CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P14-GTGGCC-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P14-GTGGCC-READ2-Sequences.txt.gz_val_2.fq.gz -o B_female_44_01  -p 23
### salmon (mapping-based) v0.12.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P14-GTGGCC-READ1-Sequences.txt.gz_val_1.fq.gz }
### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P14-GTGGCC-READ2-Sequences.txt.gz_val_2.fq.gz }
### [ output ] => { B_female_44_01 }
### [ threads ] => { 23 }
Logs will be written to B_female_44_01/logs
[2019-12-19 10:34:26.939] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-12-19 10:34:26.939] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-12-19 10:34:26.939] [jointLog] [info] parsing read library format
[2019-12-19 10:34:26.939] [jointLog] [info] There is 1 library.
[2019-12-19 10:34:26.997] [jointLog] [info] Loading Quasi index
[2019-12-19 10:34:26.997] [jointLog] [info] Loading 32-bit quasi index
[2019-12-19 10:34:26.997] [stderrLog] [info] Loading Suffix Array 
[2019-12-19 10:34:28.313] [stderrLog] [info] Loading Transcript Info 
[2019-12-19 10:34:28.753] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-12-19 10:34:28.856] [stderrLog] [info] There were 861,197 set bits in the bit array
[2019-12-19 10:34:28.925] [stderrLog] [info] Computing transcript lengths
[2019-12-19 10:34:28.926] [stderrLog] [info] Waiting to finish loading hash
[2019-12-19 10:34:43.770] [stderrLog] [info] Done loading index
[2019-12-19 10:34:43.771] [jointLog] [info] done
[2019-12-19 10:34:43.771] [jointLog] [info] Index contained 861,197 targets






processed 500,001 fragments
hits: 894,289, hits per frag:  1.90658

processed 1,000,002 fragments
hits: 1,785,987, hits per frag:  2.21335

processed 1,500,001 fragments
hits: 2,683,637, hits per frag:  1.94488

processed 2,000,000 fragments
hits: 3,582,163, hits per frag:  1.81766

processed 2,500,000 fragments
hits: 4,480,067, hits per frag:  1.84143

processed 3,000,000 fragments
hits: 5,379,838, hits per frag:  1.84565

processed 3,500,000 fragments
hits: 6,275,657, hits per frag:  1.86335

processed 4,000,001 fragments
hits: 7,169,481, hits per frag:  1.83561

processed 4,500,000 fragments
hits: 8,058,847, hits per frag:  1.81318

processed 5,000,000 fragments
hits: 8,950,579, hits per frag:  1.80306

processed 5,500,000 fragments
hits: 9,842,515, hits per frag:  1.80663

processed 6,000,000 fragments
hits: 10,733,421, hits per frag:  1.82616

processed 6,500,000 fragments
hits: 11,624,603, hits per frag:  1.81131

processed 7,000,000 fragments
hits: 12,512,153, hits per frag:  1.80916

processed 7,500,000 fragments
hits: 13,400,734, hits per frag:  1.79688

processed 8,000,000 fragments
hits: 14,293,669, hits per frag:  1.833

processed 8,500,000 fragments
hits: 15,193,273, hits per frag:  1.80206

processed 9,000,001 fragments
hits: 16,092,668, hits per frag:  1.80562

processed 9,500,000 fragments
hits: 17,003,165, hits per frag:  1.81808

processed 10,000,000 fragments
hits: 17,902,865, hits per frag:  1.79335

processed 10,500,001 fragments
hits: 18,809,821, hits per frag:  1.80245

processed 11,000,000 fragments
hits: 19,717,041, hits per frag:  1.79497

processed 11,500,000 fragments
hits: 20,625,053, hits per frag:  1.80096

processed 12,000,000 fragments
hits: 21,531,726, hits per frag:  1.80064

processed 12,500,000 fragments
hits: 22,436,105, hits per frag:  1.80197

processed 13,000,001 fragments
hits: 23,338,473, hits per frag:  1.81514

processed 13,500,000 fragments
hits: 24,238,426, hits per frag:  1.80532

processed 14,000,000 fragments
hits: 25,136,720, hits per frag:  1.84443

processed 14,500,000 fragments
hits: 26,033,235, hits per frag:  1.80595

processed 15,000,000 fragments
hits: 26,931,006, hits per frag:  1.79818

processed 15,500,002 fragments
hits: 27,828,264, hits per frag:  1.81598

processed 16,000,001 fragments
hits: 28,722,596, hits per frag:  1.80211

processed 16,500,000 fragments
hits: 29,614,892, hits per frag:  1.80774

processed 17,000,001 fragments
hits: 30,507,242, hits per frag:  1.8011

processed 18,000,000 fragments
hits: 32,297,476, hits per frag:  1.82914

processed 18,500,000 fragments
hits: 33,190,641, hits per frag:  1.80539

processed 19,000,000 fragments
hits: 34,087,566, hits per frag:  1.80646

processed 19,500,000 fragments
hits: 34,982,306, hits per frag:  1.80096

processed 20,000,000 fragments
hits: 35,870,234, hits per frag:  1.80566

processed 20,500,000 fragments
hits: 36,754,811, hits per frag:  1.80457

processed 21,000,000 fragments
hits: 37,642,557, hits per frag:  1.80037

processed 21,500,000 fragments
hits: 38,532,437, hits per frag:  1.80228

processed 22,000,000 fragments
hits: 39,422,239, hits per frag:  1.79459

processed 22,500,000 fragments
hits: 40,316,237, hits per frag:  1.79926

processed 23,000,000 fragments
hits: 41,201,834, hits per frag:  1.79767

processed 23,500,001 fragments
hits: 42,089,798, hits per frag:  1.7957

processed 24,000,000 fragments
hits: 42,981,014, hits per frag:  1.79844

processed 24,500,001 fragments
hits: 43,888,296, hits per frag:  1.80176

processed 25,000,000 fragments
hits: 44,789,622, hits per frag:  1.79559

processed 25,500,000 fragments
hits: 45,700,089, hits per frag:  1.79916

processed 26,000,000 fragments
hits: 46,613,857, hits per frag:  1.79839

processed 26,500,001 fragments
hits: 47,535,602, hits per frag:  1.79783

processed 27,000,000 fragments
hits: 48,450,038, hits per frag:  1.80742

processed 27,500,000 fragments
hits: 49,358,361, hits per frag:  1.79885

processed 28,000,000 fragments
hits: 50,263,265, hits per frag:  1.79707

processed 28,500,000 fragments
hits: 51,164,371, hits per frag:  1.80145

processed 29,000,000 fragments
hits: 52,068,792, hits per frag:  1.79721

processed 29,500,001 fragments
hits: 52,978,012, hits per frag:  1.80241

processed 30,000,000 fragments
hits: 53,879,014, hits per frag:  1.80388

processed 30,500,000 fragments
hits: 54,778,310, hits per frag:  1.79959

processed 31,000,000 fragments
hits: 55,672,721, hits per frag:  1.79939

processed 31,500,000 fragments
hits: 56,567,668, hits per frag:  1.79652[2019-12-19 10:36:07.852] [jointLog] [info] Thread saw mini-batch with a maximum of 7.72% zero probability fragments
[2019-12-19 10:36:07.853] [jointLog] [info] Thread saw mini-batch with a maximum of 7.76% zero probability fragments
[2019-12-19 10:36:07.853] [jointLog] [info] Thread saw mini-batch with a maximum of 7.48% zero probability fragments
[2019-12-19 10:36:07.853] [jointLog] [info] Thread saw mini-batch with a maximum of 7.84% zero probability fragments
[2019-12-19 10:36:07.853] [jointLog] [info] Thread saw mini-batch with a maximum of 7.68% zero probability fragments
[2019-12-19 10:36:07.853] [jointLog] [info] Thread saw mini-batch with a maximum of 7.76% zero probability fragments
[2019-12-19 10:36:07.853] [jointLog] [info] Thread saw mini-batch with a maximum of 7.64% zero probability fragments
[2019-12-19 10:36:07.853] [jointLog] [info] Thread saw mini-batch with a maximum of 7.66% zero probability fragments
[2019-12-19 10:36:07.853] [jointLog] [info] Thread saw mini-batch with a maximum of 7.54% zero probability fragments
[2019-12-19 10:36:07.853] [jointLog] [info] Thread saw mini-batch with a maximum of 7.26% zero probability fragments
[2019-12-19 10:36:07.853] [jointLog] [info] Thread saw mini-batch with a maximum of 7.90% zero probability fragments
[2019-12-19 10:36:07.859] [jointLog] [info] Thread saw mini-batch with a maximum of 7.68% zero probability fragments
[2019-12-19 10:36:07.867] [jointLog] [info] Thread saw mini-batch with a maximum of 7.44% zero probability fragments
[2019-12-19 10:36:07.869] [jointLog] [info] Thread saw mini-batch with a maximum of 7.52% zero probability fragments
[2019-12-19 10:36:07.893] [jointLog] [info] Thread saw mini-batch with a maximum of 7.62% zero probability fragments
[2019-12-19 10:36:07.895] [jointLog] [info] Thread saw mini-batch with a maximum of 7.56% zero probability fragments
[2019-12-19 10:36:07.900] [jointLog] [info] Thread saw mini-batch with a maximum of 7.74% zero probability fragments
[2019-12-19 10:36:07.925] [jointLog] [info] Thread saw mini-batch with a maximum of 7.96% zero probability fragments
[2019-12-19 10:36:07.930] [jointLog] [info] Thread saw mini-batch with a maximum of 7.78% zero probability fragments
[2019-12-19 10:36:07.932] [jointLog] [info] Thread saw mini-batch with a maximum of 7.68% zero probability fragments
[2019-12-19 10:36:07.950] [jointLog] [info] Thread saw mini-batch with a maximum of 7.70% zero probability fragments
[2019-12-19 10:36:07.963] [jointLog] [info] Thread saw mini-batch with a maximum of 7.38% zero probability fragments
[2019-12-19 10:36:07.989] [jointLog] [info] Thread saw mini-batch with a maximum of 7.58% zero probability fragments










