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-P01-AGTTCC-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P01-AGTTCC-READ2-Sequences.txt.gz_val_2.fq.gz) -o male_bleached_K5_01  -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 ] => { male_bleached_K5_01 }
### [ threads ] => { 23 }
Logs will be written to male_bleached_K5_01/logs
[2019-03-14 07:46:19.860] [jointLog] [info] parsing read library format
[2019-03-14 07:46:19.860] [jointLog] [info] There is 1 library.
[2019-03-14 07:46:19.927] [stderrLog] [info] Loading Suffix Array 
[2019-03-14 07:46:19.927] [jointLog] [info] Loading Quasi index
[2019-03-14 07:46:19.927] [jointLog] [info] Loading 32-bit quasi index
[2019-03-14 07:46:19.964] [stderrLog] [info] Loading Transcript Info 
[2019-03-14 07:46:19.973] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-03-14 07:46:19.977] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-03-14 07:46:19.979] [stderrLog] [info] Computing transcript lengths
[2019-03-14 07:46:19.979] [stderrLog] [info] Waiting to finish loading hash
[2019-03-14 07:46:20.330] [jointLog] [info] done
[2019-03-14 07:46:20.330] [jointLog] [info] Index contained 5838 targets
[2019-03-14 07:46:20.330] [stderrLog] [info] Done loading index






processed 500000 fragments
hits: 96066, hits per frag:  0.212992

processed 1000000 fragments
hits: 192072, hits per frag:  0.200424

processed 1500000 fragments
hits: 287711, hits per frag:  0.206113

processed 2000000 fragments
hits: 384028, hits per frag:  0.197979

processed 2500000 fragments
hits: 480047, hits per frag:  0.199213

processed 3000001 fragments
hits: 574864, hits per frag:  0.197498

processed 3500000 fragments
hits: 671007, hits per frag:  0.19518

processed 4000000 fragments
hits: 767880, hits per frag:  0.195039

processed 4500000 fragments
hits: 863815, hits per frag:  0.195537

processed 5000001 fragments
hits: 958239, hits per frag:  0.19511

processed 5500000 fragments
hits: 1053764, hits per frag:  0.19337

processed 6000000 fragments
hits: 1149165, hits per frag:  0.193888

processed 6500001 fragments
hits: 1244434, hits per frag:  0.192663

processed 7000000 fragments
hits: 1340581, hits per frag:  0.193768

processed 7500000 fragments
hits: 1435726, hits per frag:  0.19212

processed 8000000 fragments
hits: 1532433, hits per frag:  0.192887

processed 8500000 fragments
hits: 1628303, hits per frag:  0.192561

processed 9000000 fragments
hits: 1723516, hits per frag:  0.19219

processed 9500000 fragments
hits: 1817983, hits per frag:  0.191676

processed 10000000 fragments
hits: 1913265, hits per frag:  0.193999

processed 10500001 fragments
hits: 2008622, hits per frag:  0.192309

processed 11000001 fragments
hits: 2104664, hits per frag:  0.193163

processed 11500000 fragments
hits: 2200022, hits per frag:  0.191781

processed 12000001 fragments
hits: 2295251, hits per frag:  0.191826

processed 12500001 fragments
hits: 2389899, hits per frag:  0.192561

processed 13000000 fragments
hits: 2485752, hits per frag:  0.192438

processed 13500001 fragments
hits: 2581786, hits per frag:  0.191361

processed 14000000 fragments
hits: 2676220, hits per frag:  0.192647

processed 14500001 fragments
hits: 2772463, hits per frag:  0.191469

processed 15000000 fragments
hits: 2867750, hits per frag:  0.193062

processed 15500000 fragments
hits: 2963200, hits per frag:  0.192331

processed 16000000 fragments
hits: 3059628, hits per frag:  0.191296

processed 16500000 fragments
hits: 3156089, hits per frag:  0.191352

processed 17000000 fragments
hits: 3252103, hits per frag:  0.191719

processed 17500000 fragments
hits: 3347030, hits per frag:  0.192141

processed 18000000 fragments
hits: 3442740, hits per frag:  0.191859

processed 18500001 fragments
hits: 3537853, hits per frag:  0.191696

processed 19000001 fragments
hits: 3632693, hits per frag:  0.191327

processed 19500000 fragments
hits: 3727656, hits per frag:  0.191474

processed 20000000 fragments
hits: 3823206, hits per frag:  0.192124

processed 20500000 fragments
hits: 3919085, hits per frag:  0.191576

processed 21000000 fragments
hits: 4013677, hits per frag:  0.191815

processed 21500000 fragments
hits: 4108598, hits per frag:  0.191839

processed 22000000 fragments
hits: 4204170, hits per frag:  0.191573

processed 22500000 fragments
hits: 4299725, hits per frag:  0.191244

processed 23000000 fragments
hits: 4396028, hits per frag:  0.191792

processed 23500000 fragments
hits: 4492384, hits per frag:  0.191473

processed 24000001 fragments
hits: 4587392, hits per frag:  0.191569

processed 24500000 fragments
hits: 4684371, hits per frag:  0.191593









[2019-03-14 07:47:18.170] [jointLog] [info] Computed 7374 rich equivalence classes for further processing
[2019-03-14 07:47:18.170] [jointLog] [info] Counted 2259062 total reads in the equivalence classes 
[2019-03-14 07:47:18.180] [jointLog] [warning] 0.00989258% 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 07:47:18.181] [jointLog] [warning] Only 2259062 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 07:47:18.181] [jointLog] [info] Mapping rate = 9.09192%

