CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/get_Trinity_gene_to_trans_map.pl /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta > /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map
CMD: salmon index -t /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx --type quasi -k 31 -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.
###
index ["/media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx"] did not previously exist  . . . creating it
[2019-01-30 21:09:07.237] [jLog] [info] building index
RapMap Indexer

[Step 1 of 4] : counting k-mers
Elapsed time: 0.677656s

Replaced 0 non-ATCG nucleotides
Clipped poly-A tails from 5 transcripts
Building rank-select dictionary and saving to disk done
Elapsed time: 0.000857991s
Writing sequence data to file . . . done
Elapsed time: 0.00843078s
[info] Building 32-bit suffix array (length of generalized text is 13191960)
Building suffix array . . . success
saving to disk . . . done
Elapsed time: 0.0309615s
done
Elapsed time: 1.18323s


processed 0 positions

processed 1000000 positions

processed 2000000 positions

processed 3000000 positions

processed 4000000 positions

processed 5000000 positions

processed 6000000 positions

processed 7000000 positions

processed 8000000 positions

processed 9000000 positions

processed 10000000 positions

processed 11000000 positions

processed 12000000 positions

processed 13000000 positions
khash had 7291711 keys
saving hash to disk . . . done
Elapsed time: 0.417489s
[2019-01-30 21:09:24.258] [jLog] [info] done building index
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 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 ] => { bleached_K5_01 }
### [ threads ] => { 23 }
Logs will be written to bleached_K5_01/logs
[2019-01-30 21:09:24.289] [jointLog] [info] parsing read library format
[2019-01-30 21:09:24.289] [jointLog] [info] There is 1 library.
[2019-01-30 21:09:24.350] [stderrLog] [info] Loading Suffix Array 
[2019-01-30 21:09:24.350] [jointLog] [info] Loading Quasi index
[2019-01-30 21:09:24.350] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:09:24.390] [stderrLog] [info] Loading Transcript Info 
[2019-01-30 21:09:24.400] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-01-30 21:09:24.403] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-01-30 21:09:24.405] [stderrLog] [info] Computing transcript lengths
[2019-01-30 21:09:24.405] [stderrLog] [info] Waiting to finish loading hash
[2019-01-30 21:09:24.747] [jointLog] [info] done
[2019-01-30 21:09:24.747] [jointLog] [info] Index contained 5838 targets




[2019-01-30 21:09:24.747] [stderrLog] [info] Done loading index


processed 500001 fragments
hits: 144905, hits per frag:  0.304553

processed 1000000 fragments
hits: 192128, hits per frag:  0.211677

processed 1500000 fragments
hits: 287819, hits per frag:  0.197027

processed 2000000 fragments
hits: 383955, hits per frag:  0.200056

processed 2500000 fragments
hits: 480105, hits per frag:  0.194121

processed 3000001 fragments
hits: 574812, hits per frag:  0.19428

processed 3500000 fragments
hits: 671024, hits per frag:  0.193222

processed 4000000 fragments
hits: 767941, hits per frag:  0.195392

processed 4500000 fragments
hits: 863744, hits per frag:  0.194765

processed 5000000 fragments
hits: 958238, hits per frag:  0.196151

processed 5500000 fragments
hits: 1053824, hits per frag:  0.192519

processed 6000000 fragments
hits: 1149261, hits per frag:  0.193516

processed 6500000 fragments
hits: 1244528, hits per frag:  0.193067

processed 7000000 fragments
hits: 1340501, hits per frag:  0.193391

processed 7500000 fragments
hits: 1435359, hits per frag:  0.192964

processed 8000000 fragments
hits: 1532327, hits per frag:  0.194235

processed 8500001 fragments
hits: 1628264, hits per frag:  0.192175

processed 9000000 fragments
hits: 1723596, hits per frag:  0.191656

processed 9500000 fragments
hits: 1817984, hits per frag:  0.191804

processed 10000000 fragments
hits: 1913284, hits per frag:  0.193067

processed 10500000 fragments
hits: 2008646, hits per frag:  0.193069

processed 11000000 fragments
hits: 2104714, hits per frag:  0.192731

processed 11500001 fragments
hits: 2200030, hits per frag:  0.192438

processed 12000000 fragments
hits: 2295244, hits per frag:  0.191678

processed 12500001 fragments
hits: 2389842, hits per frag:  0.191641

processed 13000000 fragments
hits: 2485755, hits per frag:  0.191917

processed 13500000 fragments
hits: 2581722, hits per frag:  0.191753

processed 14000000 fragments
hits: 2676110, hits per frag:  0.192517

processed 14500000 fragments
hits: 2772567, hits per frag:  0.192065

processed 15000000 fragments
hits: 2867775, hits per frag:  0.191461

processed 15500000 fragments
hits: 2963253, hits per frag:  0.192898

processed 16000001 fragments
hits: 3059541, hits per frag:  0.191726

processed 16500000 fragments
hits: 3156126, hits per frag:  0.191773

processed 17000000 fragments
hits: 3252098, hits per frag:  0.192222

processed 17500000 fragments
hits: 3347019, hits per frag:  0.191932

processed 18000000 fragments
hits: 3442803, hits per frag:  0.192358

processed 18500001 fragments
hits: 3537902, hits per frag:  0.191557

processed 19000000 fragments
hits: 3632736, hits per frag:  0.191583

processed 19500000 fragments
hits: 3727713, hits per frag:  0.191468

processed 20000000 fragments
hits: 3823259, hits per frag:  0.191192

processed 20500001 fragments
hits: 3918993, hits per frag:  0.19201

processed 21000000 fragments
hits: 4013642, hits per frag:  0.191258

processed 21500000 fragments
hits: 4108600, hits per frag:  0.191297

processed 22000000 fragments
hits: 4204224, hits per frag:  0.191946

processed 22000044 fragments
hits: 4204242, hits per frag:  0.191349

processed 22500000 fragments
hits: 4299823, hits per frag:  0.191965

processed 23000000 fragments
hits: 4396059, hits per frag:  0.19203

processed 23500000 fragments
hits: 4492280, hits per frag:  0.192364

processed 24000000 fragments
hits: 4587383, hits per frag:  0.191388

processed 24500000 fragments
hits: 4684506, hits per frag:  0.19194









[2019-01-30 21:10:24.843] [jointLog] [info] Computed 7374 rich equivalence classes for further processing
[2019-01-30 21:10:24.843] [jointLog] [info] Counted 2259062 total reads in the equivalence classes 
[2019-01-30 21:10:24.854] [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.


[2019-01-30 21:10:24.855] [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.

[2019-01-30 21:10:24.855] [jointLog] [info] Mapping rate = 9.09192%

[2019-01-30 21:10:24.855] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:10:24.855] [jointLog] [info] Starting optimizer
[2019-01-30 21:10:24.861] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:10:24.861] [jointLog] [info] iteration = 0 | max rel diff. = 556.404
[2019-01-30 21:10:24.882] [jointLog] [info] iteration = 100 | max rel diff. = 0.11871
[2019-01-30 21:10:24.897] [jointLog] [info] iteration = 200 | max rel diff. = 0.0618657
[2019-01-30 21:10:24.912] [jointLog] [info] iteration = 300 | max rel diff. = 0.0435088
[2019-01-30 21:10:24.927] [jointLog] [info] iteration = 400 | max rel diff. = 0.0267594
[2019-01-30 21:10:24.943] [jointLog] [info] iteration = 500 | max rel diff. = 0.0203618
[2019-01-30 21:10:24.960] [jointLog] [info] iteration = 600 | max rel diff. = 0.0172348
[2019-01-30 21:10:24.978] [jointLog] [info] iteration = 700 | max rel diff. = 0.0139803
[2019-01-30 21:10:24.995] [jointLog] [info] iteration = 800 | max rel diff. = 0.0121048
[2019-01-30 21:10:25.013] [jointLog] [info] iteration = 900 | max rel diff. = 0.0120494
[2019-01-30 21:10:25.030] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0101032
[2019-01-30 21:10:25.033] [jointLog] [info] iteration = 1015 | max rel diff. = 0.00970086
[2019-01-30 21:10:25.033] [jointLog] [info] Finished optimizer
[2019-01-30 21:10:25.033] [jointLog] [info] writing output 

[2019-01-30 21:10:25.044] [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: 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 bleached_K5_01/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > 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 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 ] => { bleached_K5_02 }
### [ threads ] => { 23 }
Logs will be written to bleached_K5_02/logs
[2019-01-30 21:10:25.436] [jointLog] [info] parsing read library format
[2019-01-30 21:10:25.436] [jointLog] [info] There is 1 library.
[2019-01-30 21:10:25.497] [stderrLog] [info] Loading Suffix Array 
[2019-01-30 21:10:25.497] [jointLog] [info] Loading Quasi index
[2019-01-30 21:10:25.497] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:10:25.533] [stderrLog] [info] Loading Transcript Info 
[2019-01-30 21:10:25.542] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-01-30 21:10:25.545] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-01-30 21:10:25.547] [stderrLog] [info] Computing transcript lengths
[2019-01-30 21:10:25.547] [stderrLog] [info] Waiting to finish loading hash
[2019-01-30 21:10:25.896] [jointLog] [info] done
[2019-01-30 21:10:25.896] [jointLog] [info] Index contained 5838 targets
[2019-01-30 21:10:25.896] [stderrLog] [info] Done loading index






processed 500001 fragments
hits: 84910, hits per frag:  0.206999

processed 1000000 fragments
hits: 170084, hits per frag:  0.180878

processed 1500000 fragments
hits: 255968, hits per frag:  0.175424

processed 2000000 fragments
hits: 340913, hits per frag:  0.177583

processed 2500001 fragments
hits: 425501, hits per frag:  0.17467

processed 3000000 fragments
hits: 510854, hits per frag:  0.177581

processed 3500001 fragments
hits: 595785, hits per frag:  0.172139

processed 4000001 fragments
hits: 680641, hits per frag:  0.175301

processed 4500000 fragments
hits: 765540, hits per frag:  0.171637

processed 5000000 fragments
hits: 850923, hits per frag:  0.171477

processed 5500002 fragments
hits: 935707, hits per frag:  0.171985

processed 6000000 fragments
hits: 1019554, hits per frag:  0.171454

processed 6500000 fragments
hits: 1104996, hits per frag:  0.173046

processed 7000000 fragments
hits: 1190202, hits per frag:  0.172789

processed 7500000 fragments
hits: 1275421, hits per frag:  0.170791

processed 8000001 fragments
hits: 1360184, hits per frag:  0.171467

processed 8500001 fragments
hits: 1444909, hits per frag:  0.171597

processed 9000000 fragments
hits: 1530171, hits per frag:  0.171097

processed 10000001 fragments
hits: 1700467, hits per frag:  0.171064

processed 10500000 fragments
hits: 1785771, hits per frag:  0.171468

processed 11000000 fragments
hits: 1870686, hits per frag:  0.171385

processed 11500000 fragments
hits: 1955892, hits per frag:  0.170933

processed 12000000 fragments
hits: 2041516, hits per frag:  0.171285

processed 12500000 fragments
hits: 2125109, hits per frag:  0.170774

processed 13000000 fragments
hits: 2209775, hits per frag:  0.170787

processed 13500000 fragments
hits: 2295091, hits per frag:  0.172041

processed 14000000 fragments
hits: 2380843, hits per frag:  0.171291

processed 14500000 fragments
hits: 2465722, hits per frag:  0.171315

processed 15000000 fragments
hits: 2552045, hits per frag:  0.171202

processed 15500000 fragments
hits: 2637210, hits per frag:  0.171263

processed 16000000 fragments
hits: 2723024, hits per frag:  0.170828

processed 16500001 fragments
hits: 2808567, hits per frag:  0.171479

processed 17000000 fragments
hits: 2893244, hits per frag:  0.170316

processed 17500000 fragments
hits: 2978203, hits per frag:  0.170979

processed 18000000 fragments
hits: 3064087, hits per frag:  0.170966









[2019-01-30 21:11:10.326] [jointLog] [info] Computed 7296 rich equivalence classes for further processing
[2019-01-30 21:11:10.326] [jointLog] [info] Counted 1550851 total reads in the equivalence classes 
[2019-01-30 21:11:10.337] [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.


[2019-01-30 21:11:10.338] [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.

