CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ2-Sequences.txt.gz_val_2.fq.gz) -o b_F_K5_04  -p 23
Version Info: ### PLEASE UPGRADE SALMON ###
### A newer version of Salmon with important bug fixes and improvements is available. ####
###
The newest version, available at https://github.com/COMBINE-lab/salmon/releases
contains new features, improvements, and bug fixes; please upgrade at your
earliest convenience.
###
### salmon (mapping-based) v0.9.1
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /dev/fd/63 }
### [ mates2 ] => { /dev/fd/62 }
### [ output ] => { b_F_K5_04 }
### [ threads ] => { 23 }
Logs will be written to b_F_K5_04/logs
[2019-03-14 21:12:47.387] [jointLog] [info] parsing read library format
[2019-03-14 21:12:47.387] [jointLog] [info] There is 1 library.
[2019-03-14 21:12:47.450] [stderrLog] [info] Loading Suffix Array 
[2019-03-14 21:12:47.450] [jointLog] [info] Loading Quasi index
[2019-03-14 21:12:47.450] [jointLog] [info] Loading 32-bit quasi index
[2019-03-14 21:12:47.483] [stderrLog] [info] Loading Transcript Info 
[2019-03-14 21:12:47.492] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-03-14 21:12:47.495] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-03-14 21:12:47.497] [stderrLog] [info] Computing transcript lengths
[2019-03-14 21:12:47.497] [stderrLog] [info] Waiting to finish loading hash
[2019-03-14 21:12:47.835] [jointLog] [info] done
[2019-03-14 21:12:47.835] [jointLog] [info] Index contained 5838 targets




[2019-03-14 21:12:47.835] [stderrLog] [info] Done loading index


processed 500000 fragments
hits: 96405, hits per frag:  0.229877

processed 1000002 fragments
hits: 192608, hits per frag:  0.195235

processed 1500000 fragments
hits: 289426, hits per frag:  0.197389

processed 2000001 fragments
hits: 385688, hits per frag:  0.196246

processed 2500000 fragments
hits: 481916, hits per frag:  0.195897

processed 3000000 fragments
hits: 577832, hits per frag:  0.193303

processed 3500000 fragments
hits: 673436, hits per frag:  0.195744

processed 4000000 fragments
hits: 770521, hits per frag:  0.197806

processed 4500000 fragments
hits: 867650, hits per frag:  0.196804

processed 5000000 fragments
hits: 963783, hits per frag:  0.194861

processed 5500000 fragments
hits: 1060885, hits per frag:  0.196025

processed 6000000 fragments
hits: 1157680, hits per frag:  0.195531

processed 6500000 fragments
hits: 1253645, hits per frag:  0.193796

processed 7000000 fragments
hits: 1351193, hits per frag:  0.194221

processed 7500000 fragments
hits: 1447913, hits per frag:  0.193499

processed 8000000 fragments
hits: 1543269, hits per frag:  0.19342

processed 8500000 fragments
hits: 1638938, hits per frag:  0.195079

processed 9000000 fragments
hits: 1735078, hits per frag:  0.194848

processed 9500000 fragments
hits: 1831512, hits per frag:  0.194674

processed 10000001 fragments
hits: 1926836, hits per frag:  0.193175

processed 10500000 fragments
hits: 2022014, hits per frag:  0.193089

processed 11000000 fragments
hits: 2118411, hits per frag:  0.192984

processed 11500000 fragments
hits: 2215205, hits per frag:  0.194407

processed 12000000 fragments
hits: 2311953, hits per frag:  0.193106

processed 12500001 fragments
hits: 2406342, hits per frag:  0.192849

processed 13000000 fragments
hits: 2501303, hits per frag:  0.194106

processed 13500001 fragments
hits: 2597628, hits per frag:  0.192524

processed 14000000 fragments
hits: 2694107, hits per frag:  0.19277

processed 14500000 fragments
hits: 2790495, hits per frag:  0.193809

processed 15000000 fragments
hits: 2887056, hits per frag:  0.193551

processed 15500000 fragments
hits: 2982998, hits per frag:  0.193164

processed 16000001 fragments
hits: 3078675, hits per frag:  0.193104

processed 16500000 fragments
hits: 3174668, hits per frag:  0.193125

processed 17000001 fragments
hits: 3270783, hits per frag:  0.192786

processed 17500001 fragments
hits: 3366899, hits per frag:  0.193288

processed 18000001 fragments
hits: 3463015, hits per frag:  0.192968

processed 18500000 fragments
hits: 3558799, hits per frag:  0.192867

processed 19000000 fragments
hits: 3655523, hits per frag:  0.192714

processed 19500000 fragments
hits: 3751212, hits per frag:  0.193043

processed 20000000 fragments
hits: 3847928, hits per frag:  0.193333

processed 20500000 fragments
hits: 3944476, hits per frag:  0.192855

processed 21000000 fragments
hits: 4040784, hits per frag:  0.193528

processed 21500001 fragments
hits: 4137724, hits per frag:  0.19299

processed 22000000 fragments
hits: 4233659, hits per frag:  0.19356

processed 22500001 fragments
hits: 4329702, hits per frag:  0.193265

processed 23000000 fragments
hits: 4426415, hits per frag:  0.193025

processed 23500000 fragments
hits: 4522474, hits per frag:  0.192885

processed 24000000 fragments
hits: 4618628, hits per frag:  0.193091

processed 24500000 fragments
hits: 4715068, hits per frag:  0.19269

processed 25000000 fragments
hits: 4812227, hits per frag:  0.193138

processed 25500000 fragments
hits: 4908470, hits per frag:  0.19322

processed 26000000 fragments
hits: 5004211, hits per frag:  0.192568

processed 26500000 fragments
hits: 5101321, hits per frag:  0.193189

processed 27000001 fragments
hits: 5197073, hits per frag:  0.192753

processed 27500000 fragments
hits: 5292224, hits per frag:  0.192992

processed 28000000 fragments
hits: 5389062, hits per frag:  0.192914









[2019-03-14 21:13:55.812] [jointLog] [info] Computed 7401 rich equivalence classes for further processing
[2019-03-14 21:13:55.812] [jointLog] [info] Counted 2716216 total reads in the equivalence classes 
[2019-03-14 21:13:55.823] [jointLog] [warning] 0.0118102% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2019-03-14 21:13:55.823] [jointLog] [warning] Only 2716216 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2019-03-14 21:13:55.823] [jointLog] [info] Mapping rate = 9.59013%

