77,126,963, hits per frag:  1.95327

processed 40,000,000 fragments
hits: 78,107,063, hits per frag:  1.95382

processed 40,500,000 fragments
hits: 79,096,295, hits per frag:  1.95746

processed 41,000,000 fragments
hits: 80,082,527, hits per frag:  1.95876

processed 41,500,000 fragments
hits: 81,037,294, hits per frag:  1.95486

processed 42,000,000 fragments
hits: 82,009,479, hits per frag:  1.95452

processed 42,500,000 fragments
hits: 82,983,582, hits per frag:  1.95539

processed 43,000,000 fragments
hits: 83,910,673, hits per frag:  1.95403

processed 43,500,000 fragments
hits: 84,863,388, hits per frag:  1.95576

processed 44,000,000 fragments
hits: 85,840,790, hits per frag:  1.9553

processed 44,500,000 fragments
hits: 86,794,815, hits per frag:  1.9526[2020-04-16 22:10:27.897] [jointLog] [info] Thread saw mini-batch with a maximum of 56.46% zero probability fragments
[2020-04-16 22:10:27.904] [jointLog] [info] Thread saw mini-batch with a maximum of 56.68% zero probability fragments
[2020-04-16 22:10:27.909] [jointLog] [info] Thread saw mini-batch with a maximum of 56.26% zero probability fragments
[2020-04-16 22:10:27.909] [jointLog] [info] Thread saw mini-batch with a maximum of 56.80% zero probability fragments
[2020-04-16 22:10:27.940] [jointLog] [info] Thread saw mini-batch with a maximum of 56.86% zero probability fragments
[2020-04-16 22:10:27.940] [jointLog] [info] Thread saw mini-batch with a maximum of 56.58% zero probability fragments
[2020-04-16 22:10:27.966] [jointLog] [info] Thread saw mini-batch with a maximum of 56.52% zero probability fragments
[2020-04-16 22:10:27.974] [jointLog] [info] Thread saw mini-batch with a maximum of 56.18% zero probability fragments
[2020-04-16 22:10:27.974] [jointLog] [info] Thread saw mini-batch with a maximum of 56.32% zero probability fragments
[2020-04-16 22:10:28.004] [jointLog] [info] Thread saw mini-batch with a maximum of 56.68% zero probability fragments
[2020-04-16 22:10:28.021] [jointLog] [info] Thread saw mini-batch with a maximum of 56.32% zero probability fragments
[2020-04-16 22:10:28.080] [jointLog] [info] Thread saw mini-batch with a maximum of 56.66% zero probability fragments
[2020-04-16 22:10:28.106] [jointLog] [info] Thread saw mini-batch with a maximum of 56.96% zero probability fragments
[2020-04-16 22:10:28.112] [jointLog] [info] Thread saw mini-batch with a maximum of 57.42% zero probability fragments
[2020-04-16 22:10:28.152] [jointLog] [info] Thread saw mini-batch with a maximum of 56.48% zero probability fragments
[2020-04-16 22:10:28.179] [jointLog] [info] Thread saw mini-batch with a maximum of 57.18% zero probability fragments
[2020-04-16 22:10:28.218] [jointLog] [info] Thread saw mini-batch with a maximum of 57.06% zero probability fragments
[2020-04-16 22:10:28.231] [jointLog] [info] Thread saw mini-batch with a maximum of 56.20% zero probability fragments
[2020-04-16 22:10:28.233] [jointLog] [info] Thread saw mini-batch with a maximum of 56.36% zero probability fragments
[2020-04-16 22:10:28.248] [jointLog] [info] Thread saw mini-batch with a maximum of 56.36% zero probability fragments
[2020-04-16 22:10:28.248] [jointLog] [info] Thread saw mini-batch with a maximum of 56.36% zero probability fragments
[2020-04-16 22:10:28.258] [jointLog] [info] Thread saw mini-batch with a maximum of 55.92% zero probability fragments
[2020-04-16 22:10:28.290] [jointLog] [info] Thread saw mini-batch with a maximum of 56.40% zero probability fragments
[2020-04-16 22:10:28.312] [jointLog] [info] Thread saw mini-batch with a maximum of 56.36% zero probability fragments
[2020-04-16 22:10:28.332] [jointLog] [info] Thread saw mini-batch with a maximum of 56.98% zero probability fragments
[2020-04-16 22:10:28.338] [jointLog] [info] Thread saw mini-batch with a maximum of 56.18% zero probability fragments
[2020-04-16 22:10:28.429] [jointLog] [info] Thread saw mini-batch with a maximum of 57.40% zero probability fragments
[2020-04-16 22:10:28.533] [jointLog] [info] Thread saw mini-batch with a maximum of 56.06% zero probability fragments




[2020-04-16 22:10:28.737] [jointLog] [info] Computed 82,020 rich equivalence classes for further processing
[2020-04-16 22:10:28.737] [jointLog] [info] Counted 12,916,812 total reads in the equivalence classes 






[2020-04-16 22:10:28.755] [jointLog] [warning] 1.77852e-05% of fragments were shorter than the k used to build the index.
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 21.


[2020-04-16 22:10:28.755] [jointLog] [info] Number of mappings discarded because of alignment score : 852,377,255
[2020-04-16 22:10:28.755] [jointLog] [info] Number of fragments entirely discarded because of alignment score : 2,465,423
[2020-04-16 22:10:28.755] [jointLog] [info] Number of fragments discarded because they are best-mapped to decoys : 0
[2020-04-16 22:10:28.755] [jointLog] [info] Number of fragments discarded because they have only dovetail (discordant) mappings to valid targets : 241,533
[2020-04-16 22:10:28.755] [jointLog] [info] Mapping rate = 28.716%

[2020-04-16 22:10:28.755] [jointLog] [info] finished quantifyLibrary()
[2020-04-16 22:10:28.757] [jointLog] [info] Starting optimizer
[2020-04-16 22:10:28.784] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2020-04-16 22:10:28.789] [jointLog] [info] iteration = 0 | max rel diff. = 23333.4
[2020-04-16 22:10:29.100] [jointLog] [info] iteration = 100 | max rel diff. = 4.21723
[2020-04-16 22:10:29.379] [jointLog] [info] iteration = 200 | max rel diff. = 1.22222
[2020-04-16 22:10:29.632] [jointLog] [info] iteration = 300 | max rel diff. = 2.37504
[2020-04-16 22:10:29.881] [jointLog] [info] iteration = 400 | max rel diff. = 0.0471289
[2020-04-16 22:10:30.130] [jointLog] [info] iteration = 500 | max rel diff. = 0.0434021
[2020-04-16 22:10:30.302] [jointLog] [info] iteration = 569 | max rel diff. = 0.00435499
[2020-04-16 22:10:30.303] [jointLog] [info] Finished optimizer
[2020-04-16 22:10:30.303] [jointLog] [info] writing output 

CMD: /gscratch/srlab/programs/trinityrnaseq-v2.9.0/util/support_scripts/salmon_trans_to_gene_results.pl 329777_01/quant.sf /gscratch/srlab/sam/data/C_bairdi/transcriptomes/20200408.C_bairdi.megan.Trinity.fasta.gene_trans_map > 329777_01/quant.sf.genes