[2019-01-30 21:11:10.338] [jointLog] [info] Mapping rate = 8.4437%

[2019-01-30 21:11:10.338] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:11:10.338] [jointLog] [info] Starting optimizer
[2019-01-30 21:11:10.343] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:11:10.343] [jointLog] [info] iteration = 0 | max rel diff. = 415.306
[2019-01-30 21:11:10.362] [jointLog] [info] iteration = 100 | max rel diff. = 0.123525
[2019-01-30 21:11:10.378] [jointLog] [info] iteration = 200 | max rel diff. = 0.0531477
[2019-01-30 21:11:10.395] [jointLog] [info] iteration = 300 | max rel diff. = 0.03914
[2019-01-30 21:11:10.412] [jointLog] [info] iteration = 400 | max rel diff. = 0.0282139
[2019-01-30 21:11:10.430] [jointLog] [info] iteration = 500 | max rel diff. = 0.0208173
[2019-01-30 21:11:10.447] [jointLog] [info] iteration = 600 | max rel diff. = 0.0169571
[2019-01-30 21:11:10.465] [jointLog] [info] iteration = 700 | max rel diff. = 0.0151659
[2019-01-30 21:11:10.482] [jointLog] [info] iteration = 800 | max rel diff. = 0.0115065
[2019-01-30 21:11:10.499] [jointLog] [info] iteration = 900 | max rel diff. = 0.0113234
[2019-01-30 21:11:10.515] [jointLog] [info] iteration = 987 | max rel diff. = 0.00953055
[2019-01-30 21:11:10.515] [jointLog] [info] Finished optimizer
[2019-01-30 21:11:10.515] [jointLog] [info] writing output 

[2019-01-30 21:11:10.526] [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: 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 bleached_K5_02/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > 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 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 ] => { bleached_K5_03 }
### [ threads ] => { 23 }
Logs will be written to bleached_K5_03/logs
[2019-01-30 21:11:10.918] [jointLog] [info] parsing read library format
[2019-01-30 21:11:10.918] [jointLog] [info] There is 1 library.
[2019-01-30 21:11:10.978] [jointLog] [info] Loading Quasi index
[2019-01-30 21:11:10.978] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:11:10.978] [stderrLog] [info] Loading Suffix Array 
[2019-01-30 21:11:11.013] [stderrLog] [info] Loading Transcript Info 
[2019-01-30 21:11:11.023] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-01-30 21:11:11.026] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-01-30 21:11:11.028] [stderrLog] [info] Computing transcript lengths
[2019-01-30 21:11:11.028] [stderrLog] [info] Waiting to finish loading hash
[2019-01-30 21:11:11.408] [stderrLog] [info] Done loading index




[2019-01-30 21:11:11.408] [jointLog] [info] done
[2019-01-30 21:11:11.408] [jointLog] [info] Index contained 5838 targets


processed 500000 fragments
hits: 97448, hits per frag:  0.288369

processed 1000000 fragments
hits: 195149, hits per frag:  0.216458

processed 1500000 fragments
hits: 294256, hits per frag:  0.205931

processed 2000000 fragments
hits: 392725, hits per frag:  0.206154

processed 2500000 fragments
hits: 491885, hits per frag:  0.200721

processed 3000000 fragments
hits: 591066, hits per frag:  0.204519

processed 3500000 fragments
hits: 688305, hits per frag:  0.204106

processed 4000000 fragments
hits: 785968, hits per frag:  0.200924

processed 4500000 fragments
hits: 883480, hits per frag:  0.200613

processed 5000000 fragments
hits: 982306, hits per frag:  0.199396

processed 5500000 fragments
hits: 1080385, hits per frag:  0.197703

processed 6000000 fragments
hits: 1178645, hits per frag:  0.198894

processed 6500000 fragments
hits: 1276370, hits per frag:  0.197126

processed 7000000 fragments
hits: 1375058, hits per frag:  0.199071

processed 7500000 fragments
hits: 1472008, hits per frag:  0.198145

processed 8000000 fragments
hits: 1569425, hits per frag:  0.196889

processed 8500001 fragments
hits: 1667287, hits per frag:  0.198097

processed 9000000 fragments
hits: 1765708, hits per frag:  0.200064

processed 9500001 fragments
hits: 1864238, hits per frag:  0.197241

processed 10000000 fragments
hits: 1961738, hits per frag:  0.196875

processed 10500000 fragments
hits: 2060687, hits per frag:  0.197107

processed 11000000 fragments
hits: 2160386, hits per frag:  0.197671

processed 11500000 fragments
hits: 2259372, hits per frag:  0.198306

processed 12000000 fragments
hits: 2357312, hits per frag:  0.197911

processed 12500000 fragments
hits: 2456220, hits per frag:  0.196859

processed 13000001 fragments
hits: 2554109, hits per frag:  0.197226

processed 13500000 fragments
hits: 2651886, hits per frag:  0.197736

processed 14000000 fragments
hits: 2749674, hits per frag:  0.197908

processed 14500000 fragments
hits: 2848292, hits per frag:  0.197427

processed 15000000 fragments
hits: 2946025, hits per frag:  0.196969

processed 15500000 fragments
hits: 3044696, hits per frag:  0.197305

processed 16000001 fragments
hits: 3142008, hits per frag:  0.196741

processed 16500000 fragments
hits: 3239941, hits per frag:  0.197567

processed 17000002 fragments
hits: 3337504, hits per frag:  0.197574

processed 17500000 fragments
hits: 3435832, hits per frag:  0.196555

processed 18000002 fragments
hits: 3532672, hits per frag:  0.198278

processed 18500000 fragments
hits: 3631248, hits per frag:  0.197157

processed 19000001 fragments
hits: 3730512, hits per frag:  0.197077

processed 19500000 fragments
hits: 3828358, hits per frag:  0.196719

processed 20000000 fragments
hits: 3926627, hits per frag:  0.197004

processed 20500000 fragments
hits: 4023794, hits per frag:  0.196646

processed 21000000 fragments
hits: 4122188, hits per frag:  0.196443

processed 21500000 fragments
hits: 4219688, hits per frag:  0.196846

processed 22000000 fragments
hits: 4317980, hits per frag:  0.196786

processed 22500000 fragments
hits: 4416367, hits per frag:  0.197209

processed 23000000 fragments
hits: 4514880, hits per frag:  0.19657

processed 23500001 fragments
hits: 4612646, hits per frag:  0.19661

processed 24000000 fragments
hits: 4710791, hits per frag:  0.196478

processed 24500000 fragments
hits: 4808035, hits per frag:  0.196914

processed 25000000 fragments
hits: 4906467, hits per frag:  0.196512

processed 25500000 fragments
hits: 5003685, hits per frag:  0.197064









[2019-01-30 21:12:15.580] [jointLog] [info] Computed 7398 rich equivalence classes for further processing
[2019-01-30 21:12:15.580] [jointLog] [info] Counted 2479140 total reads in the equivalence classes 
[2019-01-30 21:12:15.591] [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.


[2019-01-30 21:12:15.591] [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.

[2019-01-30 21:12:15.591] [jointLog] [info] Mapping rate = 9.56952%

[2019-01-30 21:12:15.591] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:12:15.592] [jointLog] [info] Starting optimizer
[2019-01-30 21:12:15.596] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:12:15.597] [jointLog] [info] iteration = 0 | max rel diff. = 615.829
[2019-01-30 21:12:15.614] [jointLog] [info] iteration = 100 | max rel diff. = 0.117133
[2019-01-30 21:12:15.630] [jointLog] [info] iteration = 200 | max rel diff. = 0.0562926
[2019-01-30 21:12:15.647] [jointLog] [info] iteration = 300 | max rel diff. = 0.0377845
[2019-01-30 21:12:15.663] [jointLog] [info] iteration = 400 | max rel diff. = 0.0261346
[2019-01-30 21:12:15.678] [jointLog] [info] iteration = 500 | max rel diff. = 0.0214208
[2019-01-30 21:12:15.693] [jointLog] [info] iteration = 600 | max rel diff. = 0.0177707
[2019-01-30 21:12:15.708] [jointLog] [info] iteration = 700 | max rel diff. = 0.0152763
[2019-01-30 21:12:15.723] [jointLog] [info] iteration = 800 | max rel diff. = 0.013019
[2019-01-30 21:12:15.738] [jointLog] [info] iteration = 900 | max rel diff. = 0.0119452
[2019-01-30 21:12:15.753] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0106928
[2019-01-30 21:12:15.757] [jointLog] [info] iteration = 1027 | max rel diff. = 0.00911444
[2019-01-30 21:12:15.757] [jointLog] [info] Finished optimizer
[2019-01-30 21:12:15.757] [jointLog] [info] writing output 

[2019-01-30 21:12:15.768] [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: 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 bleached_K5_03/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > 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 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 ] => { bleached_K5_04 }
### [ threads ] => { 23 }
Logs will be written to bleached_K5_04/logs
[2019-01-30 21:12:16.046] [jointLog] [info] parsing read library format
[2019-01-30 21:12:16.046] [jointLog] [info] There is 1 library.
[2019-01-30 21:12:16.106] [jointLog] [info] Loading Quasi index
[2019-01-30 21:12:16.106] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:12:16.106] [stderrLog] [info] Loading Suffix Array 
[2019-01-30 21:12:16.145] [stderrLog] [info] Loading Transcript Info 
[2019-01-30 21:12:16.155] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-01-30 21:12:16.158] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-01-30 21:12:16.160] [stderrLog] [info] Computing transcript lengths
[2019-01-30 21:12:16.160] [stderrLog] [info] Waiting to finish loading hash
[2019-01-30 21:12:16.496] [jointLog] [info] done
[2019-01-30 21:12:16.496] [jointLog] [info] Index contained 5838 targets




[2019-01-30 21:12:16.496] [stderrLog] [info] Done loading index


processed 500000 fragments
hits: 96445, hits per frag:  0.202524

processed 1000000 fragments
hits: 192504, hits per frag:  0.201983

processed 1500000 fragments
hits: 289496, hits per frag:  0.202509

processed 2000000 fragments
hits: 385814, hits per frag:  0.20411

processed 2500000 fragments
hits: 481995, hits per frag:  0.193555

processed 3000000 fragments
hits: 577816, hits per frag:  0.19467

processed 3500000 fragments
hits: 673557, hits per frag:  0.197429

processed 4000000 fragments
hits: 770471, hits per frag:  0.198057

processed 4500000 fragments
hits: 867725, hits per frag:  0.194217

processed 5000000 fragments
hits: 963724, hits per frag:  0.194914

processed 5500000 fragments
hits: 1060883, hits per frag:  0.196516

processed 6000000 fragments
hits: 1157663, hits per frag:  0.195128

processed 6500000 fragments
hits: 1253667, hits per frag:  0.195597

processed 7000000 fragments
hits: 1351179, hits per frag:  0.195613

processed 7500000 fragments
hits: 1447852, hits per frag:  0.194292

processed 8000000 fragments
hits: 1543311, hits per frag:  0.194381

processed 8500000 fragments
hits: 1639022, hits per frag:  0.193674

processed 9000000 fragments
hits: 1735049, hits per frag:  0.195171

processed 9500000 fragments
hits: 1831416, hits per frag:  0.194438

processed 10000000 fragments
hits: 1926868, hits per frag:  0.193549

processed 10500000 fragments
hits: 2022021, hits per frag:  0.194436

processed 11000001 fragments
hits: 2118317, hits per frag:  0.193042

processed 11500000 fragments
hits: 2215252, hits per frag:  0.192659

processed 12000001 fragments
hits: 2312004, hits per frag:  0.193209

processed 12500000 fragments
hits: 2406328, hits per frag:  0.19337

processed 13000000 fragments
hits: 2501309, hits per frag:  0.193125

processed 13500000 fragments
hits: 2597545, hits per frag:  0.194746

processed 14000000 fragments
hits: 2694014, hits per frag:  0.193318

processed 14500000 fragments
hits: 2790499, hits per frag:  0.192885

processed 15000000 fragments
hits: 2887041, hits per frag:  0.193414

processed 15500000 fragments
hits: 2983034, hits per frag:  0.193066

processed 16000000 fragments
hits: 3078676, hits per frag:  0.193585

processed 16500000 fragments
hits: 3174772, hits per frag:  0.192697

processed 17000000 fragments
hits: 3270674, hits per frag:  0.193007

processed 17500000 fragments
hits: 3366980, hits per frag:  0.192993

processed 18000000 fragments
hits: 3463074, hits per frag:  0.19311

processed 18500000 fragments
hits: 3558844, hits per frag:  0.192659

processed 19000000 fragments
hits: 3655497, hits per frag:  0.193034

processed 19500000 fragments
hits: 3751365, hits per frag:  0.192708

processed 20000000 fragments
hits: 3847894, hits per frag:  0.192952

processed 20500001 fragments
hits: 3944493, hits per frag:  0.193371

processed 21000000 fragments
hits: 4040721, hits per frag:  0.19328

processed 21500000 fragments
hits: 4137683, hits per frag:  0.192861

processed 22000000 fragments
hits: 4233656, hits per frag:  0.192636

processed 22500000 fragments
hits: 4329578, hits per frag:  0.192691

processed 23000000 fragments
hits: 4426354, hits per frag:  0.192532

processed 23500000 fragments
hits: 4522491, hits per frag:  0.19325

processed 24000000 fragments
hits: 4618704, hits per frag:  0.19286

processed 24500000 fragments
hits: 4715066, hits per frag:  0.192808

processed 25000000 fragments
hits: 4812182, hits per frag:  0.193085

processed 25500001 fragments
hits: 4908547, hits per frag:  0.192893

processed 26000000 fragments
hits: 5004197, hits per frag:  0.193161

processed 26500000 fragments
hits: 5101368, hits per frag:  0.193027

processed 27000001 fragments
hits: 5197190, hits per frag:  0.193188

processed 27500000 fragments
hits: 5292193, hits per frag:  0.192842

processed 28000000 fragments
hits: 5389097, hits per frag:  0.19323









[2019-01-30 21:13:24.533] [jointLog] [info] Computed 7401 rich equivalence classes for further processing
[2019-01-30 21:13:24.533] [jointLog] [info] Counted 2716216 total reads in the equivalence classes 
[2019-01-30 21:13:24.543] [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.


[2019-01-30 21:13:24.544] [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.

