CMD: salmon index -t /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta --keepDuplicates -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx --type quasi -k 31 -p 23 index ["/media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx"] did not previously exist . . . creating it [2021-07-20 11:50:25.586] [jLog] [info] building index [2021-07-20 11:50:25.592] [jointLog] [info] [Step 1 of 4] : counting k-mers counted k-mers for 10,000 transcripts counted k-mers for 20,000 transcripts counted k-mers for 30,000 transcripts counted k-mers for 40,000 transcriptsElapsed time: 0.675606s [2021-07-20 11:50:26.268] [jointLog] [info] Replaced 0 non-ATCG nucleotides [2021-07-20 11:50:26.268] [jointLog] [info] Clipped poly-A tails from 0 transcripts [2021-07-20 11:50:26.272] [jointLog] [info] Building rank-select dictionary and saving to disk [2021-07-20 11:50:26.274] [jointLog] [info] done Elapsed time: 0.00180319s [2021-07-20 11:50:26.274] [jointLog] [info] Writing sequence data to file . . . [2021-07-20 11:50:26.288] [jointLog] [info] done Elapsed time: 0.0140973s [2021-07-20 11:50:26.290] [jointLog] [info] Building 32-bit suffix array (length of generalized text is 16,384,973) [2021-07-20 11:50:26.313] [jointLog] [info] Building suffix array . . . success saving to disk . . . done Elapsed time: 0.038654s done Elapsed time: 1.42343s processed 0 positions processed 1,000,000 positions processed 2,000,000 positions processed 3,000,000 positions processed 4,000,000 positions processed 5,000,000 positions processed 6,000,000 positions processed 7,000,000 positions processed 8,000,000 positions processed 9,000,000 positions processed 10,000,000 positions processed 11,000,000 positions processed 12,000,000 positions processed 13,000,000 positions processed 14,000,000 positions processed 15,000,000 positions processed 16,000,000 positions[2021-07-20 11:50:35.720] [jointLog] [info] khash had 13,097,043 keys [2021-07-20 11:50:35.720] [jointLog] [info] saving hash to disk . . . [2021-07-20 11:50:36.626] [jointLog] [info] done Elapsed time: 0.905446s [2021-07-20 11:50:36.697] [jLog] [info] done building index CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P01-AGTTCC-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P01-AGTTCC-READ2-Sequences.txt.gz_val_2.fq.gz -o bleached_male_K5_01 -p 23 ### salmon (mapping-based) v0.12.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P01-AGTTCC-READ1-Sequences.txt.gz_val_1.fq.gz } ### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P01-AGTTCC-READ2-Sequences.txt.gz_val_2.fq.gz } ### [ output ] => { bleached_male_K5_01 } ### [ threads ] => { 23 } Logs will be written to bleached_male_K5_01/logs [2021-07-20 11:50:36.797] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2021-07-20 11:50:36.797] [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. [2021-07-20 11:50:36.797] [jointLog] [info] parsing read library format [2021-07-20 11:50:36.798] [jointLog] [info] There is 1 library. [2021-07-20 11:50:36.857] [jointLog] [info] Loading Quasi index [2021-07-20 11:50:36.857] [jointLog] [info] Loading 32-bit quasi index [2021-07-20 11:50:36.857] [stderrLog] [info] Loading Suffix Array [2021-07-20 11:50:36.899] [stderrLog] [info] Loading Transcript Info [2021-07-20 11:50:36.910] [stderrLog] [info] Loading Rank-Select Bit Array [2021-07-20 11:50:36.913] [stderrLog] [info] There were 42,425 set bits in the bit array [2021-07-20 11:50:36.915] [stderrLog] [info] Computing transcript lengths [2021-07-20 11:50:36.915] [stderrLog] [info] Waiting to finish loading hash [2021-07-20 11:50:37.613] [stderrLog] [info] Done loading index [2021-07-20 11:50:37.613] [jointLog] [info] done [2021-07-20 11:50:37.613] [jointLog] [info] Index contained 42,425 targets  processed 500,000 fragments hits: 129,807, hits per frag: 0.398318 processed 1,000,000 fragments hits: 260,409, hits per frag: 0.298657 processed 1,500,000 fragments hits: 390,341, hits per frag: 0.270164 processed 2,000,000 fragments hits: 520,834, hits per frag: 0.305509 processed 2,500,000 fragments hits: 650,765, hits per frag: 0.295734 processed 3,000,001 fragments hits: 779,549, hits per frag: 0.265795 processed 3,500,001 fragments hits: 910,051, hits per frag: 0.27179 processed 4,000,000 fragments hits: 1,040,649, hits per frag: 0.264823 processed 4,500,000 fragments hits: 1,170,049, hits per frag: 0.261023 processed 5,000,000 fragments hits: 1,299,738, hits per frag: 0.267919 processed 5,500,000 fragments hits: 1,430,639, hits per frag: 0.267777 processed 6,000,000 fragments hits: 1,561,342, hits per frag: 0.260875 processed 6,500,001 fragments hits: 1,691,106, hits per frag: 0.264877 processed 7,000,000 fragments hits: 1,821,026, hits per frag: 0.261162 processed 7,500,000 fragments hits: 1,951,624, hits per frag: 0.262232 processed 8,000,001 fragments hits: 2,081,026, hits per frag: 0.263971 processed 8,500,000 fragments hits: 2,210,488, hits per frag: 0.262224 processed 9,000,001 fragments hits: 2,339,370, hits per frag: 0.263342 processed 9,500,000 fragments hits: 2,469,030, hits