[2019-03-14 21:13:55.824] [jointLog] [info] finished quantifyLibrary()
[2019-03-14 21:13:55.824] [jointLog] [info] Starting optimizer
[2019-03-14 21:13:55.829] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-03-14 21:13:55.829] [jointLog] [info] iteration = 0 | max rel diff. = 623.186
[2019-03-14 21:13:55.848] [jointLog] [info] iteration = 100 | max rel diff. = 0.126921
[2019-03-14 21:13:55.866] [jointLog] [info] iteration = 200 | max rel diff. = 0.0631581
[2019-03-14 21:13:55.885] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433758
[2019-03-14 21:13:55.903] [jointLog] [info] iteration = 400 | max rel diff. = 0.0310137
[2019-03-14 21:13:55.920] [jointLog] [info] iteration = 500 | max rel diff. = 0.0246268
[2019-03-14 21:13:55.938] [jointLog] [info] iteration = 600 | max rel diff. = 0.0179093
[2019-03-14 21:13:55.956] [jointLog] [info] iteration = 700 | max rel diff. = 0.0152061
[2019-03-14 21:13:55.974] [jointLog] [info] iteration = 800 | max rel diff. = 0.0120247
[2019-03-14 21:13:55.991] [jointLog] [info] iteration = 900 | max rel diff. = 0.0120261
[2019-03-14 21:13:56.007] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0110934
[2019-03-14 21:13:56.012] [jointLog] [info] iteration = 1034 | max rel diff. = 0.00984526
[2019-03-14 21:13:56.012] [jointLog] [info] Finished optimizer
[2019-03-14 21:13:56.012] [jointLog] [info] writing output 

[2019-03-14 21:13:56.023] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] :

Greater than 5% of the fragments disagreed with the provided library type; check the file: b_F_K5_04/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl b_F_K5_04/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > b_F_K5_04/quant.sf.genes
CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ2-Sequences.txt.gz_val_2.fq.gz) -o b_F_K5_05  -p 23
Version Info: ### PLEASE UPGRADE SALMON ###
### A newer version of Salmon with important bug fixes and improvements is available. ####
###
The newest version, available at https://github.com/COMBINE-lab/salmon/releases
contains new features, improvements, and bug fixes; please upgrade at your
earliest convenience.
###
### salmon (mapping-based) v0.9.1
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /dev/fd/63 }
### [ mates2 ] => { /dev/fd/62 }
### [ output ] => { b_F_K5_05 }
### [ threads ] => { 23 }
Logs will be written to b_F_K5_05/logs
[2019-03-14 21:13:56.496] [jointLog] [info] parsing read library format
[2019-03-14 21:13:56.496] [jointLog] [info] There is 1 library.
[2019-03-14 21:13:56.558] [stderrLog] [info] Loading Suffix Array 
[2019-03-14 21:13:56.558] [jointLog] [info] Loading Quasi index
[2019-03-14 21:13:56.558] [jointLog] [info] Loading 32-bit quasi index
[2019-03-14 21:13:56.597] [stderrLog] [info] Loading Transcript Info 
[2019-03-14 21:13:56.606] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-03-14 21:13:56.609] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-03-14 21:13:56.611] [stderrLog] [info] Computing transcript lengths
[2019-03-14 21:13:56.611] [stderrLog] [info] Waiting to finish loading hash
[2019-03-14 21:13:56.948] [jointLog] [info] done
[2019-03-14 21:13:56.948] [jointLog] [info] Index contained 5838 targets