[2019-01-30 21:13:24.544] [jointLog] [info] Mapping rate = 9.59013%

[2019-01-30 21:13:24.544] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:13:24.544] [jointLog] [info] Starting optimizer
[2019-01-30 21:13:24.550] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:13:24.551] [jointLog] [info] iteration = 0 | max rel diff. = 623.195
[2019-01-30 21:13:24.573] [jointLog] [info] iteration = 100 | max rel diff. = 0.126869
[2019-01-30 21:13:24.591] [jointLog] [info] iteration = 200 | max rel diff. = 0.0632856
[2019-01-30 21:13:24.609] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433748
[2019-01-30 21:13:24.626] [jointLog] [info] iteration = 400 | max rel diff. = 0.0310135
[2019-01-30 21:13:24.644] [jointLog] [info] iteration = 500 | max rel diff. = 0.0246257
[2019-01-30 21:13:24.662] [jointLog] [info] iteration = 600 | max rel diff. = 0.0180863
[2019-01-30 21:13:24.680] [jointLog] [info] iteration = 700 | max rel diff. = 0.015206
[2019-01-30 21:13:24.698] [jointLog] [info] iteration = 800 | max rel diff. = 0.0135994
[2019-01-30 21:13:24.716] [jointLog] [info] iteration = 900 | max rel diff. = 0.0118754
[2019-01-30 21:13:24.735] [jointLog] [info] iteration = 1000 | max rel diff. = 0.011097
[2019-01-30 21:13:24.741] [jointLog] [info] iteration = 1035 | max rel diff. = 0.00985433
[2019-01-30 21:13:24.741] [jointLog] [info] Finished optimizer
[2019-01-30 21:13:24.741] [jointLog] [info] writing output 

[2019-01-30 21:13:24.754] [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: 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 bleached_K5_04/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > 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 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 ] => { bleached_K5_05 }
### [ threads ] => { 23 }
Logs will be written to bleached_K5_05/logs
[2019-01-30 21:13:25.175] [jointLog] [info] parsing read library format
[2019-01-30 21:13:25.175] [jointLog] [info] There is 1 library.
[2019-01-30 21:13:25.236] [stderrLog] [info] Loading Suffix Array 
[2019-01-30 21:13:25.236] [jointLog] [info] Loading Quasi index
[2019-01-30 21:13:25.236] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:13:25.273] [stderrLog] [info] Loading Transcript Info 
[2019-01-30 21:13:25.282] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-01-30 21:13:25.285] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-01-30 21:13:25.287] [stderrLog] [info] Computing transcript lengths
[2019-01-30 21:13:25.287] [stderrLog] [info] Waiting to finish loading hash
[2019-01-30 21:13:25.641] [jointLog] [info] done
[2019-01-30 21:13:25.641] [jointLog] [info] Index contained 5838 targets
[2019-01-30 21:13:25.641] [stderrLog] [info] Done loading index






processed 500000 fragments
hits: 88710, hits per frag:  0.215256

processed 1000000 fragments
hits: 177927, hits per frag:  0.183996

processed 1500000 fragments
hits: 265499, hits per frag:  0.177212

processed 2000000 fragments
hits: 354093, hits per frag:  0.183755

processed 2500000 fragments
hits: 442239, hits per frag:  0.180812

processed 3000000 fragments
hits: 531329, hits per frag:  0.182544

processed 3500000 fragments
hits: 619383, hits per frag:  0.184445

processed 4000000 fragments
hits: 707003, hits per frag:  0.181965

processed 4500000 fragments
hits: 796504, hits per frag:  0.179839

processed 5000000 fragments
hits: 884738, hits per frag:  0.179957

processed 5500001 fragments
hits: 972740, hits per frag:  0.179513

processed 6000000 fragments
hits: 1061328, hits per frag:  0.178003

processed 6500000 fragments
hits: 1149961, hits per frag:  0.179035

processed 7000000 fragments
hits: 1238352, hits per frag:  0.179525

processed 7500000 fragments
hits: 1326035, hits per frag:  0.178406

processed 8500002 fragments
hits: 1502640, hits per frag:  0.178803

processed 9000000 fragments
hits: 1591859, hits per frag:  0.179168

processed 9500000 fragments
hits: 1680388, hits per frag:  0.177398

processed 10000001 fragments
hits: 1768764, hits per frag:  0.178117

processed 10500000 fragments
hits: 1856495, hits per frag:  0.17806

processed 11000000 fragments
hits: 1943754, hits per frag:  0.177636

processed 11500000 fragments
hits: 2031796, hits per frag:  0.176984

processed 12000000 fragments
hits: 2119217, hits per frag:  0.17732

processed 12500000 fragments
hits: 2207347, hits per frag:  0.177425

processed 13000000 fragments
hits: 2294869, hits per frag:  0.176773

processed 13500000 fragments
hits: 2382970, hits per frag:  0.177354

processed 14000000 fragments
hits: 2470846, hits per frag:  0.177291

processed 14500000 fragments
hits: 2559420, hits per frag:  0.177556

processed 15000000 fragments
hits: 2647977, hits per frag:  0.176715

processed 15500000 fragments
hits: 2735927, hits per frag:  0.177597

processed 16000000 fragments
hits: 2824286, hits per frag:  0.177985

processed 16500000 fragments
hits: 2913111, hits per frag:  0.177132

processed 17000000 fragments
hits: 3001372, hits per frag:  0.176794

processed 17500000 fragments
hits: 3089736, hits per frag:  0.177466

processed 18000000 fragments
hits: 3177785, hits per frag:  0.176852

processed 18500000 fragments
hits: 3264970, hits per frag:  0.176861

processed 19000000 fragments
hits: 3352425, hits per frag:  0.177065

processed 19500000 fragments
hits: 3440217, hits per frag:  0.177424

processed 20000001 fragments
hits: 3527516, hits per frag:  0.177178

processed 20500000 fragments
hits: 3615120, hits per frag:  0.17698

processed 21000000 fragments
hits: 3703014, hits per frag:  0.177205

processed 21500001 fragments
hits: 3791545, hits per frag:  0.176989



[2019-01-30 21:14:17.684] [jointLog] [info] Computed 6922 rich equivalence classes for further processing
[2019-01-30 21:14:17.684] [jointLog] [info] Counted 1916701 total reads in the equivalence classes 






[2019-01-30 21:14:17.695] [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.


[2019-01-30 21:14:17.695] [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.

[2019-01-30 21:14:17.695] [jointLog] [info] Mapping rate = 8.75913%

[2019-01-30 21:14:17.695] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:14:17.695] [jointLog] [info] Starting optimizer
[2019-01-30 21:14:17.700] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:14:17.701] [jointLog] [info] iteration = 0 | max rel diff. = 428.666
[2019-01-30 21:14:17.718] [jointLog] [info] iteration = 100 | max rel diff. = 0.11263
[2019-01-30 21:14:17.734] [jointLog] [info] iteration = 200 | max rel diff. = 0.0561102
[2019-01-30 21:14:17.749] [jointLog] [info] iteration = 300 | max rel diff. = 0.0366455
[2019-01-30 21:14:17.764] [jointLog] [info] iteration = 400 | max rel diff. = 0.0243092
[2019-01-30 21:14:17.779] [jointLog] [info] iteration = 500 | max rel diff. = 0.0243105
[2019-01-30 21:14:17.794] [jointLog] [info] iteration = 600 | max rel diff. = 0.017536
[2019-01-30 21:14:17.812] [jointLog] [info] iteration = 700 | max rel diff. = 0.0150939
[2019-01-30 21:14:17.830] [jointLog] [info] iteration = 800 | max rel diff. = 0.0129985
[2019-01-30 21:14:17.848] [jointLog] [info] iteration = 900 | max rel diff. = 0.011836
[2019-01-30 21:14:17.865] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0118362
[2019-01-30 21:14:17.874] [jointLog] [info] iteration = 1050 | max rel diff. = 0.00947587
[2019-01-30 21:14:17.875] [jointLog] [info] Finished optimizer
[2019-01-30 21:14:17.875] [jointLog] [info] writing output 

[2019-01-30 21:14:17.885] [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: 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 bleached_K5_05/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > 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 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 ] => { bleached_K5_06 }
### [ threads ] => { 23 }
Logs will be written to bleached_K5_06/logs
[2019-01-30 21:14:18.261] [jointLog] [info] parsing read library format
[2019-01-30 21:14:18.261] [jointLog] [info] There is 1 library.
[2019-01-30 21:14:18.321] [jointLog] [info] Loading Quasi index
[2019-01-30 21:14:18.321] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:14:18.321] [stderrLog] [info] Loading Suffix Array 
[2019-01-30 21:14:18.356] [stderrLog] [info] Loading Transcript Info 
[2019-01-30 21:14:18.365] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-01-30 21:14:18.368] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-01-30 21:14:18.370] [stderrLog] [info] Computing transcript lengths
[2019-01-30 21:14:18.370] [stderrLog] [info] Waiting to finish loading hash
[2019-01-30 21:14:18.748] [stderrLog] [info] Done loading index




[2019-01-30 21:14:18.748] [jointLog] [info] done
[2019-01-30 21:14:18.748] [jointLog] [info] Index contained 5838 targets


processed 500000 fragments
hits: 74509, hits per frag:  0.17195

processed 1000000 fragments
hits: 149540, hits per frag:  0.16922

processed 1500000 fragments
hits: 224705, hits per frag:  0.151906

processed 2000000 fragments
hits: 298961, hits per frag:  0.157328

processed 2500000 fragments
hits: 373766, hits per frag:  0.153562

processed 3000000 fragments
hits: 448010, hits per frag:  0.152863

processed 3500000 fragments
hits: 522412, hits per frag:  0.151922

processed 4000000 fragments
hits: 595256, hits per frag:  0.151705

processed 4500000 fragments
hits: 669318, hits per frag:  0.152251

processed 5000001 fragments
hits: 744438, hits per frag:  0.149133

processed 5500000 fragments
hits: 819683, hits per frag:  0.152406

processed 6000000 fragments
hits: 894846, hits per frag:  0.151169

processed 6500000 fragments
hits: 968522, hits per frag:  0.151071

processed 7000000 fragments
hits: 1042069, hits per frag:  0.150081

processed 7500000 fragments
hits: 1116202, hits per frag:  0.15052

processed 8000000 fragments
hits: 1189852, hits per frag:  0.149327

processed 8500000 fragments
hits: 1262931, hits per frag:  0.148976

processed 9000000 fragments
hits: 1338149, hits per frag:  0.149148

processed 9500000 fragments
hits: 1413017, hits per frag:  0.149089

processed 10000001 fragments
hits: 1487389, hits per frag:  0.148877

processed 10500001 fragments
hits: 1561547, hits per frag:  0.149056

processed 11000001 fragments
hits: 1635734, hits per frag:  0.148941

processed 11500000 fragments
hits: 1710239, hits per frag:  0.149343

processed 12000000 fragments
hits: 1783817, hits per frag:  0.150322

processed 12500000 fragments
hits: 1857579, hits per frag:  0.15002

processed 13000000 fragments
hits: 1930614, hits per frag:  0.149441

processed 13500001 fragments
hits: 2006424, hits per frag:  0.149217

processed 14000000 fragments
hits: 2081169, hits per frag:  0.149941

processed 14500000 fragments
hits: 2156450, hits per frag:  0.149342

processed 15000001 fragments
hits: 2230469, hits per frag:  0.149024

processed 15500000 fragments
hits: 2304301, hits per frag:  0.148979

processed 16000001 fragments
hits: 2377768, hits per frag:  0.149336

processed 16500001 fragments
hits: 2451329, hits per frag:  0.148806

processed 17000000 fragments
hits: 2524270, hits per frag:  0.149002









[2019-01-30 21:14:59.925] [jointLog] [info] Computed 6627 rich equivalence classes for further processing
[2019-01-30 21:14:59.925] [jointLog] [info] Counted 1294477 total reads in the equivalence classes 
[2019-01-30 21:14:59.937] [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.


[2019-01-30 21:14:59.937] [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.