[2019-03-14 07:47:18.181] [jointLog] [info] finished quantifyLibrary()
[2019-03-14 07:47:18.181] [jointLog] [info] Starting optimizer
[2019-03-14 07:47:18.185] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-03-14 07:47:18.185] [jointLog] [info] iteration = 0 | max rel diff. = 556.424
[2019-03-14 07:47:18.203] [jointLog] [info] iteration = 100 | max rel diff. = 0.118712
[2019-03-14 07:47:18.217] [jointLog] [info] iteration = 200 | max rel diff. = 0.0618691
[2019-03-14 07:47:18.232] [jointLog] [info] iteration = 300 | max rel diff. = 0.0435063
[2019-03-14 07:47:18.246] [jointLog] [info] iteration = 400 | max rel diff. = 0.0267595
[2019-03-14 07:47:18.261] [jointLog] [info] iteration = 500 | max rel diff. = 0.0203617
[2019-03-14 07:47:18.275] [jointLog] [info] iteration = 600 | max rel diff. = 0.0172347
[2019-03-14 07:47:18.291] [jointLog] [info] iteration = 700 | max rel diff. = 0.0139827
[2019-03-14 07:47:18.307] [jointLog] [info] iteration = 800 | max rel diff. = 0.0120669
[2019-03-14 07:47:18.322] [jointLog] [info] iteration = 900 | max rel diff. = 0.012067
[2019-03-14 07:47:18.338] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0101034
[2019-03-14 07:47:18.340] [jointLog] [info] iteration = 1015 | max rel diff. = 0.00970062
[2019-03-14 07:47:18.341] [jointLog] [info] Finished optimizer
[2019-03-14 07:47:18.341] [jointLog] [info] writing output 

[2019-03-14 07:47:18.351] [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: male_bleached_K5_01/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl male_bleached_K5_01/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > male_bleached_K5_01/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-P06-GCCAAT-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P06-GCCAAT-READ2-Sequences.txt.gz_val_2.fq.gz) -o male_bleached_K5_02  -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 ] => { male_bleached_K5_02 }
### [ threads ] => { 23 }
Logs will be written to male_bleached_K5_02/logs
[2019-03-14 07:47:18.593] [jointLog] [info] parsing read library format
[2019-03-14 07:47:18.593] [jointLog] [info] There is 1 library.
[2019-03-14 07:47:18.659] [stderrLog] [info] Loading Suffix Array 
[2019-03-14 07:47:18.659] [jointLog] [info] Loading Quasi index
[2019-03-14 07:47:18.659] [jointLog] [info] Loading 32-bit quasi index
[2019-03-14 07:47:18.695] [stderrLog] [info] Loading Transcript Info 
[2019-03-14 07:47:18.704] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-03-14 07:47:18.708] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-03-14 07:47:18.709] [stderrLog] [info] Computing transcript lengths
[2019-03-14 07:47:18.710] [stderrLog] [info] Waiting to finish loading hash
[2019-03-14 07:47:19.065] [jointLog] [info] done
[2019-03-14 07:47:19.065] [jointLog] [info] Index contained 5838 targets
[2019-03-14 07:47:19.065] [stderrLog] [info] Done loading index