[2019-12-19 10:36:08.502] [jointLog] [info] Computed 602,288 rich equivalence classes for further processing
[2019-12-19 10:36:08.502] [jointLog] [info] Counted 21,728,911 total reads in the equivalence classes 
[2019-12-19 10:36:08.528] [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.


[2019-12-19 10:36:08.528] [jointLog] [info] Mapping rate = 68.6389%

[2019-12-19 10:36:08.528] [jointLog] [info] finished quantifyLibrary()
[2019-12-19 10:36:08.528] [jointLog] [info] Starting optimizer
[2019-12-19 10:36:08.945] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-12-19 10:36:08.972] [jointLog] [info] iteration = 0 | max rel diff. = 1205.26
[2019-12-19 10:36:11.647] [jointLog] [info] iteration = 100 | max rel diff. = 15.3358
[2019-12-19 10:36:14.357] [jointLog] [info] iteration = 200 | max rel diff. = 5.34607
[2019-12-19 10:36:16.887] [jointLog] [info] iteration = 300 | max rel diff. = 5.22153
[2019-12-19 10:36:19.378] [jointLog] [info] iteration = 400 | max rel diff. = 12.3097
[2019-12-19 10:36:21.872] [jointLog] [info] iteration = 500 | max rel diff. = 0.286174
[2019-12-19 10:36:24.279] [jointLog] [info] iteration = 600 | max rel diff. = 0.214552
[2019-12-19 10:36:26.708] [jointLog] [info] iteration = 700 | max rel diff. = 1.64281
[2019-12-19 10:36:29.180] [jointLog] [info] iteration = 800 | max rel diff. = 0.353817
[2019-12-19 10:36:31.617] [jointLog] [info] iteration = 900 | max rel diff. = 0.214142
[2019-12-19 10:36:34.069] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.139031
[2019-12-19 10:36:36.369] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.76428
[2019-12-19 10:36:38.788] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.746375
[2019-12-19 10:36:41.202] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0797545
[2019-12-19 10:36:43.592] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.425124
[2019-12-19 10:36:46.015] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.0296526
[2019-12-19 10:36:48.334] [jointLog] [info] iteration = 1,600 | max rel diff. = 0.190659
[2019-12-19 10:36:48.690] [jointLog] [info] iteration = 1,614 | max rel diff. = 0.00468146
[2019-12-19 10:36:48.756] [jointLog] [info] Finished optimizer
[2019-12-19 10:36:48.756] [jointLog] [info] writing output 

CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl B_female_44_01/quant.sf /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.gene_trans_map > B_female_44_01/quant.sf.genes
CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P03-ACTGAT-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P03-ACTGAT-READ2-Sequences.txt.gz_val_2.fq.gz -o B_female_44_02  -p 23
### salmon (mapping-based) v0.12.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P03-ACTGAT-READ1-Sequences.txt.gz_val_1.fq.gz }
### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P03-ACTGAT-READ2-Sequences.txt.gz_val_2.fq.gz }
### [ output ] => { B_female_44_02 }
### [ threads ] => { 23 }
Logs will be written to B_female_44_02/logs
[2019-12-19 10:37:07.415] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-12-19 10:37:07.415] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-12-19 10:37:07.415] [jointLog] [info] parsing read library format
[2019-12-19 10:37:07.415] [jointLog] [info] There is 1 library.
[2019-12-19 10:37:07.474] [jointLog] [info] Loading Quasi index
[2019-12-19 10:37:07.474] [jointLog] [info] Loading 32-bit quasi index
[2019-12-19 10:37:07.474] [stderrLog] [info] Loading Suffix Array 
[2019-12-19 10:37:08.779] [stderrLog] [info] Loading Transcript Info 
[2019-12-19 10:37:09.207] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-12-19 10:37:09.309] [stderrLog] [info] There were 861,197 set bits in the bit array
[2019-12-19 10:37:09.378] [stderrLog] [info] Computing transcript lengths
[2019-12-19 10:37:09.379] [stderrLog] [info] Waiting to finish loading hash
[2019-12-19 10:37:26.185] [stderrLog] [info] Done loading index
[2019-12-19 10:37:26.185] [jointLog] [info] done
[2019-12-19 10:37:26.185] [jointLog] [info] Index contained 861,197 targets