[2019-01-30 21:14:59.937] [jointLog] [info] Mapping rate = 7.48881%

[2019-01-30 21:14:59.937] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:14:59.938] [jointLog] [info] Starting optimizer
[2019-01-30 21:14:59.942] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:14:59.942] [jointLog] [info] iteration = 0 | max rel diff. = 305.93
[2019-01-30 21:14:59.961] [jointLog] [info] iteration = 100 | max rel diff. = 0.113977
[2019-01-30 21:14:59.976] [jointLog] [info] iteration = 200 | max rel diff. = 0.0606186
[2019-01-30 21:14:59.991] [jointLog] [info] iteration = 300 | max rel diff. = 0.043268
[2019-01-30 21:15:00.005] [jointLog] [info] iteration = 400 | max rel diff. = 0.0293288
[2019-01-30 21:15:00.019] [jointLog] [info] iteration = 500 | max rel diff. = 0.0217735
[2019-01-30 21:15:00.034] [jointLog] [info] iteration = 600 | max rel diff. = 0.0174293
[2019-01-30 21:15:00.048] [jointLog] [info] iteration = 700 | max rel diff. = 0.0147432
[2019-01-30 21:15:00.062] [jointLog] [info] iteration = 800 | max rel diff. = 0.0118476
[2019-01-30 21:15:00.079] [jointLog] [info] iteration = 900 | max rel diff. = 0.0111509
[2019-01-30 21:15:00.096] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0113565
[2019-01-30 21:15:00.111] [jointLog] [info] iteration = 1091 | max rel diff. = 0.00876264
[2019-01-30 21:15:00.111] [jointLog] [info] Finished optimizer
[2019-01-30 21:15:00.111] [jointLog] [info] writing output 

[2019-01-30 21:15:00.122] [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: 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 bleached_K5_06/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > bleached_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-P03-ACTGAT-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P03-ACTGAT-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_44_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 ] => { bleached_44_01 }
### [ threads ] => { 23 }
Logs will be written to bleached_44_01/logs
[2019-01-30 21:15:00.543] [jointLog] [info] parsing read library format
[2019-01-30 21:15:00.543] [jointLog] [info] There is 1 library.
[2019-01-30 21:15:00.603] [jointLog] [info] Loading Quasi index
[2019-01-30 21:15:00.603] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:15:00.603] [stderrLog] [info] Loading Suffix Array 
[2019-01-30 21:15:00.636] [stderrLog] [info] Loading Transcript Info 
[2019-01-30 21:15:00.644] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-01-30 21:15:00.648] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-01-30 21:15:00.649] [stderrLog] [info] Computing transcript lengths
[2019-01-30 21:15:00.649] [stderrLog] [info] Waiting to finish loading hash
[2019-01-30 21:15:01.013] [stderrLog] [info] Done loading index




[2019-01-30 21:15:01.013] [jointLog] [info] done
[2019-01-30 21:15:01.013] [jointLog] [info] Index contained 5838 targets


processed 500000 fragments
hits: 88935, hits per frag:  0.184791

processed 1000000 fragments
hits: 178158, hits per frag:  0.191149

processed 1500001 fragments
hits: 266516, hits per frag:  0.183502

processed 2000000 fragments
hits: 355354, hits per frag:  0.19054

processed 2500000 fragments
hits: 444181, hits per frag:  0.186105

processed 3000001 fragments
hits: 531514, hits per frag:  0.181597

processed 3500000 fragments
hits: 620498, hits per frag:  0.185317

processed 4000000 fragments
hits: 709216, hits per frag:  0.182005

processed 4500000 fragments
hits: 798687, hits per frag:  0.18113

processed 5000000 fragments
hits: 888213, hits per frag:  0.180557

processed 5500000 fragments
hits: 976900, hits per frag:  0.180017

processed 6000000 fragments
hits: 1064967, hits per frag:  0.18132

processed 6500000 fragments
hits: 1153899, hits per frag:  0.179101

processed 7000000 fragments
hits: 1242427, hits per frag:  0.18013

processed 7500001 fragments
hits: 1331764, hits per frag:  0.177958

processed 8000001 fragments
hits: 1420300, hits per frag:  0.179389

processed 8500000 fragments
hits: 1506875, hits per frag:  0.177574

processed 9000000 fragments
hits: 1595427, hits per frag:  0.177945

processed 9500000 fragments
hits: 1685167, hits per frag:  0.178078

processed 10000000 fragments
hits: 1773394, hits per frag:  0.178457

processed 10500001 fragments
hits: 1861767, hits per frag:  0.178642

processed 11000000 fragments
hits: 1950553, hits per frag:  0.177923

processed 11500000 fragments
hits: 2038652, hits per frag:  0.178025

processed 12000001 fragments
hits: 2127539, hits per frag:  0.177368

processed 12500001 fragments
hits: 2215361, hits per frag:  0.17804

processed 13000000 fragments
hits: 2303297, hits per frag:  0.178628

processed 13500000 fragments
hits: 2393174, hits per frag:  0.178895

processed 14000000 fragments
hits: 2481916, hits per frag:  0.177899

processed 14500000 fragments
hits: 2571205, hits per frag:  0.179279

processed 15000000 fragments
hits: 2659614, hits per frag:  0.178478

processed 15500000 fragments
hits: 2749231, hits per frag:  0.177605

processed 16000000 fragments
hits: 2839773, hits per frag:  0.177652

processed 16500000 fragments
hits: 2927927, hits per frag:  0.178193

processed 17000000 fragments
hits: 3015986, hits per frag:  0.178039

processed 17500001 fragments
hits: 3104466, hits per frag:  0.178589

processed 18000000 fragments
hits: 3192947, hits per frag:  0.177629

processed 18500000 fragments
hits: 3281386, hits per frag:  0.17764

processed 19000000 fragments
hits: 3370440, hits per frag:  0.178002

processed 19500000 fragments
hits: 3457896, hits per frag:  0.177687

processed 20000000 fragments
hits: 3545731, hits per frag:  0.177905

processed 20500000 fragments
hits: 3633895, hits per frag:  0.177483

processed 21000001 fragments
hits: 3722653, hits per frag:  0.178222

processed 21500000 fragments
hits: 3810446, hits per frag:  0.177614

processed 22000000 fragments
hits: 3898912, hits per frag:  0.17771

processed 22500000 fragments
hits: 3987501, hits per frag:  0.177803

processed 23000000 fragments
hits: 4076752, hits per frag:  0.177866









[2019-01-30 21:15:57.090] [jointLog] [info] Computed 7727 rich equivalence classes for further processing
[2019-01-30 21:15:57.090] [jointLog] [info] Counted 2025613 total reads in the equivalence classes 
[2019-01-30 21:15:57.102] [jointLog] [warning] 0.0188665% 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.


[2019-01-30 21:15:57.102] [jointLog] [warning] Only 2025613 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2019-01-30 21:15:57.102] [jointLog] [info] Mapping rate = 8.79746%

[2019-01-30 21:15:57.102] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:15:57.103] [jointLog] [info] Starting optimizer
[2019-01-30 21:15:57.108] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:15:57.108] [jointLog] [info] iteration = 0 | max rel diff. = 539.321
[2019-01-30 21:15:57.127] [jointLog] [info] iteration = 100 | max rel diff. = 0.113552
[2019-01-30 21:15:57.143] [jointLog] [info] iteration = 200 | max rel diff. = 0.0515044
[2019-01-30 21:15:57.159] [jointLog] [info] iteration = 300 | max rel diff. = 0.0363763
[2019-01-30 21:15:57.176] [jointLog] [info] iteration = 400 | max rel diff. = 0.0277539
[2019-01-30 21:15:57.193] [jointLog] [info] iteration = 500 | max rel diff. = 0.0205168
[2019-01-30 21:15:57.210] [jointLog] [info] iteration = 600 | max rel diff. = 0.0185245
[2019-01-30 21:15:57.227] [jointLog] [info] iteration = 700 | max rel diff. = 0.0164994
[2019-01-30 21:15:57.245] [jointLog] [info] iteration = 800 | max rel diff. = 0.0142163
[2019-01-30 21:15:57.261] [jointLog] [info] iteration = 900 | max rel diff. = 0.0142163
[2019-01-30 21:15:57.279] [jointLog] [info] iteration = 1000 | max rel diff. = 0.010818
[2019-01-30 21:15:57.279] [jointLog] [info] iteration = 1005 | max rel diff. = 0.00918972
[2019-01-30 21:15:57.280] [jointLog] [info] Finished optimizer
[2019-01-30 21:15:57.280] [jointLog] [info] writing output 

[2019-01-30 21:15:57.291] [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: bleached_44_01/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_44_01/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > bleached_44_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-P11-ACTTGA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P11-ACTTGA-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_44_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 ] => { bleached_44_02 }
### [ threads ] => { 23 }
Logs will be written to bleached_44_02/logs
[2019-01-30 21:15:57.648] [jointLog] [info] parsing read library format
[2019-01-30 21:15:57.648] [jointLog] [info] There is 1 library.
[2019-01-30 21:15:57.710] [stderrLog] [info] Loading Suffix Array 
[2019-01-30 21:15:57.710] [jointLog] [info] Loading Quasi index
[2019-01-30 21:15:57.710] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:15:57.745] [stderrLog] [info] Loading Transcript Info 
[2019-01-30 21:15:57.754] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-01-30 21:15:57.757] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-01-30 21:15:57.759] [stderrLog] [info] Computing transcript lengths
[2019-01-30 21:15:57.759] [stderrLog] [info] Waiting to finish loading hash
[2019-01-30 21:15:58.095] [jointLog] [info] done
[2019-01-30 21:15:58.095] [jointLog] [info] Index contained 5838 targets




[2019-01-30 21:15:58.095] [stderrLog] [info] Done loading index


processed 500000 fragments
hits: 94624, hits per frag:  0.213798

processed 1000000 fragments
hits: 189799, hits per frag:  0.201705

processed 1500000 fragments
hits: 285282, hits per frag:  0.202405

processed 2000000 fragments
hits: 380551, hits per frag:  0.193036

processed 2500001 fragments
hits: 475590, hits per frag:  0.198562

processed 3000000 fragments
hits: 571870, hits per frag:  0.192679

processed 3500000 fragments
hits: 666627, hits per frag:  0.194378

processed 4000000 fragments
hits: 761667, hits per frag:  0.194829

processed 4500001 fragments
hits: 856360, hits per frag:  0.195225

processed 5000000 fragments
hits: 951280, hits per frag:  0.190564

processed 5500000 fragments
hits: 1045270, hits per frag:  0.191656

processed 6000000 fragments
hits: 1139734, hits per frag:  0.191988

processed 6500000 fragments
hits: 1234183, hits per frag:  0.190217

processed 7000000 fragments
hits: 1328811, hits per frag:  0.19092

processed 7500000 fragments
hits: 1423445, hits per frag:  0.190709

processed 8000000 fragments
hits: 1517543, hits per frag:  0.191206

processed 8500001 fragments
hits: 1611818, hits per frag:  0.191702

processed 9000000 fragments
hits: 1705169, hits per frag:  0.190201

processed 9500000 fragments
hits: 1798492, hits per frag:  0.190899

processed 10000000 fragments
hits: 1892856, hits per frag:  0.190511

processed 10500001 fragments
hits: 1986830, hits per frag:  0.189682

processed 11000000 fragments
hits: 2081766, hits per frag:  0.189923

processed 11500000 fragments
hits: 2176792, hits per frag:  0.190231

processed 12000000 fragments
hits: 2270941, hits per frag:  0.189574

processed 12500000 fragments
hits: 2365301, hits per frag:  0.189827

processed 13000000 fragments
hits: 2460445, hits per frag:  0.190683

processed 13500000 fragments
hits: 2554990, hits per frag:  0.190909

processed 14000000 fragments
hits: 2649639, hits per frag:  0.1897

processed 14500000 fragments
hits: 2744342, hits per frag:  0.190781

processed 15000000 fragments
hits: 2838666, hits per frag:  0.190978

processed 15500001 fragments
hits: 2933541, hits per frag:  0.189771

processed 16000000 fragments
hits: 3028817, hits per frag:  0.189961

processed 16500000 fragments
hits: 3124456, hits per frag:  0.190045

processed 17000001 fragments
hits: 3217898, hits per frag:  0.189686

processed 17500000 fragments
hits: 3312063, hits per frag:  0.191183

processed 18000000 fragments
hits: 3406134, hits per frag:  0.189602

processed 18500000 fragments
hits: 3500909, hits per frag:  0.189638

processed 19000000 fragments
hits: 3594389, hits per frag:  0.189698

processed 19500000 fragments
hits: 3688697, hits per frag:  0.189619

processed 20000000 fragments
hits: 3783063, hits per frag:  0.189668

processed 20500001 fragments
hits: 3876754, hits per frag:  0.190355

processed 21000000 fragments
hits: 3972238, hits per frag:  0.189203

processed 21500000 fragments
hits: 4066654, hits per frag:  0.190159









[2019-01-30 21:16:51.711] [jointLog] [info] Computed 7631 rich equivalence classes for further processing
[2019-01-30 21:16:51.711] [jointLog] [info] Counted 2077905 total reads in the equivalence classes 
[2019-01-30 21:16:51.722] [jointLog] [warning] 0.0142576% 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.