[2019-03-14 21:13:56.948] [stderrLog] [info] Done loading index


processed 500000 fragments
hits: 88704, hits per frag:  0.208844

processed 1000000 fragments
hits: 177946, hits per frag:  0.193161

processed 1500000 fragments
hits: 265438, hits per frag:  0.180362

processed 2000001 fragments
hits: 354078, hits per frag:  0.1839

processed 2500000 fragments
hits: 442349, hits per frag:  0.181893

processed 3000000 fragments
hits: 531422, hits per frag:  0.181326

processed 3500001 fragments
hits: 619397, hits per frag:  0.182259

processed 4000000 fragments
hits: 706963, hits per frag:  0.179619

processed 4500000 fragments
hits: 796393, hits per frag:  0.178929

processed 5000000 fragments
hits: 884745, hits per frag:  0.177856

processed 5500001 fragments
hits: 972845, hits per frag:  0.180156

processed 6000000 fragments
hits: 1061253, hits per frag:  0.179793

processed 6500000 fragments
hits: 1150043, hits per frag:  0.180114

processed 7000000 fragments
hits: 1238273, hits per frag:  0.178942

processed 7500000 fragments
hits: 1326021, hits per frag:  0.178635

processed 8000000 fragments
hits: 1414033, hits per frag:  0.178323

processed 8500000 fragments
hits: 1502639, hits per frag:  0.17864

processed 9000001 fragments
hits: 1591887, hits per frag:  0.177862

processed 9500000 fragments
hits: 1680415, hits per frag:  0.179963

processed 10000000 fragments
hits: 1768823, hits per frag:  0.178002

processed 10500000 fragments
hits: 1856617, hits per frag:  0.178445

processed 11000000 fragments
hits: 1943664, hits per frag:  0.177135

processed 11500000 fragments
hits: 2031771, hits per frag:  0.178091

processed 12000000 fragments
hits: 2119293, hits per frag:  0.17759

processed 12500000 fragments
hits: 2207320, hits per frag:  0.178563

processed 13000000 fragments
hits: 2294847, hits per frag:  0.177731

processed 13500000 fragments
hits: 2382828, hits per frag:  0.177176

processed 14000000 fragments
hits: 2470901, hits per frag:  0.177308

processed 14500000 fragments
hits: 2559429, hits per frag:  0.177238

processed 15000000 fragments
hits: 2647939, hits per frag:  0.17703

processed 15500000 fragments
hits: 2735964, hits per frag:  0.176892

processed 16000001 fragments
hits: 2824312, hits per frag:  0.177413

processed 16500000 fragments
hits: 2913140, hits per frag:  0.176749

processed 17000001 fragments
hits: 3001400, hits per frag:  0.17724

processed 17500000 fragments
hits: 3089615, hits per frag:  0.176742

processed 18000001 fragments
hits: 3177730, hits per frag:  0.176803

processed 18500000 fragments
hits: 3264990, hits per frag:  0.176981

processed 19000000 fragments
hits: 3352323, hits per frag:  0.177243

processed 19500000 fragments
hits: 3440169, hits per frag:  0.177071

processed 20000000 fragments
hits: 3527616, hits per frag:  0.177222

processed 20500000 fragments
hits: 3615216, hits per frag:  0.177107

processed 21000000 fragments
hits: 3702956, hits per frag:  0.176564

processed 21500000 fragments
hits: 3791464, hits per frag:  0.177156









[2019-03-14 21:14:49.124] [jointLog] [info] Computed 6922 rich equivalence classes for further processing
[2019-03-14 21:14:49.124] [jointLog] [info] Counted 1916701 total reads in the equivalence classes 
[2019-03-14 21:14:49.135] [jointLog] [warning] 0.0194906% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2019-03-14 21:14:49.135] [jointLog] [warning] Only 1916701 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2019-03-14 21:14:49.135] [jointLog] [info] Mapping rate = 8.75913%

[2019-03-14 21:14:49.135] [jointLog] [info] finished quantifyLibrary()
[2019-03-14 21:14:49.136] [jointLog] [info] Starting optimizer
[2019-03-14 21:14:49.140] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-03-14 21:14:49.140] [jointLog] [info] iteration = 0 | max rel diff. = 428.646
[2019-03-14 21:14:49.156] [jointLog] [info] iteration = 100 | max rel diff. = 0.112607
[2019-03-14 21:14:49.171] [jointLog] [info] iteration = 200 | max rel diff. = 0.0561126
[2019-03-14 21:14:49.186] [jointLog] [info] iteration = 300 | max rel diff. = 0.0366474
[2019-03-14 21:14:49.201] [jointLog] [info] iteration = 400 | max rel diff. = 0.0243107
[2019-03-14 21:14:49.216] [jointLog] [info] iteration = 500 | max rel diff. = 0.0243121
[2019-03-14 21:14:49.233] [jointLog] [info] iteration = 600 | max rel diff. = 0.0175144
[2019-03-14 21:14:49.249] [jointLog] [info] iteration = 700 | max rel diff. = 0.0150948
[2019-03-14 21:14:49.266] [jointLog] [info] iteration = 800 | max rel diff. = 0.0129998
[2019-03-14 21:14:49.283] [jointLog] [info] iteration = 900 | max rel diff. = 0.0114931
[2019-03-14 21:14:49.299] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0114934
[2019-03-14 21:14:49.311] [jointLog] [info] iteration = 1072 | max rel diff. = 0.00919436
[2019-03-14 21:14:49.312] [jointLog] [info] Finished optimizer
[2019-03-14 21:14:49.312] [jointLog] [info] writing output 

[2019-03-14 21:14:49.323] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] :

Greater than 5% of the fragments disagreed with the provided library type; check the file: b_F_K5_05/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl b_F_K5_05/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > b_F_K5_05/quant.sf.genes
CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ2-Sequences.txt.gz_val_2.fq.gz) -o b_F_K5_06  -p 23
Version Info: ### PLEASE UPGRADE SALMON ###
### A newer version of Salmon with important bug fixes and improvements is available. ####
###
The newest version, available at https://github.com/COMBINE-lab/salmon/releases
contains new features, improvements, and bug fixes; please upgrade at your
earliest convenience.
###
### salmon (mapping-based) v0.9.1
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /dev/fd/63 }
### [ mates2 ] => { /dev/fd/62 }
### [ output ] => { b_F_K5_06 }
### [ threads ] => { 23 }
Logs will be written to b_F_K5_06/logs
[2019-03-14 21:14:49.808] [jointLog] [info] parsing read library format
[2019-03-14 21:14:49.808] [jointLog] [info] There is 1 library.
[2019-03-14 21:14:49.871] [stderrLog] [info] Loading Suffix Array 
[2019-03-14 21:14:49.871] [jointLog] [info] Loading Quasi index
[2019-03-14 21:14:49.871] [jointLog] [info] Loading 32-bit quasi index
[2019-03-14 21:14:49.908] [stderrLog] [info] Loading Transcript Info 
[2019-03-14 21:14:49.917] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-03-14 21:14:49.920] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-03-14 21:14:49.922] [stderrLog] [info] Computing transcript lengths
[2019-03-14 21:14:49.922] [stderrLog] [info] Waiting to finish loading hash
[2019-03-14 21:14:50.262] [jointLog] [info] done
[2019-03-14 21:14:50.262] [jointLog] [info] Index contained 5838 targets