processed 500,000 fragments
hits: 878,123, hits per frag:  2.36717

processed 1,000,000 fragments
hits: 1,756,648, hits per frag:  1.97137

processed 1,500,000 fragments
hits: 2,634,748, hits per frag:  1.85384

processed 2,000,000 fragments
hits: 3,515,445, hits per frag:  1.858

processed 2,500,000 fragments
hits: 4,395,437, hits per frag:  1.86423

processed 3,000,000 fragments
hits: 5,271,919, hits per frag:  1.79651

processed 3,500,000 fragments
hits: 6,146,956, hits per frag:  1.78506

processed 4,000,000 fragments
hits: 7,023,198, hits per frag:  1.86785

processed 4,500,000 fragments
hits: 7,899,699, hits per frag:  1.8444

processed 5,000,000 fragments
hits: 8,774,359, hits per frag:  1.77194

processed 5,500,000 fragments
hits: 9,646,247, hits per frag:  1.77528

processed 6,000,000 fragments
hits: 10,528,035, hits per frag:  1.7639

processed 6,500,000 fragments
hits: 11,411,098, hits per frag:  1.77239

processed 7,000,000 fragments
hits: 12,300,472, hits per frag:  1.77544

processed 7,500,001 fragments
hits: 13,185,416, hits per frag:  1.76755

processed 8,000,000 fragments
hits: 14,074,297, hits per frag:  1.78305

processed 8,500,001 fragments
hits: 14,958,585, hits per frag:  1.78668

processed 9,000,000 fragments
hits: 15,847,608, hits per frag:  1.76638

processed 9,500,000 fragments
hits: 16,731,432, hits per frag:  1.77501

processed 10,000,000 fragments
hits: 17,613,603, hits per frag:  1.76614

processed 10,500,000 fragments
hits: 18,495,453, hits per frag:  1.77792

processed 11,000,000 fragments
hits: 19,380,301, hits per frag:  1.77536

processed 11,500,000 fragments
hits: 20,258,162, hits per frag:  1.77006

processed 12,000,000 fragments
hits: 21,133,921, hits per frag:  1.76339

processed 12,500,000 fragments
hits: 22,010,650, hits per frag:  1.79588

processed 13,000,000 fragments
hits: 22,886,822, hits per frag:  1.77831

processed 13,500,000 fragments
hits: 23,762,206, hits per frag:  1.78631

processed 14,000,000 fragments
hits: 24,640,623, hits per frag:  1.76797

processed 14,500,000 fragments
hits: 25,514,315, hits per frag:  1.78254

processed 15,000,000 fragments
hits: 26,383,118, hits per frag:  1.77129

processed 15,500,000 fragments
hits: 27,256,039, hits per frag:  1.78838

processed 16,000,001 fragments
hits: 28,130,276, hits per frag:  1.77614

processed 16,500,001 fragments
hits: 29,004,138, hits per frag:  1.76266

processed 17,000,001 fragments
hits: 29,872,971, hits per frag:  1.76531

processed 17,500,000 fragments
hits: 30,743,900, hits per frag:  1.76303

processed 18,000,000 fragments
hits: 31,633,587, hits per frag:  1.77442

processed 18,500,000 fragments
hits: 32,525,610, hits per frag:  1.76362

processed 19,000,001 fragments
hits: 33,428,799, hits per frag:  1.77437

processed 19,500,000 fragments
hits: 34,327,811, hits per frag:  1.76715

processed 20,000,000 fragments
hits: 35,218,225, hits per frag:  1.76713

processed 20,500,002 fragments
hits: 36,108,770, hits per frag:  1.76708

processed 21,000,000 fragments
hits: 36,993,121, hits per frag:  1.77227

processed 21,500,001 fragments
hits: 37,887,482, hits per frag:  1.76527

processed 22,000,000 fragments
hits: 38,769,613, hits per frag:  1.76414

processed 22,500,000 fragments
hits: 39,649,027, hits per frag:  1.76538

processed 23,000,000 fragments
hits: 40,524,791, hits per frag:  1.7812[2019-12-19 10:38:26.289] [jointLog] [info] Thread saw mini-batch with a maximum of 9.10% zero probability fragments
[2019-12-19 10:38:26.289] [jointLog] [info] Thread saw mini-batch with a maximum of 9.58% zero probability fragments
[2019-12-19 10:38:26.289] [jointLog] [info] Thread saw mini-batch with a maximum of 8.80% zero probability fragments
[2019-12-19 10:38:26.289] [jointLog] [info] Thread saw mini-batch with a maximum of 9.26% zero probability fragments
[2019-12-19 10:38:26.289] [jointLog] [info] Thread saw mini-batch with a maximum of 8.78% zero probability fragments
[2019-12-19 10:38:26.289] [jointLog] [info] Thread saw mini-batch with a maximum of 9.06% zero probability fragments
[2019-12-19 10:38:26.289] [jointLog] [info] Thread saw mini-batch with a maximum of 9.70% zero probability fragments
[2019-12-19 10:38:26.289] [jointLog] [info] Thread saw mini-batch with a maximum of 8.92% zero probability fragments
[2019-12-19 10:38:26.289] [jointLog] [info] Thread saw mini-batch with a maximum of 9.10% zero probability fragments
[2019-12-19 10:38:26.289] [jointLog] [info] Thread saw mini-batch with a maximum of 8.92% zero probability fragments
[2019-12-19 10:38:26.289] [jointLog] [info] Thread saw mini-batch with a maximum of 9.18% zero probability fragments
[2019-12-19 10:38:26.298] [jointLog] [info] Thread saw mini-batch with a maximum of 9.36% zero probability fragments
[2019-12-19 10:38:26.301] [jointLog] [info] Thread saw mini-batch with a maximum of 9.34% zero probability fragments
[2019-12-19 10:38:26.308] [jointLog] [info] Thread saw mini-batch with a maximum of 9.26% zero probability fragments
[2019-12-19 10:38:26.325] [jointLog] [info] Thread saw mini-batch with a maximum of 8.88% zero probability fragments
[2019-12-19 10:38:26.334] [jointLog] [info] Thread saw mini-batch with a maximum of 9.24% zero probability fragments
[2019-12-19 10:38:26.348] [jointLog] [info] Thread saw mini-batch with a maximum of 8.88% zero probability fragments
[2019-12-19 10:38:26.354] [jointLog] [info] Thread saw mini-batch with a maximum of 8.98% zero probability fragments
[2019-12-19 10:38:26.369] [jointLog] [info] Thread saw mini-batch with a maximum of 9.14% zero probability fragments
[2019-12-19 10:38:26.383] [jointLog] [info] Thread saw mini-batch with a maximum of 9.36% zero probability fragments
[2019-12-19 10:38:26.394] [jointLog] [info] Thread saw mini-batch with a maximum of 8.94% zero probability fragments
[2019-12-19 10:38:26.405] [jointLog] [info] Thread saw mini-batch with a maximum of 9.24% zero probability fragments
[2019-12-19 10:38:26.417] [jointLog] [info] Thread saw mini-batch with a maximum of 8.92% zero probability fragments










[2019-12-19 10:38:26.914] [jointLog] [info] Computed 550,508 rich equivalence classes for further processing
[2019-12-19 10:38:26.914] [jointLog] [info] Counted 15,676,050 total reads in the equivalence classes 
[2019-12-19 10:38:26.939] [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.


[2019-12-19 10:38:26.939] [jointLog] [info] Mapping rate = 68.0828%

[2019-12-19 10:38:26.939] [jointLog] [info] finished quantifyLibrary()
[2019-12-19 10:38:26.939] [jointLog] [info] Starting optimizer
[2019-12-19 10:38:27.383] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-12-19 10:38:27.410] [jointLog] [info] iteration = 0 | max rel diff. = 942.798
[2019-12-19 10:38:29.975] [jointLog] [info] iteration = 100 | max rel diff. = 16.7608
[2019-12-19 10:38:32.404] [jointLog] [info] iteration = 200 | max rel diff. = 12.8301
[2019-12-19 10:38:34.880] [jointLog] [info] iteration = 300 | max rel diff. = 1.83995
[2019-12-19 10:38:37.189] [jointLog] [info] iteration = 400 | max rel diff. = 1.89623
[2019-12-19 10:38:39.442] [jointLog] [info] iteration = 500 | max rel diff. = 1.57078
[2019-12-19 10:38:41.903] [jointLog] [info] iteration = 600 | max rel diff. = 3.83871
[2019-12-19 10:38:44.266] [jointLog] [info] iteration = 700 | max rel diff. = 4.38262
[2019-12-19 10:38:46.611] [jointLog] [info] iteration = 800 | max rel diff. = 0.443012
[2019-12-19 10:38:48.953] [jointLog] [info] iteration = 900 | max rel diff. = 0.408845
[2019-12-19 10:38:51.266] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0970463
[2019-12-19 10:38:53.715] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.103035
[2019-12-19 10:38:56.032] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.19659
[2019-12-19 10:38:58.337] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.455581
[2019-12-19 10:39:00.667] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.013617
[2019-12-19 10:39:02.360] [jointLog] [info] iteration = 1,475 | max rel diff. = 0.00752042
[2019-12-19 10:39:02.448] [jointLog] [info] Finished optimizer
[2019-12-19 10:39:02.448] [jointLog] [info] writing output 

CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl B_female_44_02/quant.sf /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.gene_trans_map > B_female_44_02/quant.sf.genes
CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P11-ACTTGA-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P11-ACTTGA-READ2-Sequences.txt.gz_val_2.fq.gz -o B_female_44_03  -p 23
### salmon (mapping-based) v0.12.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P11-ACTTGA-READ1-Sequences.txt.gz_val_1.fq.gz }
### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P11-ACTTGA-READ2-Sequences.txt.gz_val_2.fq.gz }
### [ output ] => { B_female_44_03 }
### [ threads ] => { 23 }
Logs will be written to B_female_44_03/logs
[2019-12-19 10:39:20.724] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-12-19 10:39:20.724] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-12-19 10:39:20.724] [jointLog] [info] parsing read library format
[2019-12-19 10:39:20.724] [jointLog] [info] There is 1 library.
[2019-12-19 10:39:20.783] [jointLog] [info] Loading Quasi index
[2019-12-19 10:39:20.783] [jointLog] [info] Loading 32-bit quasi index
[2019-12-19 10:39:20.783] [stderrLog] [info] Loading Suffix Array 
[2019-12-19 10:39:22.081] [stderrLog] [info] Loading Transcript Info 
[2019-12-19 10:39:22.515] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-12-19 10:39:22.621] [stderrLog] [info] There were 861,197 set bits in the bit array
[2019-12-19 10:39:22.690] [stderrLog] [info] Computing transcript lengths
[2019-12-19 10:39:22.691] [stderrLog] [info] Waiting to finish loading hash
[2019-12-19 10:39:37.995] [stderrLog] [info] Done loading index
[2019-12-19 10:39:37.995] [jointLog] [info] done
[2019-12-19 10:39:37.995] [jointLog] [info] Index contained 861,197 targets