[2019-01-30 21:16:51.723] [jointLog] [warning] Only 2077905 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2019-01-30 21:16:51.723] [jointLog] [info] Mapping rate = 9.47121%

[2019-01-30 21:16:51.723] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:16:51.723] [jointLog] [info] Starting optimizer
[2019-01-30 21:16:51.728] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:16:51.728] [jointLog] [info] iteration = 0 | max rel diff. = 467.258
[2019-01-30 21:16:51.746] [jointLog] [info] iteration = 100 | max rel diff. = 0.12376
[2019-01-30 21:16:51.763] [jointLog] [info] iteration = 200 | max rel diff. = 0.0600567
[2019-01-30 21:16:51.780] [jointLog] [info] iteration = 300 | max rel diff. = 0.0368969
[2019-01-30 21:16:51.796] [jointLog] [info] iteration = 400 | max rel diff. = 0.0285312
[2019-01-30 21:16:51.811] [jointLog] [info] iteration = 500 | max rel diff. = 0.0204312
[2019-01-30 21:16:51.827] [jointLog] [info] iteration = 600 | max rel diff. = 0.0203213
[2019-01-30 21:16:51.842] [jointLog] [info] iteration = 700 | max rel diff. = 0.0156616
[2019-01-30 21:16:51.857] [jointLog] [info] iteration = 800 | max rel diff. = 0.0123596
[2019-01-30 21:16:51.872] [jointLog] [info] iteration = 900 | max rel diff. = 0.0116243
[2019-01-30 21:16:51.890] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0116244
[2019-01-30 21:16:51.892] [jointLog] [info] iteration = 1015 | max rel diff. = 0.00897672
[2019-01-30 21:16:51.893] [jointLog] [info] Finished optimizer
[2019-01-30 21:16:51.893] [jointLog] [info] writing output 

[2019-01-30 21:16:51.904] [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: bleached_44_02/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_44_02/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > bleached_44_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-P14-GTGGCC-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P14-GTGGCC-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_44_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 ] => { bleached_44_03 }
### [ threads ] => { 23 }
Logs will be written to bleached_44_03/logs
[2019-01-30 21:16:52.326] [jointLog] [info] parsing read library format
[2019-01-30 21:16:52.326] [jointLog] [info] There is 1 library.
[2019-01-30 21:16:52.389] [stderrLog] [info] Loading Suffix Array 
[2019-01-30 21:16:52.388] [jointLog] [info] Loading Quasi index
[2019-01-30 21:16:52.388] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:16:52.426] [stderrLog] [info] Loading Transcript Info 
[2019-01-30 21:16:52.434] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-01-30 21:16:52.438] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-01-30 21:16:52.439] [stderrLog] [info] Computing transcript lengths
[2019-01-30 21:16:52.439] [stderrLog] [info] Waiting to finish loading hash
[2019-01-30 21:16:52.775] [jointLog] [info] done
[2019-01-30 21:16:52.775] [jointLog] [info] Index contained 5838 targets




[2019-01-30 21:16:52.775] [stderrLog] [info] Done loading index


processed 500000 fragments
hits: 92803, hits per frag:  0.230419

processed 1000000 fragments
hits: 185305, hits per frag:  0.204658

processed 1500001 fragments
hits: 277551, hits per frag:  0.19317

processed 2000000 fragments
hits: 369990, hits per frag:  0.190164

processed 2500000 fragments
hits: 463381, hits per frag:  0.193565

processed 3000001 fragments
hits: 556874, hits per frag:  0.18971

processed 3500000 fragments
hits: 649897, hits per frag:  0.188824

processed 4000000 fragments
hits: 743419, hits per frag:  0.187004

processed 4500000 fragments
hits: 835456, hits per frag:  0.186999

processed 5000001 fragments
hits: 928601, hits per frag:  0.189138

processed 5500000 fragments
hits: 1021766, hits per frag:  0.186808

processed 6000001 fragments
hits: 1114250, hits per frag:  0.187069

processed 6500000 fragments
hits: 1208597, hits per frag:  0.186863

processed 7000000 fragments
hits: 1301615, hits per frag:  0.187759

processed 7500000 fragments
hits: 1395341, hits per frag:  0.187998

processed 8000000 fragments
hits: 1487837, hits per frag:  0.186406

processed 8500001 fragments
hits: 1580358, hits per frag:  0.186732

processed 9000000 fragments
hits: 1673021, hits per frag:  0.187051

processed 9500000 fragments
hits: 1765150, hits per frag:  0.187485

processed 10000001 fragments
hits: 1857879, hits per frag:  0.186986

processed 10500000 fragments
hits: 1950497, hits per frag:  0.187097

processed 11000000 fragments
hits: 2042601, hits per frag:  0.187056

processed 11500000 fragments
hits: 2135579, hits per frag:  0.186417

processed 12000001 fragments
hits: 2229188, hits per frag:  0.186517

processed 12500000 fragments
hits: 2321385, hits per frag:  0.187151

processed 13000000 fragments
hits: 2414866, hits per frag:  0.186233

processed 13500000 fragments
hits: 2506128, hits per frag:  0.185934

processed 14000000 fragments
hits: 2599445, hits per frag:  0.186265

processed 14500002 fragments
hits: 2691428, hits per frag:  0.185913

processed 15000000 fragments
hits: 2783504, hits per frag:  0.186871

processed 15500000 fragments
hits: 2876005, hits per frag:  0.187052

processed 16500000 fragments
hits: 3061656, hits per frag:  0.186482

processed 17000000 fragments
hits: 3154427, hits per frag:  0.186535

processed 17500000 fragments
hits: 3246985, hits per frag:  0.185988

processed 18000000 fragments
hits: 3338898, hits per frag:  0.186731

processed 18500000 fragments
hits: 3430927, hits per frag:  0.185512

processed 19000000 fragments
hits: 3523588, hits per frag:  0.186547

processed 19500000 fragments
hits: 3616890, hits per frag:  0.186231

processed 20000001 fragments
hits: 3709665, hits per frag:  0.186273

processed 20500000 fragments
hits: 3803304, hits per frag:  0.186383

processed 21000000 fragments
hits: 3896920, hits per frag:  0.186288

processed 21500000 fragments
hits: 3990469, hits per frag:  0.185984

processed 22000000 fragments
hits: 4083759, hits per frag:  0.185944

processed 22500000 fragments
hits: 4177392, hits per frag:  0.186438

processed 23000000 fragments
hits: 4270189, hits per frag:  0.18612

processed 23500000 fragments
hits: 4362851, hits per frag:  0.185966

processed 24000000 fragments
hits: 4455645, hits per frag:  0.185806

processed 24500000 fragments
hits: 4547848, hits per frag:  0.185984

processed 25000001 fragments
hits: 4640339, hits per frag:  0.186095

processed 25500001 fragments
hits: 4732956, hits per frag:  0.185781

processed 26000000 fragments
hits: 4825417, hits per frag:  0.185948

processed 26500001 fragments
hits: 4918642, hits per frag:  0.186281

processed 27000001 fragments
hits: 5010227, hits per frag:  0.186078

processed 27500000 fragments
hits: 5102939, hits per frag:  0.185998

processed 28000000 fragments
hits: 5195041, hits per frag:  0.186128

processed 28500000 fragments
hits: 5286792, hits per frag:  0.185611

processed 29000000 fragments
hits: 5379165, hits per frag:  0.186102

processed 29500000 fragments
hits: 5471047, hits per frag:  0.185907

processed 30000000 fragments
hits: 5563741, hits per frag:  0.186179

processed 30500000 fragments
hits: 5656014, hits per frag:  0.186063

processed 31000000 fragments
hits: 5747916, hits per frag:  0.185682

processed 31500000 fragments
hits: 5840937, hits per frag:  0.186052









[2019-01-30 21:18:08.800] [jointLog] [info] Computed 8044 rich equivalence classes for further processing
[2019-01-30 21:18:08.800] [jointLog] [info] Counted 2909485 total reads in the equivalence classes 
[2019-01-30 21:18:08.812] [jointLog] [warning] 0.0123607% 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.


[2019-01-30 21:18:08.813] [jointLog] [warning] Only 2909485 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2019-01-30 21:18:08.813] [jointLog] [info] Mapping rate = 9.19069%

[2019-01-30 21:18:08.813] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:18:08.813] [jointLog] [info] Starting optimizer
[2019-01-30 21:18:08.818] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:18:08.818] [jointLog] [info] iteration = 0 | max rel diff. = 793.502
[2019-01-30 21:18:08.835] [jointLog] [info] iteration = 100 | max rel diff. = 0.119636
[2019-01-30 21:18:08.851] [jointLog] [info] iteration = 200 | max rel diff. = 0.0542236
[2019-01-30 21:18:08.866] [jointLog] [info] iteration = 300 | max rel diff. = 0.0369931
[2019-01-30 21:18:08.882] [jointLog] [info] iteration = 400 | max rel diff. = 0.0286885
[2019-01-30 21:18:08.898] [jointLog] [info] iteration = 500 | max rel diff. = 0.023342
[2019-01-30 21:18:08.914] [jointLog] [info] iteration = 600 | max rel diff. = 0.0174684
[2019-01-30 21:18:08.929] [jointLog] [info] iteration = 700 | max rel diff. = 0.0169584
[2019-01-30 21:18:08.945] [jointLog] [info] iteration = 800 | max rel diff. = 0.0155419
[2019-01-30 21:18:08.960] [jointLog] [info] iteration = 900 | max rel diff. = 0.0113094
[2019-01-30 21:18:08.976] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0104464
[2019-01-30 21:18:08.991] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0102824
[2019-01-30 21:18:08.993] [jointLog] [info] iteration = 1114 | max rel diff. = 0.0088728
[2019-01-30 21:18:08.994] [jointLog] [info] Finished optimizer
[2019-01-30 21:18:08.994] [jointLog] [info] writing output 

[2019-01-30 21:18:09.005] [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: bleached_44_03/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_44_03/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > bleached_44_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-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 non-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 ] => { non-bleached_K5_01 }
### [ threads ] => { 23 }
Logs will be written to non-bleached_K5_01/logs
[2019-01-30 21:18:09.249] [jointLog] [info] parsing read library format
[2019-01-30 21:18:09.249] [jointLog] [info] There is 1 library.
[2019-01-30 21:18:09.309] [jointLog] [info] Loading Quasi index
[2019-01-30 21:18:09.309] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:18:09.309] [stderrLog] [info] Loading Suffix Array 
[2019-01-30 21:18:09.346] [stderrLog] [info] Loading Transcript Info 
[2019-01-30 21:18:09.355] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-01-30 21:18:09.358] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-01-30 21:18:09.360] [stderrLog] [info] Computing transcript lengths
[2019-01-30 21:18:09.360] [stderrLog] [info] Waiting to finish loading hash
[2019-01-30 21:18:09.698] [jointLog] [info] done
[2019-01-30 21:18:09.698] [jointLog] [info] Index contained 5838 targets
[2019-01-30 21:18:09.698] [stderrLog] [info] Done loading index






processed 500000 fragments
hits: 98639, hits per frag:  0.225065

processed 1000000 fragments
hits: 198038, hits per frag:  0.209894

processed 1500000 fragments
hits: 295940, hits per frag:  0.199318

processed 2000000 fragments
hits: 396437, hits per frag:  0.20777

processed 2500000 fragments
hits: 495830, hits per frag:  0.206556

processed 3000000 fragments
hits: 595343, hits per frag:  0.205286

processed 3500000 fragments
hits: 694849, hits per frag:  0.201066

processed 4000000 fragments
hits: 793672, hits per frag:  0.204497

processed 5000000 fragments
hits: 990887, hits per frag:  0.20122

processed 5500000 fragments
hits: 1089814, hits per frag:  0.20137

processed 6000000 fragments
hits: 1189010, hits per frag:  0.201417

processed 6500000 fragments
hits: 1288296, hits per frag:  0.198794

processed 7000000 fragments
hits: 1386962, hits per frag:  0.198906

processed 7500000 fragments
hits: 1485296, hits per frag:  0.199057

processed 8000000 fragments
hits: 1584496, hits per frag:  0.200523

processed 8500001 fragments
hits: 1683740, hits per frag:  0.199682

processed 9000001 fragments
hits: 1782913, hits per frag:  0.200568

processed 9500000 fragments
hits: 1881006, hits per frag:  0.198829

processed 10000000 fragments
hits: 1981145, hits per frag:  0.200269

processed 10500000 fragments
hits: 2079169, hits per frag:  0.199321

processed 11000000 fragments
hits: 2177905, hits per frag:  0.19993

processed 11500000 fragments
hits: 2276707, hits per frag:  0.199257

processed 12000000 fragments
hits: 2375417, hits per frag:  0.199701

processed 12500000 fragments
hits: 2473763, hits per frag:  0.198459

processed 13000001 fragments
hits: 2572796, hits per frag:  0.198477

processed 13500000 fragments
hits: 2670070, hits per frag:  0.199103

processed 14000000 fragments
hits: 2768432, hits per frag:  0.198178

processed 14500000 fragments
hits: 2866610, hits per frag:  0.198255

processed 15000000 fragments
hits: 2965787, hits per frag:  0.199383

processed 15500000 fragments
hits: 3065208, hits per frag:  0.198965

processed 16000002 fragments
hits: 3164215, hits per frag:  0.198599

processed 16500001 fragments
hits: 3262481, hits per frag:  0.198178

processed 17500001 fragments
hits: 3461346, hits per frag:  0.197875

processed 18000000 fragments
hits: 3560737, hits per frag:  0.198694

processed 18500002 fragments
hits: 3658779, hits per frag:  0.198677

processed 19000000 fragments
hits: 3758133, hits per frag:  0.198346

processed 19500001 fragments
hits: 3857832, hits per frag:  0.198717

processed 20000001 fragments
hits: 3956234, hits per frag:  0.19813

processed 20500000 fragments
hits: 4055363, hits per frag:  0.199005

processed 21000000 fragments
hits: 4154041, hits per frag:  0.19873

processed 21500001 fragments
hits: 4253131, hits per frag:  0.198113

processed 22000000 fragments
hits: 4352899, hits per frag:  0.198788

processed 22500000 fragments
hits: 4452312, hits per frag:  0.198816

processed 23000000 fragments
hits: 4551488, hits per frag:  0.198163

processed 23500000 fragments
hits: 4649873, hits per frag:  0.198168









[2019-01-30 21:19:06.586] [jointLog] [info] Computed 7091 rich equivalence classes for further processing
[2019-01-30 21:19:06.586] [jointLog] [info] Counted 2346516 total reads in the equivalence classes 
[2019-01-30 21:19:06.597] [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.


[2019-01-30 21:19:06.597] [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.