[2019-03-14 21:14:50.262] [stderrLog] [info] Done loading index


processed 500000 fragments
hits: 74570, hits per frag:  0.182204

processed 1000000 fragments
hits: 149554, hits per frag:  0.153446

processed 1500000 fragments
hits: 224725, hits per frag:  0.152215

processed 2000000 fragments
hits: 298991, hits per frag:  0.154634

processed 2500000 fragments
hits: 373667, hits per frag:  0.150859

processed 3000000 fragments
hits: 447898, hits per frag:  0.151659

processed 3500000 fragments
hits: 522364, hits per frag:  0.152265

processed 4000001 fragments
hits: 595364, hits per frag:  0.150692

processed 4500001 fragments
hits: 669413, hits per frag:  0.152919

processed 5000000 fragments
hits: 744479, hits per frag:  0.151729

processed 5500000 fragments
hits: 819804, hits per frag:  0.150397

processed 6000000 fragments
hits: 894796, hits per frag:  0.150933

processed 6500000 fragments
hits: 968530, hits per frag:  0.149036

processed 7000001 fragments
hits: 1042073, hits per frag:  0.150168

processed 7500001 fragments
hits: 1116308, hits per frag:  0.150234

processed 8000000 fragments
hits: 1189798, hits per frag:  0.14982

processed 8500000 fragments
hits: 1262832, hits per frag:  0.148961

processed 9000000 fragments
hits: 1338113, hits per frag:  0.14917

processed 9500000 fragments
hits: 1413026, hits per frag:  0.14944

processed 10000000 fragments
hits: 1487446, hits per frag:  0.150053

processed 10500000 fragments
hits: 1561615, hits per frag:  0.149531

processed 11000000 fragments
hits: 1635769, hits per frag:  0.148776

processed 11500000 fragments
hits: 1710084, hits per frag:  0.149214

processed 12000001 fragments
hits: 1783769, hits per frag:  0.148704

processed 12500000 fragments
hits: 1857527, hits per frag:  0.149312

processed 13000000 fragments
hits: 1930681, hits per frag:  0.149485

processed 13500002 fragments
hits: 2006531, hits per frag:  0.149411

processed 14000000 fragments
hits: 2081173, hits per frag:  0.148991

processed 14500000 fragments
hits: 2156316, hits per frag:  0.149265

processed 15000000 fragments
hits: 2230437, hits per frag:  0.149605

processed 15500000 fragments
hits: 2304392, hits per frag:  0.149759

processed 16000000 fragments
hits: 2377829, hits per frag:  0.149315

processed 16500000 fragments
hits: 2451296, hits per frag:  0.149157

processed 17000001 fragments
hits: 2524287, hits per frag:  0.149071









[2019-03-14 21:15:29.263] [jointLog] [info] Computed 6627 rich equivalence classes for further processing
[2019-03-14 21:15:29.263] [jointLog] [info] Counted 1294477 total reads in the equivalence classes 
[2019-03-14 21:15:29.273] [jointLog] [warning] 0.0100547% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2019-03-14 21:15:29.273] [jointLog] [warning] Only 1294477 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2019-03-14 21:15:29.273] [jointLog] [info] Mapping rate = 7.48881%

[2019-03-14 21:15:29.273] [jointLog] [info] finished quantifyLibrary()
[2019-03-14 21:15:29.273] [jointLog] [info] Starting optimizer
[2019-03-14 21:15:29.279] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-03-14 21:15:29.279] [jointLog] [info] iteration = 0 | max rel diff. = 305.923
[2019-03-14 21:15:29.295] [jointLog] [info] iteration = 100 | max rel diff. = 0.113946
[2019-03-14 21:15:29.311] [jointLog] [info] iteration = 200 | max rel diff. = 0.0606231
[2019-03-14 21:15:29.326] [jointLog] [info] iteration = 300 | max rel diff. = 0.0432692
[2019-03-14 21:15:29.340] [jointLog] [info] iteration = 400 | max rel diff. = 0.0293289
[2019-03-14 21:15:29.354] [jointLog] [info] iteration = 500 | max rel diff. = 0.0218005
[2019-03-14 21:15:29.368] [jointLog] [info] iteration = 600 | max rel diff. = 0.017429
[2019-03-14 21:15:29.383] [jointLog] [info] iteration = 700 | max rel diff. = 0.0147314
[2019-03-14 21:15:29.397] [jointLog] [info] iteration = 800 | max rel diff. = 0.0118523
[2019-03-14 21:15:29.413] [jointLog] [info] iteration = 900 | max rel diff. = 0.0111513
[2019-03-14 21:15:29.429] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0113568
[2019-03-14 21:15:29.445] [jointLog] [info] iteration = 1091 | max rel diff. = 0.00876297
[2019-03-14 21:15:29.445] [jointLog] [info] Finished optimizer
[2019-03-14 21:15:29.445] [jointLog] [info] writing output 

[2019-03-14 21:15:29.456] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] :

Greater than 5% of the fragments disagreed with the provided library type; check the file: b_F_K5_06/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl b_F_K5_06/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > b_F_K5_06/quant.sf.genes
CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P02-ACAGTG-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P02-ACAGTG-READ2-Sequences.txt.gz_val_2.fq.gz) -o nb_F_K5_07  -p 23
Version Info: ### PLEASE UPGRADE SALMON ###
### A newer version of Salmon with important bug fixes and improvements is available. ####
###
The newest version, available at https://github.com/COMBINE-lab/salmon/releases
contains new features, improvements, and bug fixes; please upgrade at your
earliest convenience.
###
### salmon (mapping-based) v0.9.1
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /dev/fd/63 }
### [ mates2 ] => { /dev/fd/62 }
### [ output ] => { nb_F_K5_07 }
### [ threads ] => { 23 }
Logs will be written to nb_F_K5_07/logs
[2019-03-14 21:15:29.701] [jointLog] [info] parsing read library format
[2019-03-14 21:15:29.701] [jointLog] [info] There is 1 library.
[2019-03-14 21:15:29.762] [stderrLog] [info] Loading Suffix Array 
[2019-03-14 21:15:29.762] [jointLog] [info] Loading Quasi index
[2019-03-14 21:15:29.762] [jointLog] [info] Loading 32-bit quasi index
[2019-03-14 21:15:29.802] [stderrLog] [info] Loading Transcript Info 
[2019-03-14 21:15:29.812] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-03-14 21:15:29.816] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-03-14 21:15:29.817] [stderrLog] [info] Computing transcript lengths
[2019-03-14 21:15:29.817] [stderrLog] [info] Waiting to finish loading hash
[2019-03-14 21:15:30.153] [jointLog] [info] done
[2019-03-14 21:15:30.153] [jointLog] [info] Index contained 5838 targets