processed 500000 fragments
hits: 84795, hits per frag:  0.18674

processed 1000000 fragments
hits: 169913, hits per frag:  0.184434

processed 1500000 fragments
hits: 255912, hits per frag:  0.175886

processed 2000000 fragments
hits: 340998, hits per frag:  0.176008

processed 2500001 fragments
hits: 425525, hits per frag:  0.170547

processed 3000002 fragments
hits: 511039, hits per frag:  0.174227

processed 3500001 fragments
hits: 595726, hits per frag:  0.173506

processed 4000000 fragments
hits: 680675, hits per frag:  0.17046

processed 4500000 fragments
hits: 765460, hits per frag:  0.171866

processed 5000001 fragments
hits: 850918, hits per frag:  0.171306

processed 5500000 fragments
hits: 935795, hits per frag:  0.172257

processed 6000000 fragments
hits: 1019647, hits per frag:  0.172154

processed 6500000 fragments
hits: 1105021, hits per frag:  0.172529

processed 7000000 fragments
hits: 1190098, hits per frag:  0.17046

processed 7500000 fragments
hits: 1275445, hits per frag:  0.171056

processed 8000001 fragments
hits: 1360199, hits per frag:  0.170801

processed 8500000 fragments
hits: 1444878, hits per frag:  0.171958

processed 9000001 fragments
hits: 1529985, hits per frag:  0.171704

processed 9500000 fragments
hits: 1615325, hits per frag:  0.171822

processed 10000000 fragments
hits: 1700341, hits per frag:  0.170946

processed 10500000 fragments
hits: 1785783, hits per frag:  0.171738

processed 11000000 fragments
hits: 1870724, hits per frag:  0.170966

processed 11500000 fragments
hits: 1955949, hits per frag:  0.170489

processed 12000000 fragments
hits: 2041448, hits per frag:  0.171299

processed 12500000 fragments
hits: 2125170, hits per frag:  0.17029

processed 13000000 fragments
hits: 2209826, hits per frag:  0.170977

processed 13500000 fragments
hits: 2295152, hits per frag:  0.170751

processed 14000000 fragments
hits: 2380815, hits per frag:  0.171423

processed 14500000 fragments
hits: 2465802, hits per frag:  0.170692

processed 15000000 fragments
hits: 2552193, hits per frag:  0.171013

processed 15500000 fragments
hits: 2637118, hits per frag:  0.170493

processed 16000000 fragments
hits: 2722924, hits per frag:  0.171198

processed 16500000 fragments
hits: 2808596, hits per frag:  0.171512

processed 17000000 fragments
hits: 2893297, hits per frag:  0.170524

processed 17500000 fragments
hits: 2978075, hits per frag:  0.171132

processed 18000000 fragments
hits: 3064254, hits per frag:  0.170982









[2019-03-14 07:48:02.621] [jointLog] [info] Computed 7296 rich equivalence classes for further processing
[2019-03-14 07:48:02.621] [jointLog] [info] Counted 1550851 total reads in the equivalence classes 
[2019-03-14 07:48:02.630] [jointLog] [warning] 0.0114771% 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 07:48:02.631] [jointLog] [warning] Only 1550851 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 07:48:02.631] [jointLog] [info] Mapping rate = 8.4437%

[2019-03-14 07:48:02.631] [jointLog] [info] finished quantifyLibrary()
[2019-03-14 07:48:02.631] [jointLog] [info] Starting optimizer
[2019-03-14 07:48:02.636] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-03-14 07:48:02.636] [jointLog] [info] iteration = 0 | max rel diff. = 415.309
[2019-03-14 07:48:02.656] [jointLog] [info] iteration = 100 | max rel diff. = 0.123527
[2019-03-14 07:48:02.672] [jointLog] [info] iteration = 200 | max rel diff. = 0.0531559
[2019-03-14 07:48:02.687] [jointLog] [info] iteration = 300 | max rel diff. = 0.0391319
[2019-03-14 07:48:02.702] [jointLog] [info] iteration = 400 | max rel diff. = 0.028226
[2019-03-14 07:48:02.717] [jointLog] [info] iteration = 500 | max rel diff. = 0.0208174
[2019-03-14 07:48:02.731] [jointLog] [info] iteration = 600 | max rel diff. = 0.0169562
[2019-03-14 07:48:02.746] [jointLog] [info] iteration = 700 | max rel diff. = 0.0151658
[2019-03-14 07:48:02.761] [jointLog] [info] iteration = 800 | max rel diff. = 0.0115074
[2019-03-14 07:48:02.775] [jointLog] [info] iteration = 900 | max rel diff. = 0.0113233
[2019-03-14 07:48:02.788] [jointLog] [info] iteration = 987 | max rel diff. = 0.00949143
[2019-03-14 07:48:02.788] [jointLog] [info] Finished optimizer
[2019-03-14 07:48:02.788] [jointLog] [info] writing output 

[2019-03-14 07:48:02.799] [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: male_bleached_K5_02/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl male_bleached_K5_02/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > male_bleached_K5_02/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-P07-AGTCAA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P07-AGTCAA-READ2-Sequences.txt.gz_val_2.fq.gz) -o male_bleached_K5_03  -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 ] => { male_bleached_K5_03 }
### [ threads ] => { 23 }
Logs will be written to male_bleached_K5_03/logs
[2019-03-14 07:48:03.295] [jointLog] [info] parsing read library format
[2019-03-14 07:48:03.295] [jointLog] [info] There is 1 library.
[2019-03-14 07:48:03.361] [stderrLog] [info] Loading Suffix Array 
[2019-03-14 07:48:03.361] [jointLog] [info] Loading Quasi index
[2019-03-14 07:48:03.361] [jointLog] [info] Loading 32-bit quasi index
[2019-03-14 07:48:03.397] [stderrLog] [info] Loading Transcript Info 
[2019-03-14 07:48:03.406] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-03-14 07:48:03.410] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-03-14 07:48:03.412] [stderrLog] [info] Computing transcript lengths
[2019-03-14 07:48:03.412] [stderrLog] [info] Waiting to finish loading hash
[2019-03-14 07:48:03.765] [jointLog] [info] done
[2019-03-14 07:48:03.765] [jointLog] [info] Index contained 5838 targets