[2019-01-30 21:19:06.597] [jointLog] [info] Mapping rate = 9.83271%

[2019-01-30 21:19:06.597] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:19:06.598] [jointLog] [info] Starting optimizer
[2019-01-30 21:19:06.603] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:19:06.603] [jointLog] [info] iteration = 0 | max rel diff. = 538.309
[2019-01-30 21:19:06.621] [jointLog] [info] iteration = 100 | max rel diff. = 0.118473
[2019-01-30 21:19:06.637] [jointLog] [info] iteration = 200 | max rel diff. = 0.0573747
[2019-01-30 21:19:06.652] [jointLog] [info] iteration = 300 | max rel diff. = 0.0391361
[2019-01-30 21:19:06.667] [jointLog] [info] iteration = 400 | max rel diff. = 0.0274319
[2019-01-30 21:19:06.682] [jointLog] [info] iteration = 500 | max rel diff. = 0.0220552
[2019-01-30 21:19:06.697] [jointLog] [info] iteration = 600 | max rel diff. = 0.0192187
[2019-01-30 21:19:06.713] [jointLog] [info] iteration = 700 | max rel diff. = 0.0157126
[2019-01-30 21:19:06.731] [jointLog] [info] iteration = 800 | max rel diff. = 0.0128051
[2019-01-30 21:19:06.748] [jointLog] [info] iteration = 900 | max rel diff. = 0.0111952
[2019-01-30 21:19:06.766] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0107808
[2019-01-30 21:19:06.777] [jointLog] [info] iteration = 1065 | max rel diff. = 0.00971605
[2019-01-30 21:19:06.778] [jointLog] [info] Finished optimizer
[2019-01-30 21:19:06.778] [jointLog] [info] writing output 

[2019-01-30 21:19:06.790] [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: non-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 non-bleached_K5_01/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > non-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-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 non-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 ] => { non-bleached_K5_02 }
### [ threads ] => { 23 }
Logs will be written to non-bleached_K5_02/logs
[2019-01-30 21:19:07.173] [jointLog] [info] parsing read library format
[2019-01-30 21:19:07.173] [jointLog] [info] There is 1 library.
[2019-01-30 21:19:07.233] [jointLog] [info] Loading Quasi index
[2019-01-30 21:19:07.233] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:19:07.233] [stderrLog] [info] Loading Suffix Array 
[2019-01-30 21:19:07.268] [stderrLog] [info] Loading Transcript Info 
[2019-01-30 21:19:07.276] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-01-30 21:19:07.280] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-01-30 21:19:07.282] [stderrLog] [info] Computing transcript lengths
[2019-01-30 21:19:07.282] [stderrLog] [info] Waiting to finish loading hash
[2019-01-30 21:19:07.630] [jointLog] [info] done
[2019-01-30 21:19:07.630] [jointLog] [info] Index contained 5838 targets
[2019-01-30 21:19:07.630] [stderrLog] [info] Done loading index






processed 500000 fragments
hits: 85076, hits per frag:  0.186406

processed 1000000 fragments
hits: 169838, hits per frag:  0.177748

processed 1500000 fragments
hits: 255137, hits per frag:  0.176769

processed 2000001 fragments
hits: 339711, hits per frag:  0.180956

processed 2500001 fragments
hits: 425597, hits per frag:  0.172068

processed 3000000 fragments
hits: 510682, hits per frag:  0.176354

processed 3500001 fragments
hits: 596749, hits per frag:  0.171627

processed 4000000 fragments
hits: 681957, hits per frag:  0.173574

processed 4500000 fragments
hits: 766796, hits per frag:  0.174117

processed 5000000 fragments
hits: 851472, hits per frag:  0.174217

processed 5500000 fragments
hits: 937380, hits per frag:  0.172748

processed 6000000 fragments
hits: 1022779, hits per frag:  0.173315

processed 6500000 fragments
hits: 1108134, hits per frag:  0.17261

processed 7000000 fragments
hits: 1193989, hits per frag:  0.170883

processed 7500001 fragments
hits: 1279021, hits per frag:  0.171915

processed 8000000 fragments
hits: 1364971, hits per frag:  0.172219

processed 8500000 fragments
hits: 1449836, hits per frag:  0.17124

processed 9000001 fragments
hits: 1535411, hits per frag:  0.170899

processed 9500000 fragments
hits: 1621152, hits per frag:  0.171556

processed 10000000 fragments
hits: 1706698, hits per frag:  0.172354

processed 10500000 fragments
hits: 1792392, hits per frag:  0.17202

processed 11000001 fragments
hits: 1877436, hits per frag:  0.172071

processed 11500000 fragments
hits: 1962511, hits per frag:  0.171401

processed 12000000 fragments
hits: 2047759, hits per frag:  0.172289

processed 12500000 fragments
hits: 2132645, hits per frag:  0.171359

processed 13000001 fragments
hits: 2217709, hits per frag:  0.171127

processed 13500000 fragments
hits: 2303076, hits per frag:  0.171332

processed 14000000 fragments
hits: 2387374, hits per frag:  0.171927

processed 14500000 fragments
hits: 2473362, hits per frag:  0.171425

processed 15000000 fragments
hits: 2557497, hits per frag:  0.170941

processed 15500000 fragments
hits: 2642241, hits per frag:  0.170925

processed 16000001 fragments
hits: 2726373, hits per frag:  0.170844

processed 16500000 fragments
hits: 2811769, hits per frag:  0.171003

processed 17000000 fragments
hits: 2897607, hits per frag:  0.170619

processed 17500000 fragments
hits: 2984166, hits per frag:  0.17092

processed 18000000 fragments
hits: 3068299, hits per frag:  0.170884

processed 18500001 fragments
hits: 3153100, hits per frag:  0.171003

processed 19000001 fragments
hits: 3238173, hits per frag:  0.171234

processed 19500000 fragments
hits: 3323134, hits per frag:  0.170679

processed 20000000 fragments
hits: 3409579, hits per frag:  0.17102

processed 20500001 fragments
hits: 3494828, hits per frag:  0.170843

processed 21000000 fragments
hits: 3579275, hits per frag:  0.170847

processed 21500001 fragments
hits: 3664823, hits per frag:  0.171489

processed 22000000 fragments
hits: 3749703, hits per frag:  0.171012

processed 22500000 fragments
hits: 3834744, hits per frag:  0.170729

processed 23000001 fragments
hits: 3921149, hits per frag:  0.17084

processed 23500001 fragments
hits: 4006681, hits per frag:  0.170688

processed 24000001 fragments
hits: 4092562, hits per frag:  0.170608

processed 24500001 fragments
hits: 4177917, hits per frag:  0.171146

processed 25000002 fragments
hits: 4264484, hits per frag:  0.17091

processed 25500001 fragments
hits: 4350629, hits per frag:  0.170677

processed 26000000 fragments
hits: 4436270, hits per frag:  0.171056

processed 26500000 fragments
hits: 4519727, hits per frag:  0.170677

processed 27000001 fragments
hits: 4605104, hits per frag:  0.171251

processed 27500000 fragments
hits: 4689464, hits per frag:  0.171146

processed 28000000 fragments
hits: 4775297, hits per frag:  0.170755

processed 28500001 fragments
hits: 4860008, hits per frag:  0.170819

processed 29500000 fragments
hits: 5031842, hits per frag:  0.170621

processed 30000000 fragments
hits: 5116804, hits per frag:  0.171202

processed 30500000 fragments
hits: 5202258, hits per frag:  0.170771

processed 31000000 fragments
hits: 5287789, hits per frag:  0.170694

processed 31500000 fragments
hits: 5372640, hits per frag:  0.170814

processed 32000000 fragments
hits: 5457597, hits per frag:  0.1709

processed 32500000 fragments
hits: 5541702, hits per frag:  0.170954

processed 33000000 fragments
hits: 5627060, hits per frag:  0.170758



[2019-01-30 21:20:29.283] [jointLog] [info] Computed 8127 rich equivalence classes for further processing
[2019-01-30 21:20:29.283] [jointLog] [info] Counted 2818911 total reads in the equivalence classes 






[2019-01-30 21:20:29.295] [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.


[2019-01-30 21:20:29.296] [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.

[2019-01-30 21:20:29.296] [jointLog] [info] Mapping rate = 8.52724%

[2019-01-30 21:20:29.296] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:20:29.296] [jointLog] [info] Starting optimizer
[2019-01-30 21:20:29.302] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:20:29.303] [jointLog] [info] iteration = 0 | max rel diff. = 673.377
[2019-01-30 21:20:29.323] [jointLog] [info] iteration = 100 | max rel diff. = 0.123831
[2019-01-30 21:20:29.339] [jointLog] [info] iteration = 200 | max rel diff. = 0.0596649
[2019-01-30 21:20:29.356] [jointLog] [info] iteration = 300 | max rel diff. = 0.0380999
[2019-01-30 21:20:29.373] [jointLog] [info] iteration = 400 | max rel diff. = 0.0269307
[2019-01-30 21:20:29.390] [jointLog] [info] iteration = 500 | max rel diff. = 0.0249063
[2019-01-30 21:20:29.406] [jointLog] [info] iteration = 600 | max rel diff. = 0.0157788
[2019-01-30 21:20:29.423] [jointLog] [info] iteration = 700 | max rel diff. = 0.0153608
[2019-01-30 21:20:29.440] [jointLog] [info] iteration = 800 | max rel diff. = 0.013383
[2019-01-30 21:20:29.456] [jointLog] [info] iteration = 900 | max rel diff. = 0.0109073
[2019-01-30 21:20:29.473] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0102403
[2019-01-30 21:20:29.490] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0102406
[2019-01-30 21:20:29.505] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0102406
[2019-01-30 21:20:29.509] [jointLog] [info] iteration = 1225 | max rel diff. = 0.0090297
[2019-01-30 21:20:29.509] [jointLog] [info] Finished optimizer
[2019-01-30 21:20:29.509] [jointLog] [info] writing output 

[2019-01-30 21:20:29.521] [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: non-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 non-bleached_K5_02/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > non-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-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 non-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 ] => { non-bleached_K5_03 }
### [ threads ] => { 23 }
Logs will be written to non-bleached_K5_03/logs
[2019-01-30 21:20:29.986] [jointLog] [info] parsing read library format
[2019-01-30 21:20:29.986] [jointLog] [info] There is 1 library.
[2019-01-30 21:20:30.044] [jointLog] [info] Loading Quasi index
[2019-01-30 21:20:30.044] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:20:30.044] [stderrLog] [info] Loading Suffix Array 
[2019-01-30 21:20:30.076] [stderrLog] [info] Loading Transcript Info 
[2019-01-30 21:20:30.085] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-01-30 21:20:30.088] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-01-30 21:20:30.090] [stderrLog] [info] Computing transcript lengths
[2019-01-30 21:20:30.090] [stderrLog] [info] Waiting to finish loading hash
[2019-01-30 21:20:30.425] [jointLog] [info] done
[2019-01-30 21:20:30.425] [jointLog] [info] Index contained 5838 targets