[2019-03-14 21:15:30.153] [stderrLog] [info] Done loading index


processed 500000 fragments
hits: 98567, hits per frag:  0.216033

processed 1000000 fragments
hits: 198060, hits per frag:  0.219587

processed 1500000 fragments
hits: 295917, hits per frag:  0.205702

processed 2000001 fragments
hits: 396436, hits per frag:  0.198904

processed 2500001 fragments
hits: 495814, hits per frag:  0.204032

processed 3000001 fragments
hits: 595391, hits per frag:  0.206629

processed 3500000 fragments
hits: 694628, hits per frag:  0.200206

processed 4000000 fragments
hits: 793730, hits per frag:  0.202967

processed 4500000 fragments
hits: 891919, hits per frag:  0.202764

processed 5000000 fragments
hits: 990814, hits per frag:  0.201485

processed 5500002 fragments
hits: 1089787, hits per frag:  0.202345

processed 6000000 fragments
hits: 1189232, hits per frag:  0.201372

processed 6500000 fragments
hits: 1288314, hits per frag:  0.200353

processed 7000000 fragments
hits: 1386980, hits per frag:  0.19892

processed 7500000 fragments
hits: 1485377, hits per frag:  0.198842

processed 8000000 fragments
hits: 1584438, hits per frag:  0.199471

processed 8500000 fragments
hits: 1683802, hits per frag:  0.200062

processed 9000000 fragments
hits: 1782859, hits per frag:  0.199914

processed 9500001 fragments
hits: 1881122, hits per frag:  0.199543

processed 10000003 fragments
hits: 1981100, hits per frag:  0.198779

processed 10500001 fragments
hits: 2079039, hits per frag:  0.199729

processed 11500001 fragments
hits: 2276828, hits per frag:  0.199153

processed 12000000 fragments
hits: 2375320, hits per frag:  0.199425

processed 12500001 fragments
hits: 2473825, hits per frag:  0.199708

processed 13000000 fragments
hits: 2572711, hits per frag:  0.198831

processed 13500000 fragments
hits: 2670226, hits per frag:  0.199229

processed 14000000 fragments
hits: 2768420, hits per frag:  0.19864

processed 14500000 fragments
hits: 2866561, hits per frag:  0.198543

processed 15000000 fragments
hits: 2965753, hits per frag:  0.198092

processed 15500000 fragments
hits: 3065192, hits per frag:  0.19868

processed 16000000 fragments
hits: 3164345, hits per frag:  0.198338

processed 16500000 fragments
hits: 3262478, hits per frag:  0.198506

processed 17000000 fragments
hits: 3360918, hits per frag:  0.1988

processed 17500000 fragments
hits: 3461286, hits per frag:  0.198785

processed 18000000 fragments
hits: 3560643, hits per frag:  0.198105

processed 18500000 fragments
hits: 3658846, hits per frag:  0.198515

processed 19000000 fragments
hits: 3758151, hits per frag:  0.199283

processed 19500000 fragments
hits: 3857701, hits per frag:  0.19836

processed 20000001 fragments
hits: 3956222, hits per frag:  0.197992

processed 20500000 fragments
hits: 4055280, hits per frag:  0.198316

processed 21000001 fragments
hits: 4154031, hits per frag:  0.198401

processed 21500000 fragments
hits: 4253258, hits per frag:  0.198526

processed 22000000 fragments
hits: 4352877, hits per frag:  0.198505

processed 22500000 fragments
hits: 4452307, hits per frag:  0.198633

processed 23000000 fragments
hits: 4551502, hits per frag:  0.198745

processed 23500000 fragments
hits: 4649877, hits per frag:  0.198362









[2019-03-14 21:16:25.358] [jointLog] [info] Computed 7091 rich equivalence classes for further processing
[2019-03-14 21:16:25.358] [jointLog] [info] Counted 2346516 total reads in the equivalence classes 
[2019-03-14 21:16:25.369] [jointLog] [warning] 0.0207925% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2019-03-14 21:16:25.369] [jointLog] [warning] Only 2346516 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2019-03-14 21:16:25.369] [jointLog] [info] Mapping rate = 9.83271%

[2019-03-14 21:16:25.369] [jointLog] [info] finished quantifyLibrary()
[2019-03-14 21:16:25.370] [jointLog] [info] Starting optimizer
[2019-03-14 21:16:25.375] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-03-14 21:16:25.376] [jointLog] [info] iteration = 0 | max rel diff. = 538.307
[2019-03-14 21:16:25.402] [jointLog] [info] iteration = 100 | max rel diff. = 0.118479
[2019-03-14 21:16:25.419] [jointLog] [info] iteration = 200 | max rel diff. = 0.0574428
[2019-03-14 21:16:25.437] [jointLog] [info] iteration = 300 | max rel diff. = 0.0391362
[2019-03-14 21:16:25.455] [jointLog] [info] iteration = 400 | max rel diff. = 0.0273949
[2019-03-14 21:16:25.473] [jointLog] [info] iteration = 500 | max rel diff. = 0.0220548
[2019-03-14 21:16:25.491] [jointLog] [info] iteration = 600 | max rel diff. = 0.019218
[2019-03-14 21:16:25.509] [jointLog] [info] iteration = 700 | max rel diff. = 0.0157131
[2019-03-14 21:16:25.526] [jointLog] [info] iteration = 800 | max rel diff. = 0.013467
[2019-03-14 21:16:25.544] [jointLog] [info] iteration = 900 | max rel diff. = 0.0111952
[2019-03-14 21:16:25.562] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0107554
[2019-03-14 21:16:25.574] [jointLog] [info] iteration = 1068 | max rel diff. = 0.00971556
[2019-03-14 21:16:25.575] [jointLog] [info] Finished optimizer
[2019-03-14 21:16:25.575] [jointLog] [info] writing output 

[2019-03-14 21:16:25.586] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] :