processed 500,001 fragments
hits: 897,357, hits per frag:  1.90803

processed 1,000,000 fragments
hits: 1,797,177, hits per frag:  1.92556

processed 1,500,000 fragments
hits: 2,697,815, hits per frag:  2.13113

processed 2,000,000 fragments
hits: 3,599,500, hits per frag:  1.82678

processed 2,500,000 fragments
hits: 4,499,740, hits per frag:  1.83114

processed 3,000,001 fragments
hits: 5,398,305, hits per frag:  1.86538

processed 3,500,000 fragments
hits: 6,295,304, hits per frag:  1.8683

processed 4,000,001 fragments
hits: 7,193,086, hits per frag:  1.835

processed 4,500,000 fragments
hits: 8,087,666, hits per frag:  1.82155

processed 5,000,000 fragments
hits: 8,982,988, hits per frag:  1.84436

processed 5,500,000 fragments
hits: 9,879,972, hits per frag:  1.82933

processed 6,000,000 fragments
hits: 10,786,800, hits per frag:  1.81616

processed 6,500,000 fragments
hits: 11,695,513, hits per frag:  1.81016

processed 7,500,000 fragments
hits: 13,511,510, hits per frag:  1.81402

processed 8,000,000 fragments
hits: 14,421,235, hits per frag:  1.82051

processed 8,500,001 fragments
hits: 15,327,882, hits per frag:  1.81127

processed 9,000,000 fragments
hits: 16,233,663, hits per frag:  1.81272

processed 9,500,001 fragments
hits: 17,135,386, hits per frag:  1.83422

processed 10,000,000 fragments
hits: 18,036,752, hits per frag:  1.81111

processed 10,500,001 fragments
hits: 18,940,687, hits per frag:  1.8201

processed 11,000,000 fragments
hits: 19,840,563, hits per frag:  1.81069

processed 11,500,000 fragments
hits: 20,734,979, hits per frag:  1.81101

processed 12,000,000 fragments
hits: 21,633,979, hits per frag:  1.81567

processed 12,500,000 fragments
hits: 22,530,943, hits per frag:  1.81391

processed 13,000,001 fragments
hits: 23,432,439, hits per frag:  1.81107

processed 13,500,001 fragments
hits: 24,334,968, hits per frag:  1.81023

processed 14,000,001 fragments
hits: 25,229,104, hits per frag:  1.80884

processed 14,500,000 fragments
hits: 26,118,875, hits per frag:  1.80998

processed 15,000,001 fragments
hits: 27,011,952, hits per frag:  1.819

processed 15,500,002 fragments
hits: 27,905,635, hits per frag:  1.80849

processed 16,000,000 fragments
hits: 28,800,195, hits per frag:  1.80965

processed 16,500,000 fragments
hits: 29,689,983, hits per frag:  1.80397

processed 17,000,000 fragments
hits: 30,598,224, hits per frag:  1.8037

processed 17,500,001 fragments
hits: 31,507,501, hits per frag:  1.80704

processed 18,000,000 fragments
hits: 32,424,260, hits per frag:  1.80544

processed 18,500,000 fragments
hits: 33,352,835, hits per frag:  1.81301

processed 19,000,000 fragments
hits: 34,260,646, hits per frag:  1.8209

processed 19,500,000 fragments
hits: 35,170,602, hits per frag:  1.81258

processed 20,000,000 fragments
hits: 36,076,020, hits per frag:  1.81207

processed 20,500,000 fragments
hits: 36,990,459, hits per frag:  1.81735

processed 21,000,000 fragments
hits: 37,892,407, hits per frag:  1.81663

processed 21,500,000 fragments
hits: 38,794,268, hits per frag:  1.8069[2019-12-19 10:40:35.864] [jointLog] [info] Thread saw mini-batch with a maximum of 10.64% zero probability fragments
[2019-12-19 10:40:35.864] [jointLog] [info] Thread saw mini-batch with a maximum of 10.10% zero probability fragments
[2019-12-19 10:40:35.864] [jointLog] [info] Thread saw mini-batch with a maximum of 10.38% zero probability fragments
[2019-12-19 10:40:35.864] [jointLog] [info] Thread saw mini-batch with a maximum of 10.26% zero probability fragments
[2019-12-19 10:40:35.864] [jointLog] [info] Thread saw mini-batch with a maximum of 10.26% zero probability fragments
[2019-12-19 10:40:35.864] [jointLog] [info] Thread saw mini-batch with a maximum of 10.30% zero probability fragments
[2019-12-19 10:40:35.865] [jointLog] [info] Thread saw mini-batch with a maximum of 10.34% zero probability fragments
[2019-12-19 10:40:35.865] [jointLog] [info] Thread saw mini-batch with a maximum of 10.46% zero probability fragments
[2019-12-19 10:40:35.865] [jointLog] [info] Thread saw mini-batch with a maximum of 10.54% zero probability fragments
[2019-12-19 10:40:35.865] [jointLog] [info] Thread saw mini-batch with a maximum of 10.10% zero probability fragments
[2019-12-19 10:40:35.871] [jointLog] [info] Thread saw mini-batch with a maximum of 10.22% zero probability fragments
[2019-12-19 10:40:35.880] [jointLog] [info] Thread saw mini-batch with a maximum of 10.34% zero probability fragments
[2019-12-19 10:40:35.883] [jointLog] [info] Thread saw mini-batch with a maximum of 10.44% zero probability fragments
[2019-12-19 10:40:35.897] [jointLog] [info] Thread saw mini-batch with a maximum of 10.32% zero probability fragments
[2019-12-19 10:40:35.905] [jointLog] [info] Thread saw mini-batch with a maximum of 11.00% zero probability fragments
[2019-12-19 10:40:35.928] [jointLog] [info] Thread saw mini-batch with a maximum of 10.60% zero probability fragments
[2019-12-19 10:40:35.935] [jointLog] [info] Thread saw mini-batch with a maximum of 10.56% zero probability fragments
[2019-12-19 10:40:35.937] [jointLog] [info] Thread saw mini-batch with a maximum of 10.28% zero probability fragments
[2019-12-19 10:40:35.943] [jointLog] [info] Thread saw mini-batch with a maximum of 11.22% zero probability fragments
[2019-12-19 10:40:35.958] [jointLog] [info] Thread saw mini-batch with a maximum of 10.12% zero probability fragments
[2019-12-19 10:40:35.974] [jointLog] [info] Thread saw mini-batch with a maximum of 10.38% zero probability fragments
[2019-12-19 10:40:35.985] [jointLog] [info] Thread saw mini-batch with a maximum of 10.12% zero probability fragments
[2019-12-19 10:40:35.994] [jointLog] [info] Thread saw mini-batch with a maximum of 10.16% zero probability fragments




[2019-12-19 10:40:36.380] [jointLog] [info] Computed 477,999 rich equivalence classes for further processing
[2019-12-19 10:40:36.380] [jointLog] [info] Counted 14,593,282 total reads in the equivalence classes 






[2019-12-19 10:40:36.426] [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.


[2019-12-19 10:40:36.426] [jointLog] [info] Mapping rate = 66.517%

[2019-12-19 10:40:36.426] [jointLog] [info] finished quantifyLibrary()
[2019-12-19 10:40:36.426] [jointLog] [info] Starting optimizer
[2019-12-19 10:40:36.778] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-12-19 10:40:36.804] [jointLog] [info] iteration = 0 | max rel diff. = 763.173
[2019-12-19 10:40:39.212] [jointLog] [info] iteration = 100 | max rel diff. = 8.61921
[2019-12-19 10:40:41.557] [jointLog] [info] iteration = 200 | max rel diff. = 11.163
[2019-12-19 10:40:43.913] [jointLog] [info] iteration = 300 | max rel diff. = 1.8828
[2019-12-19 10:40:46.234] [jointLog] [info] iteration = 400 | max rel diff. = 0.353528
[2019-12-19 10:40:48.520] [jointLog] [info] iteration = 500 | max rel diff. = 3.56142
[2019-12-19 10:40:50.778] [jointLog] [info] iteration = 600 | max rel diff. = 3.38315
[2019-12-19 10:40:53.063] [jointLog] [info] iteration = 700 | max rel diff. = 2.15119
[2019-12-19 10:40:55.308] [jointLog] [info] iteration = 800 | max rel diff. = 0.134975
[2019-12-19 10:40:57.466] [jointLog] [info] iteration = 900 | max rel diff. = 0.0870457
[2019-12-19 10:40:59.616] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.489488
[2019-12-19 10:41:01.781] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.181531
[2019-12-19 10:41:02.679] [jointLog] [info] iteration = 1,140 | max rel diff. = 0.00909102
[2019-12-19 10:41:02.737] [jointLog] [info] Finished optimizer
[2019-12-19 10:41:02.737] [jointLog] [info] writing output 

CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl B_female_44_03/quant.sf /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.gene_trans_map > B_female_44_03/quant.sf.genes
CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P04-GTCCGC-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P04-GTCCGC-READ2-Sequences.txt.gz_val_2.fq.gz -o NB_female_44_01  -p 23
### salmon (mapping-based) v0.12.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P04-GTCCGC-READ1-Sequences.txt.gz_val_1.fq.gz }
### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P04-GTCCGC-READ2-Sequences.txt.gz_val_2.fq.gz }
### [ output ] => { NB_female_44_01 }
### [ threads ] => { 23 }
Logs will be written to NB_female_44_01/logs
[2019-12-19 10:41:21.388] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-12-19 10:41:21.388] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-12-19 10:41:21.388] [jointLog] [info] parsing read library format
[2019-12-19 10:41:21.388] [jointLog] [info] There is 1 library.
[2019-12-19 10:41:21.447] [jointLog] [info] Loading Quasi index
[2019-12-19 10:41:21.447] [jointLog] [info] Loading 32-bit quasi index
[2019-12-19 10:41:21.447] [stderrLog] [info] Loading Suffix Array 
[2019-12-19 10:41:22.751] [stderrLog] [info] Loading Transcript Info 
[2019-12-19 10:41:23.185] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-12-19 10:41:23.292] [stderrLog] [info] There were 861,197 set bits in the bit array
[2019-12-19 10:41:23.361] [stderrLog] [info] Computing transcript lengths
[2019-12-19 10:41:23.362] [stderrLog] [info] Waiting to finish loading hash
[2019-12-19 10:41:37.833] [stderrLog] [info] Done loading index
[2019-12-19 10:41:37.833] [jointLog] [info] done
[2019-12-19 10:41:37.833] [jointLog] [info] Index contained 861,197 targets






processed 500,000 fragments
hits: 945,638, hits per frag:  1.99709

processed 1,000,000 fragments
hits: 1,893,058, hits per frag:  2.1562

processed 1,500,000 fragments
hits: 2,840,862, hits per frag:  1.98007

processed 2,000,000 fragments
hits: 3,790,871, hits per frag:  1.95326

processed 2,500,000 fragments
hits: 4,740,438, hits per frag:  1.96375

processed 3,000,000 fragments
hits: 5,687,275, hits per frag:  1.94076

processed 3,500,001 fragments
hits: 6,631,626, hits per frag:  1.91574

processed 4,000,000 fragments
hits: 7,574,734, hits per frag:  1.93399

processed 4,500,000 fragments
hits: 8,519,822, hits per frag:  1.95601

processed 5,000,001 fragments
hits: 9,462,434, hits per frag:  1.94478

processed 5,500,000 fragments
hits: 10,402,059, hits per frag:  1.92653

processed 6,000,000 fragments
hits: 11,351,116, hits per frag:  1.94223

processed 6,500,000 fragments
hits: 12,300,502, hits per frag:  1.9264

processed 7,000,000 fragments
hits: 13,253,319, hits per frag:  1.96171

processed 7,500,000 fragments
hits: 14,209,867, hits per frag:  1.90784

processed 8,000,001 fragments
hits: 15,168,236, hits per frag:  1.9014

processed 8,500,000 fragments
hits: 16,125,020, hits per frag:  1.89835

processed 9,000,001 fragments
hits: 17,079,696, hits per frag:  1.9095

processed 9,500,001 fragments
hits: 18,029,649, hits per frag:  1.91264

processed 10,000,001 fragments
hits: 18,977,765, hits per frag:  1.91205

processed 10,500,000 fragments
hits: 19,924,950, hits per frag:  1.91572

processed 11,000,000 fragments
hits: 20,872,976, hits per frag:  1.90436

processed 11,500,000 fragments
hits: 21,815,554, hits per frag:  1.90066

processed 12,000,002 fragments
hits: 22,761,339, hits per frag:  1.90453

processed 12,500,000 fragments
hits: 23,706,309, hits per frag:  1.9043

processed 13,000,000 fragments
hits: 24,650,920, hits per frag:  1.92103

processed 13,500,000 fragments
hits: 25,596,081, hits per frag:  1.90431

processed 14,000,000 fragments
hits: 26,541,072, hits per frag:  1.921

processed 14,500,001 fragments
hits: 27,481,755, hits per frag:  1.91453

processed 15,000,000 fragments
hits: 28,422,463, hits per frag:  1.94279

processed 15,500,001 fragments
hits: 29,364,065, hits per frag:  1.9054

processed 16,000,001 fragments
hits: 30,304,748, hits per frag:  1.90226

processed 16,500,000 fragments
hits: 31,244,643, hits per frag:  1.90063

processed 17,000,000 fragments
hits: 32,184,623, hits per frag:  1.90301

processed 17,500,000 fragments
hits: 33,143,992, hits per frag:  1.90121

processed 18,000,000 fragments
hits: 34,099,024, hits per frag:  1.89764

processed 18,500,000 fragments
hits: 35,062,837, hits per frag:  1.9001

processed 19,000,000 fragments
hits: 36,031,382, hits per frag:  1.90492

processed 19,500,000 fragments
hits: 36,987,908, hits per frag:  1.91114

processed 20,000,000 fragments
hits: 37,946,286, hits per frag:  1.90035

processed 20,500,000 fragments
hits: 38,898,085, hits per frag:  1.90125

processed 21,000,001 fragments
hits: 39,857,507, hits per frag:  1.89908

processed 21,500,000 fragments
hits: 40,805,939, hits per frag:  1.90424

processed 22,000,000 fragments
hits: 41,754,013, hits per frag:  1.90123[2019-12-19 10:42:37.301] [jointLog] [info] Thread saw mini-batch with a maximum of 12.48% zero probability fragments
[2019-12-19 10:42:37.301] [jointLog] [info] Thread saw mini-batch with a maximum of 12.10% zero probability fragments
[2019-12-19 10:42:37.301] [jointLog] [info] Thread saw mini-batch with a maximum of 12.30% zero probability fragments
[2019-12-19 10:42:37.301] [jointLog] [info] Thread saw mini-batch with a maximum of 12.48% zero probability fragments
[2019-12-19 10:42:37.301] [jointLog] [info] Thread saw mini-batch with a maximum of 12.12% zero probability fragments
[2019-12-19 10:42:37.301] [jointLog] [info] Thread saw mini-batch with a maximum of 12.06% zero probability fragments
[2019-12-19 10:42:37.302] [jointLog] [info] Thread saw mini-batch with a maximum of 12.28% zero probability fragments
[2019-12-19 10:42:37.302] [jointLog] [info] Thread saw mini-batch with a maximum of 12.16% zero probability fragments
[2019-12-19 10:42:37.302] [jointLog] [info] Thread saw mini-batch with a maximum of 13.14% zero probability fragments
[2019-12-19 10:42:37.302] [jointLog] [info] Thread saw mini-batch with a maximum of 12.26% zero probability fragments
[2019-12-19 10:42:37.302] [jointLog] [info] Thread saw mini-batch with a maximum of 12.12% zero probability fragments
[2019-12-19 10:42:37.302] [jointLog] [info] Thread saw mini-batch with a maximum of 11.92% zero probability fragments
[2019-12-19 10:42:37.302] [jointLog] [info] Thread saw mini-batch with a maximum of 12.14% zero probability fragments
[2019-12-19 10:42:37.316] [jointLog] [info] Thread saw mini-batch with a maximum of 12.30% zero probability fragments
[2019-12-19 10:42:37.325] [jointLog] [info] Thread saw mini-batch with a maximum of 12.04% zero probability fragments
[2019-12-19 10:42:37.340] [jointLog] [info] Thread saw mini-batch with a maximum of 12.40% zero probability fragments
[2019-12-19 10:42:37.349] [jointLog] [info] Thread saw mini-batch with a maximum of 12.30% zero probability fragments
[2019-12-19 10:42:37.361] [jointLog] [info] Thread saw mini-batch with a maximum of 12.04% zero probability fragments
[2019-12-19 10:42:37.369] [jointLog] [info] Thread saw mini-batch with a maximum of 12.28% zero probability fragments
[2019-12-19 10:42:37.381] [jointLog] [info] Thread saw mini-batch with a maximum of 11.96% zero probability fragments
[2019-12-19 10:42:37.402] [jointLog] [info] Thread saw mini-batch with a maximum of 12.48% zero probability fragments
[2019-12-19 10:42:37.418] [jointLog] [info] Thread saw mini-batch with a maximum of 12.10% zero probability fragments
[2019-12-19 10:42:37.424] [jointLog] [info] Thread saw mini-batch with a maximum of 12.16% zero probability fragments










[2019-12-19 10:42:37.824] [jointLog] [info] Computed 503,725 rich equivalence classes for further processing
[2019-12-19 10:42:37.824] [jointLog] [info] Counted 15,218,617 total reads in the equivalence classes 
[2019-12-19 10:42:37.854] [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.