[2019-01-30 21:20:30.425] [stderrLog] [info] Done loading index


processed 500000 fragments
hits: 92982, hits per frag:  0.246771

processed 1000001 fragments
hits: 184970, hits per frag:  0.205916

processed 1500000 fragments
hits: 277386, hits per frag:  0.200633

processed 2000000 fragments
hits: 370298, hits per frag:  0.193836

processed 2500000 fragments
hits: 462998, hits per frag:  0.187256

processed 3000001 fragments
hits: 555585, hits per frag:  0.187799

processed 3500000 fragments
hits: 648521, hits per frag:  0.185633

processed 4000001 fragments
hits: 741525, hits per frag:  0.187568

processed 4500000 fragments
hits: 834125, hits per frag:  0.186943

processed 5000000 fragments
hits: 926549, hits per frag:  0.185885

processed 5500000 fragments
hits: 1019023, hits per frag:  0.188624

processed 6000000 fragments
hits: 1111421, hits per frag:  0.187108

processed 6500000 fragments
hits: 1204439, hits per frag:  0.186568

processed 7000002 fragments
hits: 1295972, hits per frag:  0.185825

processed 7500001 fragments
hits: 1388493, hits per frag:  0.186306

processed 8000000 fragments
hits: 1480576, hits per frag:  0.185837

processed 8500000 fragments
hits: 1572506, hits per frag:  0.187231

processed 9000001 fragments
hits: 1665938, hits per frag:  0.186014

processed 9500000 fragments
hits: 1758312, hits per frag:  0.187641

processed 10000000 fragments
hits: 1851332, hits per frag:  0.185589

processed 10500001 fragments
hits: 1944336, hits per frag:  0.187482

processed 11000000 fragments
hits: 2036466, hits per frag:  0.18637

processed 11500000 fragments
hits: 2130351, hits per frag:  0.186069

processed 12000000 fragments
hits: 2223409, hits per frag:  0.186549

processed 12500001 fragments
hits: 2316654, hits per frag:  0.18638

processed 13000002 fragments
hits: 2409223, hits per frag:  0.186695

processed 13500000 fragments
hits: 2502562, hits per frag:  0.186229

processed 14000000 fragments
hits: 2595807, hits per frag:  0.1875

processed 14500000 fragments
hits: 2688622, hits per frag:  0.185785

processed 15000000 fragments
hits: 2781280, hits per frag:  0.186236

processed 15500000 fragments
hits: 2873530, hits per frag:  0.185696

processed 16000000 fragments
hits: 2965245, hits per frag:  0.186679

processed 16500000 fragments
hits: 3058271, hits per frag:  0.186495

processed 17000001 fragments
hits: 3150742, hits per frag:  0.186495

processed 17500001 fragments
hits: 3243771, hits per frag:  0.18559

processed 18000000 fragments
hits: 3336587, hits per frag:  0.185904

processed 18500000 fragments
hits: 3428926, hits per frag:  0.186183

processed 19000000 fragments
hits: 3520917, hits per frag:  0.185978

processed 19500001 fragments
hits: 3612684, hits per frag:  0.186441

processed 20000000 fragments
hits: 3704911, hits per frag:  0.185648

processed 20500000 fragments
hits: 3796823, hits per frag:  0.185326

processed 21000000 fragments
hits: 3889201, hits per frag:  0.185738

processed 21500000 fragments
hits: 3981814, hits per frag:  0.185835

processed 22000000 fragments
hits: 4074296, hits per frag:  0.185476

processed 22500000 fragments
hits: 4165651, hits per frag:  0.185439

processed 23000000 fragments
hits: 4259811, hits per frag:  0.185451

processed 23500000 fragments
hits: 4351694, hits per frag:  0.185944

processed 24000000 fragments
hits: 4445455, hits per frag:  0.185716

processed 24500000 fragments
hits: 4537310, hits per frag:  0.185812

processed 25000000 fragments
hits: 4630130, hits per frag:  0.185715

processed 25500001 fragments
hits: 4721301, hits per frag:  0.185223

processed 26000002 fragments
hits: 4814366, hits per frag:  0.185858

processed 26500000 fragments
hits: 4907670, hits per frag:  0.185744

processed 27000000 fragments
hits: 4999925, hits per frag:  0.186745

processed 27500000 fragments
hits: 5092219, hits per frag:  0.185285

processed 28000001 fragments
hits: 5185904, hits per frag:  0.185702

processed 28500000 fragments
hits: 5278275, hits per frag:  0.185586

processed 29000000 fragments
hits: 5369819, hits per frag:  0.186108

processed 29500001 fragments
hits: 5461591, hits per frag:  0.185163

processed 30000000 fragments
hits: 5554842, hits per frag:  0.185585

processed 30500001 fragments
hits: 5647164, hits per frag:  0.185445

processed 31000000 fragments
hits: 5740319, hits per frag:  0.185697

processed 31500002 fragments
hits: 5832360, hits per frag:  0.185716

processed 32000000 fragments
hits: 5924056, hits per frag:  0.185435

processed 32500001 fragments
hits: 6017272, hits per frag:  0.185644

processed 33000000 fragments
hits: 6110421, hits per frag:  0.185872

processed 33500000 fragments
hits: 6202947, hits per frag:  0.185394

processed 34000000 fragments
hits: 6295239, hits per frag:  0.185252

processed 34500001 fragments
hits: 6387352, hits per frag:  0.185623









[2019-01-30 21:21:54.063] [jointLog] [info] Computed 7671 rich equivalence classes for further processing
[2019-01-30 21:21:54.063] [jointLog] [info] Counted 3126572 total reads in the equivalence classes 
[2019-01-30 21:21:54.074] [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.


[2019-01-30 21:21:54.075] [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.

[2019-01-30 21:21:54.075] [jointLog] [info] Mapping rate = 9.05407%

[2019-01-30 21:21:54.075] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:21:54.075] [jointLog] [info] Starting optimizer
[2019-01-30 21:21:54.080] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:21:54.081] [jointLog] [info] iteration = 0 | max rel diff. = 713.328
[2019-01-30 21:21:54.097] [jointLog] [info] iteration = 100 | max rel diff. = 0.11543
[2019-01-30 21:21:54.112] [jointLog] [info] iteration = 200 | max rel diff. = 0.0575008
[2019-01-30 21:21:54.127] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433146
[2019-01-30 21:21:54.142] [jointLog] [info] iteration = 400 | max rel diff. = 0.0297493
[2019-01-30 21:21:54.157] [jointLog] [info] iteration = 500 | max rel diff. = 0.0247589
[2019-01-30 21:21:54.173] [jointLog] [info] iteration = 600 | max rel diff. = 0.0191493
[2019-01-30 21:21:54.188] [jointLog] [info] iteration = 700 | max rel diff. = 0.0155013
[2019-01-30 21:21:54.202] [jointLog] [info] iteration = 800 | max rel diff. = 0.0129275
[2019-01-30 21:21:54.219] [jointLog] [info] iteration = 900 | max rel diff. = 0.0101359
[2019-01-30 21:21:54.235] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0101357
[2019-01-30 21:21:54.252] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0101357
[2019-01-30 21:21:54.260] [jointLog] [info] iteration = 1143 | max rel diff. = 0.0089613
[2019-01-30 21:21:54.260] [jointLog] [info] Finished optimizer
[2019-01-30 21:21:54.260] [jointLog] [info] writing output 

[2019-01-30 21:21:54.271] [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: non-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 non-bleached_K5_03/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > non-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-P04-GTCCGC-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P04-GTCCGC-READ2-Sequences.txt.gz_val_2.fq.gz) -o non-bleached_44_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 ] => { non-bleached_44_01 }
### [ threads ] => { 23 }
Logs will be written to non-bleached_44_01/logs
[2019-01-30 21:21:54.703] [jointLog] [info] parsing read library format
[2019-01-30 21:21:54.703] [jointLog] [info] There is 1 library.
[2019-01-30 21:21:54.764] [stderrLog] [info] Loading Suffix Array 
[2019-01-30 21:21:54.764] [jointLog] [info] Loading Quasi index
[2019-01-30 21:21:54.764] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:21:54.803] [stderrLog] [info] Loading Transcript Info 
[2019-01-30 21:21:54.813] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-01-30 21:21:54.816] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-01-30 21:21:54.818] [stderrLog] [info] Computing transcript lengths
[2019-01-30 21:21:54.818] [stderrLog] [info] Waiting to finish loading hash
[2019-01-30 21:21:55.157] [jointLog] [info] done
[2019-01-30 21:21:55.157] [jointLog] [info] Index contained 5838 targets




[2019-01-30 21:21:55.157] [stderrLog] [info] Done loading index


processed 500000 fragments
hits: 92803, hits per frag:  0.225661

processed 1000001 fragments
hits: 185754, hits per frag:  0.205614

processed 1500001 fragments
hits: 278895, hits per frag:  0.203479

processed 2000000 fragments
hits: 372253, hits per frag:  0.193117

processed 2500000 fragments
hits: 465399, hits per frag:  0.191711

processed 3000000 fragments
hits: 557419, hits per frag:  0.188377

processed 3500000 fragments
hits: 649304, hits per frag:  0.187307

processed 4000000 fragments
hits: 742597, hits per frag:  0.191799

processed 4500000 fragments
hits: 834977, hits per frag:  0.186138

processed 5000001 fragments
hits: 927949, hits per frag:  0.190106

processed 5500000 fragments
hits: 1020682, hits per frag:  0.188221

processed 6000000 fragments
hits: 1113563, hits per frag:  0.187233

processed 6500000 fragments
hits: 1205582, hits per frag:  0.186034

processed 7000001 fragments
hits: 1298085, hits per frag:  0.18624

processed 7500000 fragments
hits: 1390984, hits per frag:  0.185706

processed 8000000 fragments
hits: 1483372, hits per frag:  0.186698

processed 8500001 fragments
hits: 1576420, hits per frag:  0.187994

processed 9000000 fragments
hits: 1669206, hits per frag:  0.186721

processed 9500000 fragments
hits: 1762697, hits per frag:  0.187137

processed 10000000 fragments
hits: 1855365, hits per frag:  0.18614

processed 10500000 fragments
hits: 1948362, hits per frag:  0.186674

processed 11000000 fragments
hits: 2041538, hits per frag:  0.185852

processed 11500000 fragments
hits: 2133973, hits per frag:  0.187881

processed 12000000 fragments
hits: 2226566, hits per frag:  0.186538

processed 12500001 fragments
hits: 2318520, hits per frag:  0.186578

processed 13000000 fragments
hits: 2410881, hits per frag:  0.186457

processed 13500001 fragments
hits: 2503207, hits per frag:  0.185848

processed 14000000 fragments
hits: 2595546, hits per frag:  0.18625

processed 14500000 fragments
hits: 2687895, hits per frag:  0.187233

processed 15000000 fragments
hits: 2779947, hits per frag:  0.186478

processed 15500000 fragments
hits: 2872922, hits per frag:  0.186711

processed 16000000 fragments
hits: 2963998, hits per frag:  0.185635

processed 16500000 fragments
hits: 3056264, hits per frag:  0.185372

processed 17000000 fragments
hits: 3148552, hits per frag:  0.186318

processed 17500000 fragments
hits: 3241835, hits per frag:  0.186119

processed 18000000 fragments
hits: 3334148, hits per frag:  0.185886

processed 18500000 fragments
hits: 3426307, hits per frag:  0.185453

processed 19000000 fragments
hits: 3519512, hits per frag:  0.185796

processed 19500000 fragments
hits: 3612381, hits per frag:  0.185515

processed 20000000 fragments
hits: 3704787, hits per frag:  0.186074

processed 20500000 fragments
hits: 3796465, hits per frag:  0.185666

processed 21000001 fragments
hits: 3888769, hits per frag:  0.186037

processed 21500000 fragments
hits: 3981776, hits per frag:  0.185639

processed 22000001 fragments
hits: 4075502, hits per frag:  0.18598









[2019-01-30 21:22:48.469] [jointLog] [info] Computed 7356 rich equivalence classes for further processing
[2019-01-30 21:22:48.469] [jointLog] [info] Counted 2065907 total reads in the equivalence classes 
[2019-01-30 21:22:48.480] [jointLog] [warning] 0.0315555% 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.


[2019-01-30 21:22:48.480] [jointLog] [warning] Only 2065907 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2019-01-30 21:22:48.480] [jointLog] [info] Mapping rate = 9.18309%

[2019-01-30 21:22:48.480] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:22:48.481] [jointLog] [info] Starting optimizer
[2019-01-30 21:22:48.487] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:22:48.487] [jointLog] [info] iteration = 0 | max rel diff. = 551.059
[2019-01-30 21:22:48.506] [jointLog] [info] iteration = 100 | max rel diff. = 0.124265
[2019-01-30 21:22:48.521] [jointLog] [info] iteration = 200 | max rel diff. = 0.0621501
[2019-01-30 21:22:48.536] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433954
[2019-01-30 21:22:48.550] [jointLog] [info] iteration = 400 | max rel diff. = 0.0270718
[2019-01-30 21:22:48.565] [jointLog] [info] iteration = 500 | max rel diff. = 0.0244143
[2019-01-30 21:22:48.579] [jointLog] [info] iteration = 600 | max rel diff. = 0.016607
[2019-01-30 21:22:48.594] [jointLog] [info] iteration = 700 | max rel diff. = 0.0147562
[2019-01-30 21:22:48.608] [jointLog] [info] iteration = 800 | max rel diff. = 0.0137182
[2019-01-30 21:22:48.623] [jointLog] [info] iteration = 900 | max rel diff. = 0.0104647
[2019-01-30 21:22:48.638] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0104646
[2019-01-30 21:22:48.648] [jointLog] [info] iteration = 1068 | max rel diff. = 0.00877226
[2019-01-30 21:22:48.648] [jointLog] [info] Finished optimizer
[2019-01-30 21:22:48.648] [jointLog] [info] writing output 

[2019-01-30 21:22:48.659] [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: non-bleached_44_01/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_44_01/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > non-bleached_44_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-P05-GAGTGG-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P05-GAGTGG-READ2-Sequences.txt.gz_val_2.fq.gz) -o non-bleached_44_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 ] => { non-bleached_44_02 }
### [ threads ] => { 23 }
Logs will be written to non-bleached_44_02/logs
[2019-01-30 21:22:49.017] [jointLog] [info] parsing read library format
[2019-01-30 21:22:49.017] [jointLog] [info] There is 1 library.
[2019-01-30 21:22:49.078] [stderrLog] [info] Loading Suffix Array 
[2019-01-30 21:22:49.078] [jointLog] [info] Loading Quasi index
[2019-01-30 21:22:49.078] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:22:49.115] [stderrLog] [info] Loading Transcript Info 
[2019-01-30 21:22:49.124] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-01-30 21:22:49.127] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-01-30 21:22:49.129] [stderrLog] [info] Computing transcript lengths
[2019-01-30 21:22:49.129] [stderrLog] [info] Waiting to finish loading hash
[2019-01-30 21:22:49.478] [jointLog] [info] done
[2019-01-30 21:22:49.478] [jointLog] [info] Index contained 5838 targets