Greater than 5% of the fragments disagreed with the provided library type; check the file: nb_F_K5_07/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl nb_F_K5_07/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > nb_F_K5_07/quant.sf.genes
CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P10-TAGCTT-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P10-TAGCTT-READ2-Sequences.txt.gz_val_2.fq.gz) -o nb_F_K5_08  -p 23
Version Info: ### PLEASE UPGRADE SALMON ###
### A newer version of Salmon with important bug fixes and improvements is available. ####
###
The newest version, available at https://github.com/COMBINE-lab/salmon/releases
contains new features, improvements, and bug fixes; please upgrade at your
earliest convenience.
###
### salmon (mapping-based) v0.9.1
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /dev/fd/63 }
### [ mates2 ] => { /dev/fd/62 }
### [ output ] => { nb_F_K5_08 }
### [ threads ] => { 23 }
Logs will be written to nb_F_K5_08/logs
[2019-03-14 21:16:25.815] [jointLog] [info] parsing read library format
[2019-03-14 21:16:25.815] [jointLog] [info] There is 1 library.
[2019-03-14 21:16:25.876] [stderrLog] [info] Loading Suffix Array 
[2019-03-14 21:16:25.876] [jointLog] [info] Loading Quasi index
[2019-03-14 21:16:25.876] [jointLog] [info] Loading 32-bit quasi index
[2019-03-14 21:16:25.910] [stderrLog] [info] Loading Transcript Info 
[2019-03-14 21:16:25.919] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-03-14 21:16:25.923] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-03-14 21:16:25.924] [stderrLog] [info] Computing transcript lengths
[2019-03-14 21:16:25.924] [stderrLog] [info] Waiting to finish loading hash
[2019-03-14 21:16:26.263] [jointLog] [info] done
[2019-03-14 21:16:26.263] [jointLog] [info] Index contained 5838 targets




[2019-03-14 21:16:26.263] [stderrLog] [info] Done loading index


processed 500000 fragments
hits: 85063, hits per frag:  0.200587

processed 1000000 fragments
hits: 169837, hits per frag:  0.186069

processed 1500000 fragments
hits: 255150, hits per frag:  0.176947

processed 2000000 fragments
hits: 339748, hits per frag:  0.173201

processed 2500001 fragments
hits: 425559, hits per frag:  0.174427

processed 3000000 fragments
hits: 510692, hits per frag:  0.170955

processed 3500001 fragments
hits: 596800, hits per frag:  0.172096

processed 4000000 fragments
hits: 681973, hits per frag:  0.171529

processed 4500000 fragments
hits: 766839, hits per frag:  0.176655

processed 5000001 fragments
hits: 851562, hits per frag:  0.173012

processed 5500001 fragments
hits: 937385, hits per frag:  0.171679

processed 6000000 fragments
hits: 1022817, hits per frag:  0.173508

processed 6500000 fragments
hits: 1108132, hits per frag:  0.17186

processed 7000000 fragments
hits: 1193928, hits per frag:  0.173325

processed 7500000 fragments
hits: 1278935, hits per frag:  0.172519

processed 8000000 fragments
hits: 1365184, hits per frag:  0.172334

processed 8500000 fragments
hits: 1449790, hits per frag:  0.17127

processed 9000000 fragments
hits: 1535530, hits per frag:  0.17372

processed 9500001 fragments
hits: 1621186, hits per frag:  0.170865

processed 10000000 fragments
hits: 1706659, hits per frag:  0.173302

processed 10500000 fragments
hits: 1792435, hits per frag:  0.171722

processed 11000001 fragments
hits: 1877497, hits per frag:  0.171665

processed 11500000 fragments
hits: 1962495, hits per frag:  0.171955

processed 12500000 fragments
hits: 2132545, hits per frag:  0.17112

processed 13000000 fragments
hits: 2217753, hits per frag:  0.171715

processed 13500000 fragments
hits: 2303039, hits per frag:  0.17142

processed 14000000 fragments
hits: 2387390, hits per frag:  0.171416

processed 14500001 fragments
hits: 2473292, hits per frag:  0.170967

processed 15000001 fragments
hits: 2557499, hits per frag:  0.17153

processed 15500000 fragments
hits: 2642234, hits per frag:  0.17083

processed 16000000 fragments
hits: 2726493, hits per frag:  0.171545

processed 16500001 fragments
hits: 2811778, hits per frag:  0.171132

processed 17000000 fragments
hits: 2897568, hits per frag:  0.170675

processed 17500000 fragments
hits: 2984186, hits per frag:  0.170879

processed 18000003 fragments
hits: 3068271, hits per frag:  0.170574

processed 18500000 fragments
hits: 3153065, hits per frag:  0.171505

processed 19000000 fragments
hits: 3238300, hits per frag:  0.171192

processed 19500001 fragments
hits: 3323154, hits per frag:  0.1713

processed 20000001 fragments
hits: 3409452, hits per frag:  0.170774

processed 20500000 fragments
hits: 3494749, hits per frag:  0.170861

processed 21000000 fragments
hits: 3579223, hits per frag:  0.170889

processed 21500000 fragments
hits: 3664780, hits per frag:  0.171061

processed 22000000 fragments
hits: 3749762, hits per frag:  0.170813

processed 22500000 fragments
hits: 3834838, hits per frag:  0.170784

processed 23000000 fragments
hits: 3921099, hits per frag:  0.171105

processed 23500001 fragments
hits: 4006721, hits per frag:  0.170803

processed 24000002 fragments
hits: 4092591, hits per frag:  0.170778

processed 24500000 fragments
hits: 4177843, hits per frag:  0.171417

processed 25000001 fragments
hits: 4264408, hits per frag:  0.17119

processed 25500000 fragments
hits: 4350663, hits per frag:  0.171135

processed 26000000 fragments
hits: 4436347, hits per frag:  0.17075

processed 26500001 fragments
hits: 4519575, hits per frag:  0.171264

processed 27000000 fragments
hits: 4605079, hits per frag:  0.170938

processed 27500000 fragments
hits: 4689385, hits per frag:  0.171484

processed 28000000 fragments
hits: 4775319, hits per frag:  0.170607

processed 28500000 fragments
hits: 4859846, hits per frag:  0.170984

processed 29000000 fragments
hits: 4945177, hits per frag:  0.170964

processed 29500000 fragments
hits: 5031851, hits per frag:  0.170702

processed 30000000 fragments
hits: 5116702, hits per frag:  0.171376

processed 30500000 fragments
hits: 5202368, hits per frag:  0.171189

processed 31000000 fragments
hits: 5287724, hits per frag:  0.171101

processed 31500000 fragments
hits: 5372616, hits per frag:  0.170842

processed 32000000 fragments
hits: 5457410, hits per frag:  0.170991

processed 32500000 fragments
hits: 5541651, hits per frag:  0.170925

processed 33000000 fragments
hits: 5627175, hits per frag:  0.171047









[2019-03-14 21:17:45.386] [jointLog] [info] Computed 8127 rich equivalence classes for further processing
[2019-03-14 21:17:45.386] [jointLog] [info] Counted 2818911 total reads in the equivalence classes 
[2019-03-14 21:17:45.397] [jointLog] [warning] 0.0111532% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2019-03-14 21:17:45.398] [jointLog] [warning] Only 2818911 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2019-03-14 21:17:45.398] [jointLog] [info] Mapping rate = 8.52724%