[2019-12-19 10:42:37.854] [jointLog] [info] Mapping rate = 67.6478%

[2019-12-19 10:42:37.854] [jointLog] [info] finished quantifyLibrary()
[2019-12-19 10:42:37.854] [jointLog] [info] Starting optimizer
[2019-12-19 10:42:38.238] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-12-19 10:42:38.264] [jointLog] [info] iteration = 0 | max rel diff. = 832.156
[2019-12-19 10:42:40.847] [jointLog] [info] iteration = 100 | max rel diff. = 19.5165
[2019-12-19 10:42:43.363] [jointLog] [info] iteration = 200 | max rel diff. = 15.9487
[2019-12-19 10:42:45.765] [jointLog] [info] iteration = 300 | max rel diff. = 3.24676
[2019-12-19 10:42:48.223] [jointLog] [info] iteration = 400 | max rel diff. = 20.2375
[2019-12-19 10:42:50.577] [jointLog] [info] iteration = 500 | max rel diff. = 15.2544
[2019-12-19 10:42:52.860] [jointLog] [info] iteration = 600 | max rel diff. = 10.7618
[2019-12-19 10:42:55.211] [jointLog] [info] iteration = 700 | max rel diff. = 1.58329
[2019-12-19 10:42:57.571] [jointLog] [info] iteration = 800 | max rel diff. = 3.10174
[2019-12-19 10:42:59.885] [jointLog] [info] iteration = 900 | max rel diff. = 0.463221
[2019-12-19 10:43:02.220] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.38425
[2019-12-19 10:43:04.526] [jointLog] [info] iteration = 1,100 | max rel diff. = 1.12894
[2019-12-19 10:43:06.930] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.63467
[2019-12-19 10:43:09.242] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.060202
[2019-12-19 10:43:11.566] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.050893
[2019-12-19 10:43:13.939] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.0300286
[2019-12-19 10:43:16.230] [jointLog] [info] iteration = 1,600 | max rel diff. = 0.181949
[2019-12-19 10:43:18.610] [jointLog] [info] iteration = 1,700 | max rel diff. = 0.0141141
[2019-12-19 10:43:20.160] [jointLog] [info] iteration = 1,768 | max rel diff. = 0.00777887
[2019-12-19 10:43:20.217] [jointLog] [info] Finished optimizer
[2019-12-19 10:43:20.217] [jointLog] [info] writing output 

CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl NB_female_44_01/quant.sf /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.gene_trans_map > NB_female_44_01/quant.sf.genes
CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P05-GAGTGG-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P05-GAGTGG-READ2-Sequences.txt.gz_val_2.fq.gz -o NB_female_44_02  -p 23
### salmon (mapping-based) v0.12.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P05-GAGTGG-READ1-Sequences.txt.gz_val_1.fq.gz }
### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P05-GAGTGG-READ2-Sequences.txt.gz_val_2.fq.gz }
### [ output ] => { NB_female_44_02 }
### [ threads ] => { 23 }
Logs will be written to NB_female_44_02/logs
[2019-12-19 10:43:38.170] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-12-19 10:43:38.170] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-12-19 10:43:38.170] [jointLog] [info] parsing read library format
[2019-12-19 10:43:38.170] [jointLog] [info] There is 1 library.
[2019-12-19 10:43:38.228] [jointLog] [info] Loading Quasi index
[2019-12-19 10:43:38.228] [jointLog] [info] Loading 32-bit quasi index
[2019-12-19 10:43:38.228] [stderrLog] [info] Loading Suffix Array 
[2019-12-19 10:43:39.423] [stderrLog] [info] Loading Transcript Info 
[2019-12-19 10:43:39.829] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-12-19 10:43:39.928] [stderrLog] [info] There were 861,197 set bits in the bit array
[2019-12-19 10:43:39.997] [stderrLog] [info] Computing transcript lengths
[2019-12-19 10:43:39.999] [stderrLog] [info] Waiting to finish loading hash
[2019-12-19 10:43:55.255] [stderrLog] [info] Done loading index
[2019-12-19 10:43:55.255] [jointLog] [info] done
[2019-12-19 10:43:55.255] [jointLog] [info] Index contained 861,197 targets