[2019-03-14 07:48:03.765] [stderrLog] [info] Done loading index


processed 500000 fragments
hits: 97477, hits per frag:  0.198503

processed 1000002 fragments
hits: 195163, hits per frag:  0.209573

processed 1500000 fragments
hits: 294177, hits per frag:  0.212027

processed 2000000 fragments
hits: 392754, hits per frag:  0.205193

processed 2500000 fragments
hits: 492012, hits per frag:  0.20243

processed 3000000 fragments
hits: 590943, hits per frag:  0.203971

processed 3500000 fragments
hits: 688351, hits per frag:  0.19885

processed 4000000 fragments
hits: 786020, hits per frag:  0.199521

processed 4500000 fragments
hits: 883541, hits per frag:  0.199087

processed 5000000 fragments
hits: 982284, hits per frag:  0.200351

processed 5500000 fragments
hits: 1080394, hits per frag:  0.201546

processed 6000000 fragments
hits: 1178530, hits per frag:  0.198076

processed 6500000 fragments
hits: 1276360, hits per frag:  0.197087

processed 7000000 fragments
hits: 1375152, hits per frag:  0.199352

processed 7500000 fragments
hits: 1472015, hits per frag:  0.197689

processed 8000000 fragments
hits: 1569404, hits per frag:  0.198224

processed 8500000 fragments
hits: 1667327, hits per frag:  0.198076

processed 9000000 fragments
hits: 1765715, hits per frag:  0.19713

processed 9500000 fragments
hits: 1864146, hits per frag:  0.1966

processed 10000000 fragments
hits: 1961607, hits per frag:  0.196788

processed 10500000 fragments
hits: 2060578, hits per frag:  0.197121

processed 11000000 fragments
hits: 2160379, hits per frag:  0.197761

processed 11500000 fragments
hits: 2259469, hits per frag:  0.197901

processed 12000000 fragments
hits: 2357404, hits per frag:  0.197107

processed 12500000 fragments
hits: 2456268, hits per frag:  0.197174

processed 13000001 fragments
hits: 2554295, hits per frag:  0.198021

processed 13500000 fragments
hits: 2651927, hits per frag:  0.197314

processed 14000001 fragments
hits: 2749706, hits per frag:  0.197669

processed 14500000 fragments
hits: 2848426, hits per frag:  0.197297

processed 15000000 fragments
hits: 2946038, hits per frag:  0.197842

processed 15500000 fragments
hits: 3044545, hits per frag:  0.197913

processed 16000001 fragments
hits: 3141972, hits per frag:  0.196709

processed 16500000 fragments
hits: 3239889, hits per frag:  0.19703

processed 17000000 fragments
hits: 3337558, hits per frag:  0.197349

processed 17500000 fragments
hits: 3435793, hits per frag:  0.196886

processed 18000000 fragments
hits: 3532758, hits per frag:  0.197042

processed 18500001 fragments
hits: 3631334, hits per frag:  0.197028

processed 19000001 fragments
hits: 3730508, hits per frag:  0.19693

processed 19500000 fragments
hits: 3828512, hits per frag:  0.196857

processed 20000000 fragments
hits: 3926560, hits per frag:  0.196805

processed 20500000 fragments
hits: 4023847, hits per frag:  0.197628

processed 21000000 fragments
hits: 4122201, hits per frag:  0.197306

processed 21500000 fragments
hits: 4219809, hits per frag:  0.197338

processed 22000000 fragments
hits: 4317908, hits per frag:  0.196904

processed 22500000 fragments
hits: 4416325, hits per frag:  0.19691

processed 23000000 fragments
hits: 4514895, hits per frag:  0.196867

processed 23500000 fragments
hits: 4612622, hits per frag:  0.196399

processed 24000000 fragments
hits: 4710745, hits per frag:  0.197007

processed 24500000 fragments
hits: 4808010, hits per frag:  0.196476

processed 25000000 fragments
hits: 4906337, hits per frag:  0.196793

processed 25500001 fragments
hits: 5003743, hits per frag:  0.196339









[2019-03-14 07:49:05.922] [jointLog] [info] Computed 7398 rich equivalence classes for further processing
[2019-03-14 07:49:05.922] [jointLog] [info] Counted 2479140 total reads in the equivalence classes 
[2019-03-14 07:49:05.932] [jointLog] [warning] 0.0136297% 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 07:49:05.932] [jointLog] [warning] Only 2479140 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 07:49:05.932] [jointLog] [info] Mapping rate = 9.56952%

[2019-03-14 07:49:05.932] [jointLog] [info] finished quantifyLibrary()
[2019-03-14 07:49:05.933] [jointLog] [info] Starting optimizer
[2019-03-14 07:49:05.938] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-03-14 07:49:05.938] [jointLog] [info] iteration = 0 | max rel diff. = 615.834
[2019-03-14 07:49:05.956] [jointLog] [info] iteration = 100 | max rel diff. = 0.117134
[2019-03-14 07:49:05.972] [jointLog] [info] iteration = 200 | max rel diff. = 0.0572327
[2019-03-14 07:49:05.990] [jointLog] [info] iteration = 300 | max rel diff. = 0.037784
[2019-03-14 07:49:06.007] [jointLog] [info] iteration = 400 | max rel diff. = 0.02534
[2019-03-14 07:49:06.025] [jointLog] [info] iteration = 500 | max rel diff. = 0.0214197
[2019-03-14 07:49:06.042] [jointLog] [info] iteration = 600 | max rel diff. = 0.017772
[2019-03-14 07:49:06.060] [jointLog] [info] iteration = 700 | max rel diff. = 0.0152762
[2019-03-14 07:49:06.077] [jointLog] [info] iteration = 800 | max rel diff. = 0.0123923
[2019-03-14 07:49:06.095] [jointLog] [info] iteration = 900 | max rel diff. = 0.0119455
[2019-03-14 07:49:06.112] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0106927
[2019-03-14 07:49:06.117] [jointLog] [info] iteration = 1027 | max rel diff. = 0.00914205
[2019-03-14 07:49:06.117] [jointLog] [info] Finished optimizer
[2019-03-14 07:49:06.117] [jointLog] [info] writing output 