[2019-01-30 21:22:49.478] [stderrLog] [info] Done loading index


processed 500000 fragments
hits: 91790, hits per frag:  0.201103

processed 1000000 fragments
hits: 183124, hits per frag:  0.199498

processed 1500000 fragments
hits: 275560, hits per frag:  0.197048

processed 2000000 fragments
hits: 368188, hits per frag:  0.195884

processed 2500000 fragments
hits: 459520, hits per frag:  0.187015

processed 3000000 fragments
hits: 551344, hits per frag:  0.191881

processed 3500000 fragments
hits: 643087, hits per frag:  0.191891

processed 4000000 fragments
hits: 734791, hits per frag:  0.187092

processed 4500000 fragments
hits: 825573, hits per frag:  0.187179

processed 5000000 fragments
hits: 917806, hits per frag:  0.184481

processed 5500000 fragments
hits: 1009123, hits per frag:  0.184484

processed 6000001 fragments
hits: 1100737, hits per frag:  0.188022

processed 6500000 fragments
hits: 1192580, hits per frag:  0.183636

processed 7000001 fragments
hits: 1283895, hits per frag:  0.18432

processed 7500000 fragments
hits: 1375386, hits per frag:  0.184269

processed 8000000 fragments
hits: 1467720, hits per frag:  0.185835

processed 8500000 fragments
hits: 1559914, hits per frag:  0.184513

processed 9000001 fragments
hits: 1653325, hits per frag:  0.184247

processed 9500000 fragments
hits: 1744264, hits per frag:  0.185589

processed 10000000 fragments
hits: 1836451, hits per frag:  0.184389

processed 10500000 fragments
hits: 1928248, hits per frag:  0.184703

processed 11000000 fragments
hits: 2020711, hits per frag:  0.18448

processed 11500000 fragments
hits: 2113149, hits per frag:  0.185645

processed 12000000 fragments
hits: 2204378, hits per frag:  0.185486

processed 12500000 fragments
hits: 2296301, hits per frag:  0.1855

processed 13000000 fragments
hits: 2388245, hits per frag:  0.184632

processed 13500000 fragments
hits: 2479252, hits per frag:  0.184048

processed 14000000 fragments
hits: 2571858, hits per frag:  0.184427

processed 14500000 fragments
hits: 2663911, hits per frag:  0.18494

processed 15000000 fragments
hits: 2755162, hits per frag:  0.185102

processed 15500000 fragments
hits: 2846567, hits per frag:  0.184709

processed 16000000 fragments
hits: 2937016, hits per frag:  0.183957

processed 16500000 fragments
hits: 3028837, hits per frag:  0.184017

processed 17000000 fragments
hits: 3119923, hits per frag:  0.184098

processed 17500000 fragments
hits: 3212036, hits per frag:  0.183627

processed 18000000 fragments
hits: 3303768, hits per frag:  0.184371

processed 18500001 fragments
hits: 3395575, hits per frag:  0.184021

processed 19000000 fragments
hits: 3487516, hits per frag:  0.183846

processed 19500000 fragments
hits: 3579746, hits per frag:  0.184467

processed 20000000 fragments
hits: 3671988, hits per frag:  0.184248

processed 20500001 fragments
hits: 3763545, hits per frag:  0.184042

processed 21000000 fragments
hits: 3856100, hits per frag:  0.184263

processed 21500000 fragments
hits: 3948569, hits per frag:  0.184246

processed 22000000 fragments
hits: 4041104, hits per frag:  0.184184

processed 22500000 fragments
hits: 4133741, hits per frag:  0.184427

processed 23000000 fragments
hits: 4225156, hits per frag:  0.184074

processed 23500000 fragments
hits: 4317481, hits per frag:  0.184191

processed 24000000 fragments
hits: 4408661, hits per frag:  0.184313

processed 24500000 fragments
hits: 4500575, hits per frag:  0.18381

processed 25000000 fragments
hits: 4593331, hits per frag:  0.184038

processed 25500000 fragments
hits: 4683889, hits per frag:  0.184364

processed 26000000 fragments
hits: 4774206, hits per frag:  0.184239









[2019-01-30 21:23:52.963] [jointLog] [info] Computed 7419 rich equivalence classes for further processing
[2019-01-30 21:23:52.963] [jointLog] [info] Counted 2384873 total reads in the equivalence classes 
[2019-01-30 21:23:52.973] [jointLog] [warning] 0.047308% 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.


[2019-01-30 21:23:52.974] [jointLog] [warning] Only 2384873 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2019-01-30 21:23:52.974] [jointLog] [info] Mapping rate = 9.14069%

[2019-01-30 21:23:52.974] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:23:52.974] [jointLog] [info] Starting optimizer
[2019-01-30 21:23:52.981] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:23:52.981] [jointLog] [info] iteration = 0 | max rel diff. = 587.786
[2019-01-30 21:23:52.999] [jointLog] [info] iteration = 100 | max rel diff. = 0.116773
[2019-01-30 21:23:53.016] [jointLog] [info] iteration = 200 | max rel diff. = 0.0557389
[2019-01-30 21:23:53.032] [jointLog] [info] iteration = 300 | max rel diff. = 0.0365148
[2019-01-30 21:23:53.047] [jointLog] [info] iteration = 400 | max rel diff. = 0.0289878
[2019-01-30 21:23:53.062] [jointLog] [info] iteration = 500 | max rel diff. = 0.0204643
[2019-01-30 21:23:53.078] [jointLog] [info] iteration = 600 | max rel diff. = 0.0174253
[2019-01-30 21:23:53.093] [jointLog] [info] iteration = 700 | max rel diff. = 0.0162272
[2019-01-30 21:23:53.109] [jointLog] [info] iteration = 800 | max rel diff. = 0.012992
[2019-01-30 21:23:53.126] [jointLog] [info] iteration = 900 | max rel diff. = 0.0120714
[2019-01-30 21:23:53.143] [jointLog] [info] iteration = 1000 | max rel diff. = 0.00983096
[2019-01-30 21:23:53.143] [jointLog] [info] iteration = 1001 | max rel diff. = 0.00983096
[2019-01-30 21:23:53.144] [jointLog] [info] Finished optimizer
[2019-01-30 21:23:53.144] [jointLog] [info] writing output 

[2019-01-30 21:23:53.155] [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: non-bleached_44_02/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_44_02/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > non-bleached_44_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-P12-TGACCA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P12-TGACCA-READ2-Sequences.txt.gz_val_2.fq.gz) -o non-bleached_44_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 ] => { non-bleached_44_03 }
### [ threads ] => { 23 }
Logs will be written to non-bleached_44_03/logs
[2019-01-30 21:23:53.517] [jointLog] [info] parsing read library format
[2019-01-30 21:23:53.517] [jointLog] [info] There is 1 library.
[2019-01-30 21:23:53.579] [stderrLog] [info] Loading Suffix Array 
[2019-01-30 21:23:53.579] [jointLog] [info] Loading Quasi index
[2019-01-30 21:23:53.579] [jointLog] [info] Loading 32-bit quasi index
[2019-01-30 21:23:53.612] [stderrLog] [info] Loading Transcript Info 
[2019-01-30 21:23:53.620] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-01-30 21:23:53.624] [stderrLog] [info] There were 5838 set bits in the bit array
[2019-01-30 21:23:53.626] [stderrLog] [info] Computing transcript lengths
[2019-01-30 21:23:53.626] [stderrLog] [info] Waiting to finish loading hash
[2019-01-30 21:23:53.990] [jointLog] [info] done
[2019-01-30 21:23:53.990] [jointLog] [info] Index contained 5838 targets
[2019-01-30 21:23:53.990] [stderrLog] [info] Done loading index






processed 500000 fragments
hits: 87976, hits per frag:  0.210981

processed 1000000 fragments
hits: 176081, hits per frag:  0.194577

processed 1500000 fragments
hits: 264390, hits per frag:  0.177947

processed 2000000 fragments
hits: 352064, hits per frag:  0.185549

processed 2500000 fragments
hits: 439599, hits per frag:  0.182051

processed 3000000 fragments
hits: 526000, hits per frag:  0.182159

processed 3500000 fragments
hits: 614432, hits per frag:  0.182317

processed 4000000 fragments
hits: 701994, hits per frag:  0.180919

processed 4500000 fragments
hits: 790233, hits per frag:  0.17715

processed 5000000 fragments
hits: 878822, hits per frag:  0.177077

processed 5500000 fragments
hits: 967145, hits per frag:  0.17826

processed 6000000 fragments
hits: 1054826, hits per frag:  0.17787

processed 6500000 fragments
hits: 1142247, hits per frag:  0.177238

processed 7000000 fragments
hits: 1229454, hits per frag:  0.176178

processed 7500000 fragments
hits: 1316430, hits per frag:  0.175998

processed 8000000 fragments
hits: 1402860, hits per frag:  0.176303

processed 8500000 fragments
hits: 1490561, hits per frag:  0.176184

processed 9000000 fragments
hits: 1577768, hits per frag:  0.176798

processed 9500000 fragments
hits: 1665036, hits per frag:  0.176799

processed 10000001 fragments
hits: 1752667, hits per frag:  0.175729

processed 10500000 fragments
hits: 1840232, hits per frag:  0.176613

processed 11000000 fragments
hits: 1929304, hits per frag:  0.176447

processed 11500000 fragments
hits: 2017693, hits per frag:  0.176284

processed 12000001 fragments
hits: 2103901, hits per frag:  0.17648

processed 12500000 fragments
hits: 2190042, hits per frag:  0.176725

processed 13000000 fragments
hits: 2277607, hits per frag:  0.176953

processed 13500000 fragments
hits: 2365306, hits per frag:  0.176136

processed 14000000 fragments
hits: 2453144, hits per frag:  0.176049

processed 14500001 fragments
hits: 2540910, hits per frag:  0.176438

processed 15000000 fragments
hits: 2628361, hits per frag:  0.175636

processed 15500000 fragments
hits: 2715685, hits per frag:  0.176302

processed 16000000 fragments
hits: 2803241, hits per frag:  0.176064

processed 16500000 fragments
hits: 2890343, hits per frag:  0.176334

processed 17000000 fragments
hits: 2979623, hits per frag:  0.175969

processed 17500000 fragments
hits: 3067621, hits per frag:  0.176341

processed 18000000 fragments
hits: 3156000, hits per frag:  0.175896

processed 18500000 fragments
hits: 3243263, hits per frag:  0.175524

processed 19000001 fragments
hits: 3331346, hits per frag:  0.175678

processed 19500001 fragments
hits: 3419607, hits per frag:  0.175867

processed 20000000 fragments
hits: 3507491, hits per frag:  0.176356

processed 20500001 fragments
hits: 3596455, hits per frag:  0.175694

processed 21000000 fragments
hits: 3683515, hits per frag:  0.175959

processed 21500000 fragments
hits: 3771046, hits per frag:  0.176513

processed 22000000 fragments
hits: 3858780, hits per frag:  0.176007

processed 22500000 fragments
hits: 3946393, hits per frag:  0.176007

processed 23000001 fragments
hits: 4033652, hits per frag:  0.17596

processed 23500000 fragments
hits: 4120552, hits per frag:  0.176182

processed 24000000 fragments
hits: 4208926, hits per frag:  0.176065

processed 24500000 fragments
hits: 4296432, hits per frag:  0.175924

processed 25000000 fragments
hits: 4384090, hits per frag:  0.17578

processed 25500000 fragments
hits: 4471819, hits per frag:  0.176103

processed 26000000 fragments
hits: 4558485, hits per frag:  0.175581









[2019-01-30 21:24:58.227] [jointLog] [info] Computed 7721 rich equivalence classes for further processing
[2019-01-30 21:24:58.227] [jointLog] [info] Counted 2334407 total reads in the equivalence classes 
[2019-01-30 21:24:58.238] [jointLog] [warning] 0.0152392% 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.


[2019-01-30 21:24:58.238] [jointLog] [warning] Only 2334407 fragments were mapped, but the number of burn-in fragments was set to 5000000.
The effective lengths have been computed using the observed mappings.

[2019-01-30 21:24:58.238] [jointLog] [info] Mapping rate = 8.82085%

[2019-01-30 21:24:58.238] [jointLog] [info] finished quantifyLibrary()
[2019-01-30 21:24:58.239] [jointLog] [info] Starting optimizer
[2019-01-30 21:24:58.244] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-01-30 21:24:58.244] [jointLog] [info] iteration = 0 | max rel diff. = 595.466
[2019-01-30 21:24:58.262] [jointLog] [info] iteration = 100 | max rel diff. = 0.123189
[2019-01-30 21:24:58.278] [jointLog] [info] iteration = 200 | max rel diff. = 0.055328
[2019-01-30 21:24:58.295] [jointLog] [info] iteration = 300 | max rel diff. = 0.0417837
[2019-01-30 21:24:58.311] [jointLog] [info] iteration = 400 | max rel diff. = 0.0269787
[2019-01-30 21:24:58.327] [jointLog] [info] iteration = 500 | max rel diff. = 0.0220706
[2019-01-30 21:24:58.342] [jointLog] [info] iteration = 600 | max rel diff. = 0.0194603
[2019-01-30 21:24:58.357] [jointLog] [info] iteration = 700 | max rel diff. = 0.0201996
[2019-01-30 21:24:58.373] [jointLog] [info] iteration = 800 | max rel diff. = 0.0124207
[2019-01-30 21:24:58.390] [jointLog] [info] iteration = 900 | max rel diff. = 0.0124209
[2019-01-30 21:24:58.406] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0102374
[2019-01-30 21:24:58.412] [jointLog] [info] iteration = 1034 | max rel diff. = 0.00882132
[2019-01-30 21:24:58.412] [jointLog] [info] Finished optimizer
[2019-01-30 21:24:58.412] [jointLog] [info] writing output 

[2019-01-30 21:24:58.423] [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: non-bleached_44_03/lib_format_counts.json for details

CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_44_03/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > non-bleached_44_03/quant.sf.genes