processed 500,000 fragments
hits: 975,881, hits per frag:  2.11943

processed 1,000,001 fragments
hits: 1,951,299, hits per frag:  2.14678

processed 1,500,000 fragments
hits: 2,928,935, hits per frag:  2.35598

processed 2,000,002 fragments
hits: 3,909,906, hits per frag:  2.08724

processed 2,500,000 fragments
hits: 4,889,830, hits per frag:  1.98911

processed 3,000,000 fragments
hits: 5,865,218, hits per frag:  2.03174

processed 3,500,000 fragments
hits: 6,840,933, hits per frag:  1.97037

processed 4,000,000 fragments
hits: 7,814,801, hits per frag:  2.00147

processed 4,500,000 fragments
hits: 8,788,929, hits per frag:  1.9822

processed 5,000,000 fragments
hits: 9,764,291, hits per frag:  2.00177

processed 5,500,001 fragments
hits: 10,735,738, hits per frag:  1.96671

processed 6,000,000 fragments
hits: 11,708,519, hits per frag:  1.97328

processed 6,500,000 fragments
hits: 12,681,634, hits per frag:  1.95906

processed 7,000,001 fragments
hits: 13,660,738, hits per frag:  1.97673

processed 7,500,000 fragments
hits: 14,641,019, hits per frag:  1.95712

processed 8,000,000 fragments
hits: 15,627,439, hits per frag:  1.96333

processed 8,500,001 fragments
hits: 16,612,946, hits per frag:  2.0277

processed 9,000,000 fragments
hits: 17,599,212, hits per frag:  1.97535

processed 9,500,000 fragments
hits: 18,583,965, hits per frag:  1.95775

processed 10,000,001 fragments
hits: 19,568,085, hits per frag:  1.98662

processed 10,500,001 fragments
hits: 20,554,195, hits per frag:  1.96698

processed 11,000,000 fragments
hits: 21,536,663, hits per frag:  1.97375

processed 11,500,000 fragments
hits: 22,517,875, hits per frag:  1.98248

processed 12,000,000 fragments
hits: 23,498,352, hits per frag:  1.96959

processed 12,500,000 fragments
hits: 24,479,730, hits per frag:  1.98214

processed 13,000,000 fragments
hits: 25,456,248, hits per frag:  1.96493

processed 13,500,000 fragments
hits: 26,428,859, hits per frag:  1.99097

processed 14,000,000 fragments
hits: 27,407,430, hits per frag:  1.97533

processed 14,500,000 fragments
hits: 28,385,868, hits per frag:  1.96965

processed 15,000,000 fragments
hits: 29,362,995, hits per frag:  1.96456

processed 15,500,000 fragments
hits: 30,340,209, hits per frag:  1.96227

processed 16,000,000 fragments
hits: 31,318,965, hits per frag:  1.98517

processed 16,500,001 fragments
hits: 32,293,059, hits per frag:  1.96801

processed 17,000,000 fragments
hits: 33,263,972, hits per frag:  1.95958

processed 17,500,000 fragments
hits: 34,234,814, hits per frag:  1.96787

processed 18,000,000 fragments
hits: 35,209,076, hits per frag:  1.97205

processed 18,500,001 fragments
hits: 36,183,435, hits per frag:  1.96133

processed 19,000,000 fragments
hits: 37,153,214, hits per frag:  1.9757

processed 19,500,000 fragments
hits: 38,122,067, hits per frag:  1.9744

processed 20,000,000 fragments
hits: 39,106,045, hits per frag:  1.95999

processed 20,500,000 fragments
hits: 40,092,548, hits per frag:  1.96359

processed 21,000,000 fragments
hits: 41,086,537, hits per frag:  1.96089

processed 21,500,000 fragments
hits: 42,090,180, hits per frag:  1.96404

processed 22,000,000 fragments
hits: 43,089,255, hits per frag:  1.97396

processed 22,500,000 fragments
hits: 44,078,305, hits per frag:  1.9624

processed 23,000,001 fragments
hits: 45,070,461, hits per frag:  1.96793

processed 23,500,000 fragments
hits: 46,054,469, hits per frag:  1.97054

processed 24,000,000 fragments
hits: 47,045,283, hits per frag:  1.96372

processed 24,500,000 fragments
hits: 48,033,087, hits per frag:  1.96837

processed 25,000,000 fragments
hits: 49,015,235, hits per frag:  1.96978

processed 25,500,000 fragments
hits: 49,994,462, hits per frag:  1.96499

processed 26,000,001 fragments
hits: 50,967,046, hits per frag:  1.97657[2019-12-19 10:45:04.645] [jointLog] [info] Thread saw mini-batch with a maximum of 18.26% zero probability fragments
[2019-12-19 10:45:04.645] [jointLog] [info] Thread saw mini-batch with a maximum of 19.10% zero probability fragments
[2019-12-19 10:45:04.645] [jointLog] [info] Thread saw mini-batch with a maximum of 18.70% zero probability fragments
[2019-12-19 10:45:04.645] [jointLog] [info] Thread saw mini-batch with a maximum of 18.12% zero probability fragments
[2019-12-19 10:45:04.645] [jointLog] [info] Thread saw mini-batch with a maximum of 18.36% zero probability fragments
[2019-12-19 10:45:04.645] [jointLog] [info] Thread saw mini-batch with a maximum of 18.38% zero probability fragments
[2019-12-19 10:45:04.645] [jointLog] [info] Thread saw mini-batch with a maximum of 18.34% zero probability fragments
[2019-12-19 10:45:04.645] [jointLog] [info] Thread saw mini-batch with a maximum of 18.12% zero probability fragments
[2019-12-19 10:45:04.645] [jointLog] [info] Thread saw mini-batch with a maximum of 18.20% zero probability fragments
[2019-12-19 10:45:04.645] [jointLog] [info] Thread saw mini-batch with a maximum of 18.94% zero probability fragments
[2019-12-19 10:45:04.651] [jointLog] [info] Thread saw mini-batch with a maximum of 18.54% zero probability fragments
[2019-12-19 10:45:04.662] [jointLog] [info] Thread saw mini-batch with a maximum of 18.36% zero probability fragments
[2019-12-19 10:45:04.669] [jointLog] [info] Thread saw mini-batch with a maximum of 18.64% zero probability fragments
[2019-12-19 10:45:04.673] [jointLog] [info] Thread saw mini-batch with a maximum of 18.66% zero probability fragments
[2019-12-19 10:45:04.674] [jointLog] [info] Thread saw mini-batch with a maximum of 18.64% zero probability fragments
[2019-12-19 10:45:04.706] [jointLog] [info] Thread saw mini-batch with a maximum of 18.40% zero probability fragments
[2019-12-19 10:45:04.707] [jointLog] [info] Thread saw mini-batch with a maximum of 18.36% zero probability fragments
[2019-12-19 10:45:04.709] [jointLog] [info] Thread saw mini-batch with a maximum of 18.62% zero probability fragments
[2019-12-19 10:45:04.720] [jointLog] [info] Thread saw mini-batch with a maximum of 18.80% zero probability fragments
[2019-12-19 10:45:04.736] [jointLog] [info] Thread saw mini-batch with a maximum of 18.62% zero probability fragments
[2019-12-19 10:45:04.754] [jointLog] [info] Thread saw mini-batch with a maximum of 18.64% zero probability fragments
[2019-12-19 10:45:04.763] [jointLog] [info] Thread saw mini-batch with a maximum of 18.14% zero probability fragments
[2019-12-19 10:45:04.773] [jointLog] [info] Thread saw mini-batch with a maximum of 18.56% zero probability fragments










[2019-12-19 10:45:05.257] [jointLog] [info] Computed 534,612 rich equivalence classes for further processing
[2019-12-19 10:45:05.257] [jointLog] [info] Counted 16,212,376 total reads in the equivalence classes 
[2019-12-19 10:45:05.281] [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.


[2019-12-19 10:45:05.281] [jointLog] [info] Mapping rate = 62.1384%

[2019-12-19 10:45:05.281] [jointLog] [info] finished quantifyLibrary()
[2019-12-19 10:45:05.281] [jointLog] [info] Starting optimizer
[2019-12-19 10:45:05.684] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-12-19 10:45:05.711] [jointLog] [info] iteration = 0 | max rel diff. = 717.219
[2019-12-19 10:45:08.271] [jointLog] [info] iteration = 100 | max rel diff. = 18.0384
[2019-12-19 10:45:10.796] [jointLog] [info] iteration = 200 | max rel diff. = 17.3584
[2019-12-19 10:45:13.247] [jointLog] [info] iteration = 300 | max rel diff. = 2.70342
[2019-12-19 10:45:15.620] [jointLog] [info] iteration = 400 | max rel diff. = 0.590737
[2019-12-19 10:45:17.980] [jointLog] [info] iteration = 500 | max rel diff. = 2.39159
[2019-12-19 10:45:20.264] [jointLog] [info] iteration = 600 | max rel diff. = 0.289139
[2019-12-19 10:45:22.501] [jointLog] [info] iteration = 700 | max rel diff. = 10.1244
[2019-12-19 10:45:24.855] [jointLog] [info] iteration = 800 | max rel diff. = 0.253879
[2019-12-19 10:45:27.135] [jointLog] [info] iteration = 900 | max rel diff. = 1.93585
[2019-12-19 10:45:29.345] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.0758083
[2019-12-19 10:45:31.582] [jointLog] [info] iteration = 1,100 | max rel diff. = 0.0989469
[2019-12-19 10:45:33.808] [jointLog] [info] iteration = 1,200 | max rel diff. = 10.28
[2019-12-19 10:45:34.689] [jointLog] [info] iteration = 1,240 | max rel diff. = 0.00925688
[2019-12-19 10:45:34.745] [jointLog] [info] Finished optimizer
[2019-12-19 10:45:34.745] [jointLog] [info] writing output 

CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl NB_female_44_02/quant.sf /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.gene_trans_map > NB_female_44_02/quant.sf.genes
CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P12-TGACCA-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P12-TGACCA-READ2-Sequences.txt.gz_val_2.fq.gz -o NB_female_44_03  -p 23
### salmon (mapping-based) v0.12.0
### [ program ] => salmon 
### [ command ] => quant 
### [ index ] => { /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.salmon_quasi.idx }
### [ libType ] => { ISR }
### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P12-TGACCA-READ1-Sequences.txt.gz_val_1.fq.gz }
### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P12-TGACCA-READ2-Sequences.txt.gz_val_2.fq.gz }
### [ output ] => { NB_female_44_03 }
### [ threads ] => { 23 }
Logs will be written to NB_female_44_03/logs
[2019-12-19 10:45:53.335] [jointLog] [info] Fragment incompatibility prior below threshold.  Incompatible fragments will be ignored.
[2019-12-19 10:45:53.335] [jointLog] [warning] 

NOTE: It appears you are running salmon without the `--validateMappings` option.
Mapping validation can generally improve both the sensitivity and specificity of mapping,
with only a moderate increase in use of computational resources. 
Unless there is a specific reason to do this (e.g. testing on clean simulated data),
`--validateMappings` is generally recommended.

[2019-12-19 10:45:53.335] [jointLog] [info] parsing read library format
[2019-12-19 10:45:53.335] [jointLog] [info] There is 1 library.
[2019-12-19 10:45:53.393] [jointLog] [info] Loading Quasi index
[2019-12-19 10:45:53.393] [jointLog] [info] Loading 32-bit quasi index
[2019-12-19 10:45:53.393] [stderrLog] [info] Loading Suffix Array 
[2019-12-19 10:45:54.683] [stderrLog] [info] Loading Transcript Info 
[2019-12-19 10:45:55.111] [stderrLog] [info] Loading Rank-Select Bit Array
[2019-12-19 10:45:55.213] [stderrLog] [info] There were 861,197 set bits in the bit array
[2019-12-19 10:45:55.283] [stderrLog] [info] Computing transcript lengths
[2019-12-19 10:45:55.284] [stderrLog] [info] Waiting to finish loading hash
[2019-12-19 10:46:09.649] [stderrLog] [info] Done loading index
[2019-12-19 10:46:09.649] [jointLog] [info] done
[2019-12-19 10:46:09.649] [jointLog] [info] Index contained 861,197 targets