[2019-03-14 07:49:06.128] [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: male_bleached_K5_03/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl male_bleached_K5_03/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > male_bleached_K5_03/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-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 female_bleached_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 ] => { female_bleached_K5_04 }
### [ threads ] => { 23 }
Logs will be written to female_bleached_K5_04/logs
[2019-03-14 07:49:06.616] [jointLog] [info] parsing read library format
[2019-03-14 07:49:06.616] [jointLog] [info] There is 1 library.
[2019-03-14 07:49:06.683] [stderrLog] [info] Loading Suffix Array 
[2019-03-14 07:49:06.683] [jointLog] [info] Loading Quasi index
[2019-03-14 07:49:06.683] [jointLog] [info] Loading 32-bit quasi index
[2019-03-14 07:49:06.723] [stderrLog] [info] Loading Transcript Info 
[2019-03-14 07:49:06.733] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-03-14 07:49:06.736] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-03-14 07:49:06.738] [stderrLog] [info] Computing transcript lengths
[2019-03-14 07:49:06.738] [stderrLog] [info] Waiting to finish loading hash
[2019-03-14 07:49:07.075] [jointLog] [info] done
[2019-03-14 07:49:07.075] [jointLog] [info] Index contained 5838 targets




[2019-03-14 07:49:07.075] [stderrLog] [info] Done loading index


processed 500000 fragments
hits: 96372, hits per frag:  0.224853

processed 1000000 fragments
hits: 192499, hits per frag:  0.219698

processed 1500000 fragments
hits: 289387, hits per frag:  0.199702

processed 2000000 fragments
hits: 385822, hits per frag:  0.195752

processed 2500000 fragments
hits: 481942, hits per frag:  0.195096

processed 3000001 fragments
hits: 577884, hits per frag:  0.19851

processed 3500000 fragments
hits: 673391, hits per frag:  0.194247

processed 4000000 fragments
hits: 770460, hits per frag:  0.197779

processed 4500000 fragments
hits: 867691, hits per frag:  0.195097

processed 5000000 fragments
hits: 963895, hits per frag:  0.197278

processed 5500000 fragments
hits: 1060867, hits per frag:  0.194289

processed 6000000 fragments
hits: 1157709, hits per frag:  0.193413

processed 6500000 fragments
hits: 1253637, hits per frag:  0.195344

processed 7000000 fragments
hits: 1351198, hits per frag:  0.194569

processed 7500000 fragments
hits: 1447856, hits per frag:  0.194386

processed 8000000 fragments
hits: 1543397, hits per frag:  0.195313

processed 8500002 fragments
hits: 1638981, hits per frag:  0.195868

processed 9000000 fragments
hits: 1735151, hits per frag:  0.193463

processed 9500000 fragments
hits: 1831442, hits per frag:  0.193669

processed 10000000 fragments
hits: 1926808, hits per frag:  0.193645

processed 10500000 fragments
hits: 2022099, hits per frag:  0.193168

processed 11000001 fragments
hits: 2118361, hits per frag:  0.193513

processed 11500000 fragments
hits: 2215408, hits per frag:  0.194944

processed 12000000 fragments
hits: 2312082, hits per frag:  0.193482

processed 12500000 fragments
hits: 2406371, hits per frag:  0.193489

processed 13000000 fragments
hits: 2501286, hits per frag:  0.192886

processed 13500000 fragments
hits: 2597605, hits per frag:  0.192793

processed 14000000 fragments
hits: 2694018, hits per frag:  0.193762

processed 14500000 fragments
hits: 2790496, hits per frag:  0.193053

processed 15000001 fragments
hits: 2886996, hits per frag:  0.192836

processed 15500000 fragments
hits: 2983009, hits per frag:  0.193

processed 16000000 fragments
hits: 3078523, hits per frag:  0.193247

processed 16500000 fragments
hits: 3174707, hits per frag:  0.194945

processed 17000000 fragments
hits: 3270740, hits per frag:  0.193476

processed 17500001 fragments
hits: 3366895, hits per frag:  0.193275

processed 18000000 fragments
hits: 3463062, hits per frag:  0.192686

processed 18500000 fragments
hits: 3558892, hits per frag:  0.193376

processed 19000000 fragments
hits: 3655550, hits per frag:  0.193376

processed 19500000 fragments
hits: 3751275, hits per frag:  0.194249

processed 20000001 fragments
hits: 3847905, hits per frag:  0.192808

processed 20500000 fragments