[2019-03-14 21:17:45.398] [jointLog] [info] finished quantifyLibrary()
[2019-03-14 21:17:45.398] [jointLog] [info] Starting optimizer
[2019-03-14 21:17:45.403] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-03-14 21:17:45.404] [jointLog] [info] iteration = 0 | max rel diff. = 673.376
[2019-03-14 21:17:45.423] [jointLog] [info] iteration = 100 | max rel diff. = 0.123867
[2019-03-14 21:17:45.438] [jointLog] [info] iteration = 200 | max rel diff. = 0.0599776
[2019-03-14 21:17:45.454] [jointLog] [info] iteration = 300 | max rel diff. = 0.0380154
[2019-03-14 21:17:45.469] [jointLog] [info] iteration = 400 | max rel diff. = 0.0271345
[2019-03-14 21:17:45.484] [jointLog] [info] iteration = 500 | max rel diff. = 0.0249077
[2019-03-14 21:17:45.500] [jointLog] [info] iteration = 600 | max rel diff. = 0.015315
[2019-03-14 21:17:45.515] [jointLog] [info] iteration = 700 | max rel diff. = 0.0153262
[2019-03-14 21:17:45.530] [jointLog] [info] iteration = 800 | max rel diff. = 0.0135082
[2019-03-14 21:17:45.545] [jointLog] [info] iteration = 900 | max rel diff. = 0.0108925
[2019-03-14 21:17:45.560] [jointLog] [info] iteration = 1000 | max rel diff. = 0.010303
[2019-03-14 21:17:45.575] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0103032
[2019-03-14 21:17:45.590] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0103033
[2019-03-14 21:17:45.592] [jointLog] [info] iteration = 1217 | max rel diff. = 0.00902936
[2019-03-14 21:17:45.593] [jointLog] [info] Finished optimizer
[2019-03-14 21:17:45.593] [jointLog] [info] writing output 

[2019-03-14 21:17:45.605] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] :

Greater than 5% of the fragments disagreed with the provided library type; check the file: nb_F_K5_08/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl nb_F_K5_08/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > nb_F_K5_08/quant.sf.genes
CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P15-GTTTCG-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P15-GTTTCG-READ2-Sequences.txt.gz_val_2.fq.gz) -o nb_F_K5_09  -p 23
Version Info: ### PLEASE UPGRADE SALMON ###
### A newer version of Salmon with important bug fixes and improvements is available. ####
###
The newest version, available at https://github.com/COMBINE-lab/salmon/releases
contains new features, improvements, and bug fixes; please upgrade at your
earliest convenience.
###
### salmon (mapping-based) v0.9.1
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /dev/fd/63 }
### [ mates2 ] => { /dev/fd/62 }
### [ output ] => { nb_F_K5_09 }
### [ threads ] => { 23 }
Logs will be written to nb_F_K5_09/logs
[2019-03-14 21:17:45.920] [jointLog] [info] parsing read library format
[2019-03-14 21:17:45.920] [jointLog] [info] There is 1 library.
[2019-03-14 21:17:45.982] [stderrLog] [info] Loading Suffix Array 
[2019-03-14 21:17:45.982] [jointLog] [info] Loading Quasi index
[2019-03-14 21:17:45.982] [jointLog] [info] Loading 32-bit quasi index
[2019-03-14 21:17:46.018] [stderrLog] [info] Loading Transcript Info 
[2019-03-14 21:17:46.028] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-03-14 21:17:46.031] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-03-14 21:17:46.033] [stderrLog] [info] Computing transcript lengths
[2019-03-14 21:17:46.033] [stderrLog] [info] Waiting to finish loading hash
[2019-03-14 21:17:46.384] [jointLog] [info] done
[2019-03-14 21:17:46.384] [jointLog] [info] Index contained 5838 targets