processed 500,001 fragments
hits: 891,559, hits per frag:  2.28477

processed 1,000,000 fragments
hits: 1,779,170, hits per frag:  1.87895

processed 1,500,000 fragments
hits: 2,676,300, hits per frag:  2.08808

processed 2,000,001 fragments
hits: 3,566,800, hits per frag:  1.79919

processed 2,500,000 fragments
hits: 4,460,709, hits per frag:  1.8326

processed 3,000,001 fragments
hits: 5,352,823, hits per frag:  1.81848

processed 3,500,000 fragments
hits: 6,242,600, hits per frag:  1.83694

processed 4,000,001 fragments
hits: 7,129,994, hits per frag:  1.79553

processed 4,500,000 fragments
hits: 8,018,563, hits per frag:  1.82882

processed 5,000,000 fragments
hits: 8,908,327, hits per frag:  1.88369

processed 5,500,000 fragments
hits: 9,797,518, hits per frag:  1.78953

processed 6,000,000 fragments
hits: 10,685,015, hits per frag:  1.81059

processed 6,500,000 fragments
hits: 11,570,142, hits per frag:  1.81105

processed 7,000,000 fragments
hits: 12,462,186, hits per frag:  1.79068

processed 7,500,000 fragments
hits: 13,357,438, hits per frag:  1.78375

processed 8,000,000 fragments
hits: 14,258,448, hits per frag:  1.80488

processed 8,500,000 fragments
hits: 15,155,825, hits per frag:  1.79075

processed 9,000,000 fragments
hits: 16,056,553, hits per frag:  1.7944

processed 9,500,000 fragments
hits: 16,958,870, hits per frag:  1.79506

processed 10,000,000 fragments
hits: 17,859,141, hits per frag:  1.79585

processed 10,500,000 fragments
hits: 18,757,688, hits per frag:  1.79312

processed 11,000,000 fragments
hits: 19,655,577, hits per frag:  1.80402

processed 11,500,000 fragments
hits: 20,551,681, hits per frag:  1.79956

processed 12,000,001 fragments
hits: 21,445,599, hits per frag:  1.79547

processed 12,500,000 fragments
hits: 22,341,614, hits per frag:  1.80213

processed 13,000,001 fragments
hits: 23,234,434, hits per frag:  1.79342

processed 13,500,000 fragments
hits: 24,122,376, hits per frag:  1.79243

processed 14,000,000 fragments
hits: 25,015,265, hits per frag:  1.7895

processed 14,500,000 fragments
hits: 25,909,475, hits per frag:  1.79302

processed 15,000,000 fragments
hits: 26,798,136, hits per frag:  1.78931

processed 15,500,001 fragments
hits: 27,686,714, hits per frag:  1.80504

processed 16,000,000 fragments
hits: 28,575,565, hits per frag:  1.79472

processed 16,500,000 fragments
hits: 29,462,489, hits per frag:  1.79682

processed 17,000,000 fragments
hits: 30,346,414, hits per frag:  1.79038

processed 17,500,001 fragments
hits: 31,233,678, hits per frag:  1.79313

processed 18,000,001 fragments
hits: 32,118,760, hits per frag:  1.81124

processed 18,500,000 fragments
hits: 33,007,039, hits per frag:  1.79228

processed 19,000,000 fragments
hits: 33,894,379, hits per frag:  1.78806

processed 19,500,000 fragments
hits: 34,776,933, hits per frag:  1.79008

processed 20,000,000 fragments
hits: 35,660,149, hits per frag:  1.78782

processed 20,500,001 fragments
hits: 36,560,899, hits per frag:  1.78798

processed 21,000,000 fragments
hits: 37,459,029, hits per frag:  1.78958

processed 21,500,002 fragments
hits: 38,365,217, hits per frag:  1.78788

processed 22,000,000 fragments
hits: 39,284,777, hits per frag:  1.78852

processed 22,500,000 fragments
hits: 40,195,530, hits per frag:  1.7929

processed 23,000,003 fragments
hits: 41,097,290, hits per frag:  1.79633

processed 23,500,000 fragments
hits: 41,999,998, hits per frag:  1.79223

processed 24,000,000 fragments
hits: 42,899,399, hits per frag:  1.7963

processed 24,500,000 fragments
hits: 43,809,274, hits per frag:  1.79042

processed 25,000,000 fragments
hits: 44,707,333, hits per frag:  1.79583

processed 25,500,000 fragments
hits: 45,600,215, hits per frag:  1.7959

processed 26,000,000 fragments
hits: 46,491,358, hits per frag:  1.79353[2019-12-19 10:47:21.799] [jointLog] [info] Thread saw mini-batch with a maximum of 10.02% zero probability fragments
[2019-12-19 10:47:21.799] [jointLog] [info] Thread saw mini-batch with a maximum of 10.26% zero probability fragments
[2019-12-19 10:47:21.799] [jointLog] [info] Thread saw mini-batch with a maximum of 10.48% zero probability fragments
[2019-12-19 10:47:21.799] [jointLog] [info] Thread saw mini-batch with a maximum of 10.48% zero probability fragments
[2019-12-19 10:47:21.799] [jointLog] [info] Thread saw mini-batch with a maximum of 10.26% zero probability fragments
[2019-12-19 10:47:21.799] [jointLog] [info] Thread saw mini-batch with a maximum of 10.14% zero probability fragments
[2019-12-19 10:47:21.799] [jointLog] [info] Thread saw mini-batch with a maximum of 10.34% zero probability fragments
[2019-12-19 10:47:21.799] [jointLog] [info] Thread saw mini-batch with a maximum of 10.08% zero probability fragments
[2019-12-19 10:47:21.800] [jointLog] [info] Thread saw mini-batch with a maximum of 10.24% zero probability fragments
[2019-12-19 10:47:21.800] [jointLog] [info] Thread saw mini-batch with a maximum of 10.52% zero probability fragments
[2019-12-19 10:47:21.800] [jointLog] [info] Thread saw mini-batch with a maximum of 10.12% zero probability fragments
[2019-12-19 10:47:21.800] [jointLog] [info] Thread saw mini-batch with a maximum of 10.30% zero probability fragments
[2019-12-19 10:47:21.800] [jointLog] [info] Thread saw mini-batch with a maximum of 10.56% zero probability fragments
[2019-12-19 10:47:21.806] [jointLog] [info] Thread saw mini-batch with a maximum of 10.36% zero probability fragments
[2019-12-19 10:47:21.821] [jointLog] [info] Thread saw mini-batch with a maximum of 10.36% zero probability fragments
[2019-12-19 10:47:21.835] [jointLog] [info] Thread saw mini-batch with a maximum of 10.22% zero probability fragments
[2019-12-19 10:47:21.850] [jointLog] [info] Thread saw mini-batch with a maximum of 10.64% zero probability fragments
[2019-12-19 10:47:21.877] [jointLog] [info] Thread saw mini-batch with a maximum of 10.14% zero probability fragments
[2019-12-19 10:47:21.883] [jointLog] [info] Thread saw mini-batch with a maximum of 10.24% zero probability fragments
[2019-12-19 10:47:21.901] [jointLog] [info] Thread saw mini-batch with a maximum of 10.18% zero probability fragments
[2019-12-19 10:47:21.904] [jointLog] [info] Thread saw mini-batch with a maximum of 10.28% zero probability fragments
[2019-12-19 10:47:21.924] [jointLog] [info] Thread saw mini-batch with a maximum of 9.96% zero probability fragments
[2019-12-19 10:47:21.925] [jointLog] [info] Thread saw mini-batch with a maximum of 10.28% zero probability fragments










[2019-12-19 10:47:22.475] [jointLog] [info] Computed 541,349 rich equivalence classes for further processing
[2019-12-19 10:47:22.475] [jointLog] [info] Counted 17,707,811 total reads in the equivalence classes 
[2019-12-19 10:47:22.500] [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.


[2019-12-19 10:47:22.500] [jointLog] [info] Mapping rate = 66.9112%

[2019-12-19 10:47:22.500] [jointLog] [info] finished quantifyLibrary()
[2019-12-19 10:47:22.500] [jointLog] [info] Starting optimizer
[2019-12-19 10:47:22.960] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate
[2019-12-19 10:47:22.986] [jointLog] [info] iteration = 0 | max rel diff. = 968.082
[2019-12-19 10:47:25.400] [jointLog] [info] iteration = 100 | max rel diff. = 17.9924
[2019-12-19 10:47:27.802] [jointLog] [info] iteration = 200 | max rel diff. = 16.6194
[2019-12-19 10:47:30.208] [jointLog] [info] iteration = 300 | max rel diff. = 13.3336
[2019-12-19 10:47:32.563] [jointLog] [info] iteration = 400 | max rel diff. = 15.5376
[2019-12-19 10:47:34.929] [jointLog] [info] iteration = 500 | max rel diff. = 0.869299
[2019-12-19 10:47:37.250] [jointLog] [info] iteration = 600 | max rel diff. = 0.0897497
[2019-12-19 10:47:39.615] [jointLog] [info] iteration = 700 | max rel diff. = 0.069784
[2019-12-19 10:47:41.909] [jointLog] [info] iteration = 800 | max rel diff. = 3.05967
[2019-12-19 10:47:44.235] [jointLog] [info] iteration = 900 | max rel diff. = 7.09089
[2019-12-19 10:47:46.615] [jointLog] [info] iteration = 1,000 | max rel diff. = 0.304477
[2019-12-19 10:47:48.915] [jointLog] [info] iteration = 1,100 | max rel diff. = 2.01322
[2019-12-19 10:47:51.294] [jointLog] [info] iteration = 1,200 | max rel diff. = 0.056529
[2019-12-19 10:47:53.623] [jointLog] [info] iteration = 1,300 | max rel diff. = 0.0605105
[2019-12-19 10:47:55.961] [jointLog] [info] iteration = 1,400 | max rel diff. = 0.505294
[2019-12-19 10:47:58.260] [jointLog] [info] iteration = 1,500 | max rel diff. = 0.0137049
[2019-12-19 10:48:00.577] [jointLog] [info] iteration = 1,600 | max rel diff. = 0.0232803
[2019-12-19 10:48:02.896] [jointLog] [info] iteration = 1,700 | max rel diff. = 0.0272759
[2019-12-19 10:48:05.189] [jointLog] [info] iteration = 1,800 | max rel diff. = 0.0122339
[2019-12-19 10:48:07.620] [jointLog] [info] iteration = 1,900 | max rel diff. = 0.0287303
[2019-12-19 10:48:09.759] [jointLog] [info] iteration = 1,990 | max rel diff. = 0.00187491
[2019-12-19 10:48:09.820] [jointLog] [info] Finished optimizer
[2019-12-19 10:48:09.820] [jointLog] [info] writing output 

CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl NB_female_44_03/quant.sf /media/sam/4TB_toshiba/porites/20180419_trinity/Trinity.fasta.gene_trans_map > NB_female_44_03/quant.sf.genes