hits: 3944524, hits per frag:  0.19283

processed 21000000 fragments
hits: 4040776, hits per frag:  0.192918

processed 21500001 fragments
hits: 4137750, hits per frag:  0.193199

processed 22000000 fragments
hits: 4233667, hits per frag:  0.193393

processed 22500000 fragments
hits: 4329667, hits per frag:  0.192934

processed 23000000 fragments
hits: 4426385, hits per frag:  0.192708

processed 23500000 fragments
hits: 4522504, hits per frag:  0.19294

processed 24000000 fragments
hits: 4618647, hits per frag:  0.193066

processed 24500000 fragments
hits: 4714971, hits per frag:  0.192906

processed 25000001 fragments
hits: 4812131, hits per frag:  0.192949

processed 25500000 fragments
hits: 4908642, hits per frag:  0.192723

processed 26000000 fragments
hits: 5004217, hits per frag:  0.193197

processed 26500000 fragments
hits: 5101240, hits per frag:  0.192726

processed 27000000 fragments
hits: 5197144, hits per frag:  0.193267

processed 27500000 fragments
hits: 5292266, hits per frag:  0.192951

processed 28000000 fragments
hits: 5389117, hits per frag:  0.192716









[2019-03-14 07:50:15.657] [jointLog] [info] Computed 7401 rich equivalence classes for further processing
[2019-03-14 07:50:15.657] [jointLog] [info] Counted 2716216 total reads in the equivalence classes 
[2019-03-14 07:50:15.667] [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 07:50:15.668] [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 07:50:15.668] [jointLog] [info] Mapping rate = 9.59013%

[2019-03-14 07:50:15.668] [jointLog] [info] finished quantifyLibrary()
[2019-03-14 07:50:15.668] [jointLog] [info] Starting optimizer
[2019-03-14 07:50:15.672] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-03-14 07:50:15.673] [jointLog] [info] iteration = 0 | max rel diff. = 623.231
[2019-03-14 07:50:15.691] [jointLog] [info] iteration = 100 | max rel diff. = 0.126924
[2019-03-14 07:50:15.707] [jointLog] [info] iteration = 200 | max rel diff. = 0.063358
[2019-03-14 07:50:15.723] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433714
[2019-03-14 07:50:15.738] [jointLog] [info] iteration = 400 | max rel diff. = 0.0310132
[2019-03-14 07:50:15.753] [jointLog] [info] iteration = 500 | max rel diff. = 0.0246222
[2019-03-14 07:50:15.768] [jointLog] [info] iteration = 600 | max rel diff. = 0.0180039
[2019-03-14 07:50:15.783] [jointLog] [info] iteration = 700 | max rel diff. = 0.0152048
[2019-03-14 07:50:15.799] [jointLog] [info] iteration = 800 | max rel diff. = 0.0121776
[2019-03-14 07:50:15.814] [jointLog] [info] iteration = 900 | max rel diff. = 0.0118751
[2019-03-14 07:50:15.829] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0110757
[2019-03-14 07:50:15.835] [jointLog] [info] iteration = 1034 | max rel diff. = 0.00984625
[2019-03-14 07:50:15.835] [jointLog] [info] Finished optimizer
[2019-03-14 07:50:15.835] [jointLog] [info] writing output 

[2019-03-14 07:50:15.846] [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: female_bleached_K5_04/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl female_bleached_K5_04/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > female_bleached_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 female_bleached_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 ] => { female_bleached_K5_05 }
### [ threads ] => { 23 }
Logs will be written to female_bleached_K5_05/logs
[2019-03-14 07:50:16.139] [jointLog] [info] parsing read library format
[2019-03-14 07:50:16.139] [jointLog] [info] There is 1 library.
[2019-03-14 07:50:16.206] [stderrLog] [info] Loading Suffix Array 
[2019-03-14 07:50:16.206] [jointLog] [info] Loading Quasi index
[2019-03-14 07:50:16.206] [jointLog] [info] Loading 32-bit quasi index
[2019-03-14 07:50:16.248] [stderrLog] [info] Loading Transcript Info 
[2019-03-14 07:50:16.258] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-03-14 07:50:16.262] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-03-14 07:50:16.264] [stderrLog] [info] Computing transcript lengths
[2019-03-14 07:50:16.264] [stderrLog] [info] Waiting to finish loading hash
[2019-03-14 07:50:16.624] [stderrLog] [info] Done loading index




[2019-03-14 07:50:16.624] [jointLog] [info] done
[2019-03-14 07:50:16.624] [jointLog] [info] Index contained 5838 targets