[2019-03-14 21:17:46.384] [stderrLog] [info] Done loading index


processed 500001 fragments
hits: 92978, hits per frag:  0.194803

processed 1000000 fragments
hits: 184953, hits per frag:  0.185223

processed 1500002 fragments
hits: 277415, hits per frag:  0.18554

processed 2000000 fragments
hits: 370240, hits per frag:  0.191472

processed 2500001 fragments
hits: 463025, hits per frag:  0.194559

processed 3000000 fragments
hits: 555671, hits per frag:  0.190309

processed 3500000 fragments
hits: 648556, hits per frag:  0.186832

processed 4000000 fragments
hits: 741601, hits per frag:  0.187684

processed 4500002 fragments
hits: 834113, hits per frag:  0.189903

processed 5000001 fragments
hits: 926477, hits per frag:  0.187757

processed 5500001 fragments
hits: 1018936, hits per frag:  0.186877

processed 6000001 fragments
hits: 1111509, hits per frag:  0.185348

processed 6500000 fragments
hits: 1204523, hits per frag:  0.185676

processed 7000000 fragments
hits: 1296039, hits per frag:  0.188012

processed 7500001 fragments
hits: 1388479, hits per frag:  0.186924

processed 8000001 fragments
hits: 1480552, hits per frag:  0.186285

processed 8500001 fragments
hits: 1572460, hits per frag:  0.187405

processed 9000000 fragments
hits: 1665987, hits per frag:  0.185358

processed 9500000 fragments
hits: 1758429, hits per frag:  0.186453

processed 10000000 fragments
hits: 1851329, hits per frag:  0.186388

processed 10500000 fragments
hits: 1944324, hits per frag:  0.185679

processed 11000000 fragments
hits: 2036299, hits per frag:  0.186546

processed 11500000 fragments
hits: 2130193, hits per frag:  0.186299

processed 12000000 fragments
hits: 2223328, hits per frag:  0.18561

processed 12500000 fragments
hits: 2316708, hits per frag:  0.186134

processed 13000000 fragments
hits: 2409217, hits per frag:  0.186395

processed 13500000 fragments
hits: 2502640, hits per frag:  0.185759

processed 14000000 fragments
hits: 2595875, hits per frag:  0.185744

processed 14500001 fragments
hits: 2688607, hits per frag:  0.185849

processed 15000000 fragments
hits: 2781257, hits per frag:  0.18688

processed 15500001 fragments
hits: 2873630, hits per frag:  0.186035

processed 16000000 fragments
hits: 2965232, hits per frag:  0.186187

processed 16500000 fragments
hits: 3058358, hits per frag:  0.185643

processed 17000000 fragments
hits: 3150770, hits per frag:  0.185765

processed 17500000 fragments
hits: 3243757, hits per frag:  0.185853

processed 18000000 fragments
hits: 3336452, hits per frag:  0.186351

processed 18500001 fragments
hits: 3428984, hits per frag:  0.186256

processed 19000000 fragments
hits: 3520951, hits per frag:  0.185683

processed 19500000 fragments
hits: 3612717, hits per frag:  0.186186

processed 20000000 fragments
hits: 3704815, hits per frag:  0.186144

processed 20500000 fragments
hits: 3796827, hits per frag:  0.185301

processed 21000000 fragments
hits: 3889134, hits per frag:  0.185824

processed 21500000 fragments
hits: 3981828, hits per frag:  0.185852

processed 22000000 fragments
hits: 4074248, hits per frag:  0.185779

processed 22500002 fragments
hits: 4165635, hits per frag:  0.185631

processed 23000000 fragments
hits: 4259842, hits per frag:  0.18554

processed 23500000 fragments
hits: 4351623, hits per frag:  0.185519

processed 24000000 fragments
hits: 4445305, hits per frag:  0.185685

processed 24500000 fragments
hits: 4537405, hits per frag:  0.185271

processed 25000000 fragments
hits: 4630056, hits per frag:  0.185739

processed 25500000 fragments
hits: 4721260, hits per frag:  0.185339

processed 26000000 fragments
hits: 4814266, hits per frag:  0.185247

processed 26500000 fragments
hits: 4907611, hits per frag:  0.186082

processed 27000001 fragments
hits: 4999883, hits per frag:  0.185954

processed 27500000 fragments
hits: 5092132, hits per frag:  0.185271

processed 28000000 fragments
hits: 5185844, hits per frag:  0.185593

processed 28500000 fragments
hits: 5278153, hits per frag:  0.185952

processed 29000000 fragments
hits: 5369845, hits per frag:  0.185731

processed 29500000 fragments
hits: 5461574, hits per frag:  0.185671

processed 30000000 fragments
hits: 5554905, hits per frag:  0.185646

processed 30500000 fragments
hits: 5647115, hits per frag:  0.185407

processed 31000000 fragments
hits: 5740307, hits per frag:  0.185569

processed 31500000 fragments
hits: 5832510, hits per frag:  0.185369

processed 32000000 fragments
hits: 5924073, hits per frag:  0.185145

processed 32500000 fragments
hits: 6017341, hits per frag:  0.185743

processed 33000000 fragments
hits: 6110493, hits per frag:  0.185488

processed 33500000 fragments
hits: 6203029, hits per frag:  0.185682

processed 34000000 fragments
hits: 6295177, hits per frag:  0.185283

processed 34500000 fragments
hits: 6387260, hits per frag:  0.18554









[2019-03-14 21:19:07.727] [jointLog] [info] Computed 7671 rich equivalence classes for further processing
[2019-03-14 21:19:07.727] [jointLog] [info] Counted 3126572 total reads in the equivalence classes 
[2019-03-14 21:19:07.737] [jointLog] [warning] 0.0188954% of fragments were shorter than the k used to build the index (31).
If this fraction is too large, consider re-building the index with a smaller k.
The minimum read size found was 20.


[2019-03-14 21:19:07.738] [jointLog] [warning] Only 3126572 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2019-03-14 21:19:07.738] [jointLog] [info] Mapping rate = 9.05407%

[2019-03-14 21:19:07.738] [jointLog] [info] finished quantifyLibrary()
[2019-03-14 21:19:07.738] [jointLog] [info] Starting optimizer
[2019-03-14 21:19:07.744] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-03-14 21:19:07.744] [jointLog] [info] iteration = 0 | max rel diff. = 713.347
[2019-03-14 21:19:07.765] [jointLog] [info] iteration = 100 | max rel diff. = 0.115414
[2019-03-14 21:19:07.780] [jointLog] [info] iteration = 200 | max rel diff. = 0.0574996
[2019-03-14 21:19:07.796] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433144
[2019-03-14 21:19:07.811] [jointLog] [info] iteration = 400 | max rel diff. = 0.0297571
[2019-03-14 21:19:07.826] [jointLog] [info] iteration = 500 | max rel diff. = 0.0247571
[2019-03-14 21:19:07.842] [jointLog] [info] iteration = 600 | max rel diff. = 0.019155
[2019-03-14 21:19:07.859] [jointLog] [info] iteration = 700 | max rel diff. = 0.0155012
[2019-03-14 21:19:07.877] [jointLog] [info] iteration = 800 | max rel diff. = 0.0129266
[2019-03-14 21:19:07.895] [jointLog] [info] iteration = 900 | max rel diff. = 0.0101357
[2019-03-14 21:19:07.913] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0101356
[2019-03-14 21:19:07.932] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0101355
[2019-03-14 21:19:07.940] [jointLog] [info] iteration = 1143 | max rel diff. = 0.00896338
[2019-03-14 21:19:07.940] [jointLog] [info] Finished optimizer
[2019-03-14 21:19:07.940] [jointLog] [info] writing output 

[2019-03-14 21:19:07.951] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] :

Greater than 5% of the fragments disagreed with the provided library type; check the file: nb_F_K5_09/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl nb_F_K5_09/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > nb_F_K5_09/quant.sf.genes