processed 500000 fragments
hits: 88719, hits per frag:  0.214713

processed 1000000 fragments
hits: 177954, hits per frag:  0.178668

processed 1500001 fragments
hits: 265464, hits per frag:  0.18064

processed 2000000 fragments
hits: 354136, hits per frag:  0.185483

processed 2500000 fragments
hits: 442324, hits per frag:  0.185368

processed 3000000 fragments
hits: 531364, hits per frag:  0.181391

processed 3500000 fragments
hits: 619408, hits per frag:  0.180571

processed 4000000 fragments
hits: 706952, hits per frag:  0.178882

processed 4500000 fragments
hits: 796458, hits per frag:  0.179743

processed 5000000 fragments
hits: 884782, hits per frag:  0.180595

processed 5500000 fragments
hits: 972779, hits per frag:  0.178674

processed 6000000 fragments
hits: 1061327, hits per frag:  0.179253

processed 6500001 fragments
hits: 1150077, hits per frag:  0.178657

processed 7000001 fragments
hits: 1238239, hits per frag:  0.177441

processed 7500001 fragments
hits: 1326006, hits per frag:  0.17775

processed 8000001 fragments
hits: 1414141, hits per frag:  0.179339

processed 8500000 fragments
hits: 1502621, hits per frag:  0.177795

processed 9000000 fragments
hits: 1591912, hits per frag:  0.177641

processed 9500000 fragments
hits: 1680350, hits per frag:  0.177089

processed 10000000 fragments
hits: 1768790, hits per frag:  0.177108

processed 10500001 fragments
hits: 1856601, hits per frag:  0.178497

processed 11000001 fragments
hits: 1943744, hits per frag:  0.177185

processed 11500000 fragments
hits: 2031731, hits per frag:  0.17764

processed 12000000 fragments
hits: 2119210, hits per frag:  0.176803

processed 12500000 fragments
hits: 2207321, hits per frag:  0.177293

processed 13000000 fragments
hits: 2294894, hits per frag:  0.177514

processed 13500000 fragments
hits: 2382921, hits per frag:  0.177565

processed 14000000 fragments
hits: 2470709, hits per frag:  0.177661

processed 14500000 fragments
hits: 2559344, hits per frag:  0.177099

processed 15000000 fragments
hits: 2647984, hits per frag:  0.177649

processed 15500000 fragments
hits: 2735970, hits per frag:  0.177426

processed 16000000 fragments
hits: 2824293, hits per frag:  0.177522

processed 16500000 fragments
hits: 2913049, hits per frag:  0.177249

processed 17000000 fragments
hits: 3001330, hits per frag:  0.176912

processed 17500000 fragments
hits: 3089627, hits per frag:  0.177478

processed 18000000 fragments
hits: 3177806, hits per frag:  0.177349

processed 18500000 fragments
hits: 3265062, hits per frag:  0.17713

processed 19000000 fragments
hits: 3352245, hits per frag:  0.177403

processed 19500001 fragments
hits: 3440154, hits per frag:  0.177778

processed 20000000 fragments
hits: 3527540, hits per frag:  0.177031

processed 20500000 fragments
hits: 3615081, hits per frag:  0.176638

processed 21000000 fragments
hits: 3702982, hits per frag:  0.176692









[2019-03-14 07:51:08.957] [jointLog] [info] Computed 6922 rich equivalence classes for further processing
[2019-03-14 07:51:08.957] [jointLog] [info] Counted 1916701 total reads in the equivalence classes 
[2019-03-14 07:51:08.967] [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 07:51:08.968] [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 07:51:08.968] [jointLog] [info] Mapping rate = 8.75913%

[2019-03-14 07:51:08.968] [jointLog] [info] finished quantifyLibrary()
[2019-03-14 07:51:08.968] [jointLog] [info] Starting optimizer
[2019-03-14 07:51:08.974] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-03-14 07:51:08.974] [jointLog] [info] iteration = 0 | max rel diff. = 428.663
[2019-03-14 07:51:08.993] [jointLog] [info] iteration = 100 | max rel diff. = 0.112614
[2019-03-14 07:51:09.010] [jointLog] [info] iteration = 200 | max rel diff. = 0.0561104
[2019-03-14 07:51:09.025] [jointLog] [info] iteration = 300 | max rel diff. = 0.0366457
[2019-03-14 07:51:09.040] [jointLog] [info] iteration = 400 | max rel diff. = 0.0243093
[2019-03-14 07:51:09.056] [jointLog] [info] iteration = 500 | max rel diff. = 0.0243107
[2019-03-14 07:51:09.071] [jointLog] [info] iteration = 600 | max rel diff. = 0.0175284
[2019-03-14 07:51:09.086] [jointLog] [info] iteration = 700 | max rel diff. = 0.0150941
[2019-03-14 07:51:09.101] [jointLog] [info] iteration = 800 | max rel diff. = 0.0129989
[2019-03-14 07:51:09.116] [jointLog] [info] iteration = 900 | max rel diff. = 0.0117464
[2019-03-14 07:51:09.131] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0117466
[2019-03-14 07:51:09.140] [jointLog] [info] iteration = 1050 | max rel diff. = 0.00947599
[2019-03-14 07:51:09.140] [jointLog] [info] Finished optimizer
[2019-03-14 07:51:09.140] [jointLog] [info] writing output 

[2019-03-14 07:51:09.151] [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: female_bleached_K5_05/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl female_bleached_K5_05/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > female_bleached_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 female_bleached_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 ] => { female_bleached_K5_06 }
### [ threads ] => { 23 }
Logs will be written to female_bleached_K5_06/logs
[2019-03-14 07:51:09.666] [jointLog] [info] parsing read library format
[2019-03-14 07:51:09.666] [jointLog] [info] There is 1 library.
[2019-03-14 07:51:09.734] [stderrLog] [info] Loading Suffix Array 
[2019-03-14 07:51:09.733] [jointLog] [info] Loading Quasi index
[2019-03-14 07:51:09.734] [jointLog] [info] Loading 32-bit quasi index
[2019-03-14 07:51:09.772] [stderrLog] [info] Loading Transcript Info 
[2019-03-14 07:51:09.782] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-03-14 07:51:09.786] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-03-14 07:51:09.788] [stderrLog] [info] Computing transcript lengths
[2019-03-14 07:51:09.788] [stderrLog] [info] Waiting to finish loading hash
[2019-03-14 07:51:10.123] [jointLog] [info] done
[2019-03-14 07:51:10.123] [jointLog] [info] Index contained 5838 targets




[2019-03-14 07:51:10.123] [stderrLog] [info] Done loading index


processed 500000 fragments
hits: 74582, hits per frag:  0.178033

processed 1000000 fragments
hits: 149583, hits per frag:  0.164965

processed 1500000 fragments
hits: 224829, hits per frag:  0.153829

processed 2000000 fragments
hits: 298950, hits per frag:  0.153434

processed 2500000 fragments
hits: 373792, hits per frag:  0.153695

processed 3000001 fragments
hits: 447987, hits per frag:  0.156108

processed 3500000 fragments
hits: 522449, hits per frag:  0.149913

processed 4000000 fragments
hits: 595311, hits per frag:  0.150412

processed 4500000 fragments
hits: 669143, hits per frag:  0.150934

processed 5000000 fragments
hits: 744482, hits per frag:  0.150365

processed 5500000 fragments
hits: 819714, hits per frag:  0.149929

processed 6000000 fragments
hits: 894795, hits per frag:  0.150399

processed 6500000 fragments
hits: 968481, hits per frag:  0.150729

processed 7000000 fragments
hits: 1042037, hits per frag:  0.149763

processed 7500000 fragments
hits: 1116191, hits per frag:  0.150785

processed 8000000 fragments
hits: 1189915, hits per frag:  0.150577

processed 8500000 fragments
hits: 1262826, hits per frag:  0.149822

processed 9000000 fragments
hits: 1338093, hits per frag:  0.150509

processed 9500000 fragments
hits: 1413030, hits per frag:  0.149153

processed 10000000 fragments
hits: 1487514, hits per frag:  0.149873

processed 10500000 fragments
hits: 1561583, hits per frag:  0.149852

processed 11000000 fragments
hits: 1636034, hits per frag:  0.149645

processed 11500000 fragments
hits: 1710202, hits per frag:  0.149791

processed 12000000 fragments
hits: 1783825, hits per frag:  0.148906

processed 12500000 fragments
hits: 1857716, hits per frag:  0.149553

processed 13000000 fragments
hits: 1930674, hits per frag:  0.148927

processed 13500000 fragments
hits: 2006530, hits per frag:  0.148946

processed 14000000 fragments
hits: 2081184, hits per frag:  0.1498

processed 14500000 fragments
hits: 2156397, hits per frag:  0.149716

processed 15000000 fragments
hits: 2230565, hits per frag:  0.149133

processed 15500000 fragments
hits: 2304290, hits per frag:  0.149534

processed 16000000 fragments
hits: 2377880, hits per frag:  0.149361

processed 16500000 fragments
hits: 2451283, hits per frag:  0.149351

processed 17000000 fragments
hits: 2524226, hits per frag:  0.1489









[2019-03-14 07:51:49.754] [jointLog] [info] Computed 6627 rich equivalence classes for further processing
[2019-03-14 07:51:49.754] [jointLog] [info] Counted 1294477 total reads in the equivalence classes 
[2019-03-14 07:51:49.764] [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 07:51:49.764] [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 07:51:49.764] [jointLog] [info] Mapping rate = 7.48881%

[2019-03-14 07:51:49.764] [jointLog] [info] finished quantifyLibrary()
[2019-03-14 07:51:49.765] [jointLog] [info] Starting optimizer
[2019-03-14 07:51:49.769] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-03-14 07:51:49.770] [jointLog] [info] iteration = 0 | max rel diff. = 305.918
[2019-03-14 07:51:49.787] [jointLog] [info] iteration = 100 | max rel diff. = 0.113947
[2019-03-14 07:51:49.802] [jointLog] [info] iteration = 200 | max rel diff. = 0.0606269
[2019-03-14 07:51:49.816] [jointLog] [info] iteration = 300 | max rel diff. = 0.0432703
[2019-03-14 07:51:49.831] [jointLog] [info] iteration = 400 | max rel diff. = 0.0293281
[2019-03-14 07:51:49.846] [jointLog] [info] iteration = 500 | max rel diff. = 0.0218206
[2019-03-14 07:51:49.861] [jointLog] [info] iteration = 600 | max rel diff. = 0.0174288
[2019-03-14 07:51:49.876] [jointLog] [info] iteration = 700 | max rel diff. = 0.0147404
[2019-03-14 07:51:49.891] [jointLog] [info] iteration = 800 | max rel diff. = 0.0118515
[2019-03-14 07:51:49.908] [jointLog] [info] iteration = 900 | max rel diff. = 0.0111468
[2019-03-14 07:51:49.926] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0113525
[2019-03-14 07:51:49.942] [jointLog] [info] iteration = 1091 | max rel diff. = 0.00876308
[2019-03-14 07:51:49.942] [jointLog] [info] Finished optimizer
[2019-03-14 07:51:49.942] [jointLog] [info] writing output 

[2019-03-14 07:51:49.953] [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: female_bleached_K5_06/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl female_bleached_K5_06/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > female_bleached_K5_06/quant.sf.genes