per frag: 0.262858 processed 10,000,001 fragments hits: 2,598,371, hits per frag: 0.261799 processed 10,500,000 fragments hits: 2,727,717, hits per frag: 0.264477 processed 11,000,000 fragments hits: 2,856,307, hits per frag: 0.261767 processed 11,500,000 fragments hits: 2,986,727, hits per frag: 0.26085 processed 12,000,000 fragments hits: 3,116,669, hits per frag: 0.260377 processed 12,500,000 fragments hits: 3,296,475, hits per frag: 0.265066 processed 13,000,000 fragments hits: 3,377,363, hits per frag: 0.261284 processed 13,500,000 fragments hits: 3,507,406, hits per frag: 0.264167 processed 14,000,000 fragments hits: 3,636,674, hits per frag: 0.261204 processed 14,500,001 fragments hits: 3,766,239, hits per frag: 0.262722 processed 15,000,002 fragments hits: 3,896,264, hits per frag: 0.261526 processed 15,500,000 fragments hits: 4,026,214, hits per frag: 0.262919 processed 16,000,001 fragments hits: 4,156,337, hits per frag: 0.260649 processed 16,500,000 fragments hits: 4,287,491, hits per frag: 0.260932 processed 17,000,001 fragments hits: 4,416,989, hits per frag: 0.260174 processed 17,500,001 fragments hits: 4,547,275, hits per frag: 0.26117 processed 18,000,000 fragments hits: 4,677,696, hits per frag: 0.261794 processed 18,500,000 fragments hits: 4,807,629, hits per frag: 0.260796 processed 19,000,000 fragments hits: 4,937,797, hits per frag: 0.25993 processed 19,500,000 fragments hits: 5,068,418, hits per frag: 0.260385 processed 20,000,000 fragments hits: 5,198,862, hits per frag: 0.260839 processed 20,500,002 fragments hits: 5,329,084, hits per frag: 0.260244 processed 21,000,001 fragments hits: 5,459,277, hits per frag: 0.260694 processed 21,500,001 fragments hits: 5,588,663, hits per frag: 0.260567 processed 22,000,002 fragments hits: 5,718,756, hits per frag: 0.261771 processed 22,500,000 fragments hits: 5,848,895, hits per frag: 0.260512 processed 23,000,000 fragments hits: 5,979,014, hits per frag: 0.26264 processed 23,500,000 fragments hits: 6,108,543, hits per frag: 0.260218 processed 24,000,000 fragments hits: 6,238,007, hits per frag: 0.260892 processed 24,500,001 fragments hits: 6,368,892, hits per frag: 0.261255 [2021-07-20 11:51:42.916] [jointLog] [info] Thread saw mini-batch with a maximum of 1.66% zero probability fragments [2021-07-20 11:51:42.916] [jointLog] [info] Thread saw mini-batch with a maximum of 1.30% zero probability fragments [2021-07-20 11:51:42.916] [jointLog] [info] Thread saw mini-batch with a maximum of 1.44% zero probability fragments [2021-07-20 11:51:42.916] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 11:51:42.916] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 11:51:42.916] [jointLog] [info] Thread saw mini-batch with a maximum of 1.42% zero probability fragments [2021-07-20 11:51:42.916] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 11:51:42.916] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 11:51:42.916] [jointLog] [info] Thread saw mini-batch with a maximum of 1.44% zero probability fragments [2021-07-20 11:51:42.916] [jointLog] [info] Thread saw mini-batch with a maximum of 1.38% zero probability fragments [2021-07-20 11:51:42.920] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 11:51:42.934] [jointLog] [info] Thread saw mini-batch with a maximum of 1.40% zero probability fragments [2021-07-20 11:51:42.940] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 11:51:42.961] [jointLog] [info] Thread saw mini-batch with a maximum of 1.44% zero probability fragments [2021-07-20 11:51:42.964] [jointLog] [info] Thread saw mini-batch with a maximum of 1.51% zero probability fragments [2021-07-20 11:51:42.967] [jointLog] [info] Thread saw mini-batch with a maximum of 1.44% zero probability fragments [2021-07-20 11:51:42.984] [jointLog] [info] Thread saw mini-batch with a maximum of 1.46% zero probability fragments [2021-07-20 11:51:42.986] [jointLog] [info] Thread saw mini-batch with a maximum of 1.36% zero probability fragments [2021-07-20 11:51:42.989] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 11:51:43.019] [jointLog] [info] Thread saw mini-batch with a maximum of 1.32% zero probability fragments [2021-07-20 11:51:43.028] [jointLog] [info] Thread saw mini-batch with a maximum of 1.38% zero probability fragments [2021-07-20 11:51:43.034] [jointLog] [info] Thread saw mini-batch with a maximum of 1.38% zero probability fragments [2021-07-20 11:51:43.045] [jointLog] [info] Thread saw mini-batch with a maximum of 1.30% zero probability fragments [2021-07-20 11:51:43.228] [jointLog] [info] Computed 35,454 rich equivalence classes for further processing [2021-07-20 11:51:43.228] [jointLog] [info] Counted 4,430,611 total reads in the equivalence classes [2021-07-20 11:51:43.245] [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. [2021-07-20 11:51:43.248] [jointLog] [warning] Only 4430611 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2021-07-20 11:51:43.248] [jointLog] [info] Mapping rate = 17.8316% [2021-07-20 11:51:43.248] [jointLog] [info] finished quantifyLibrary() [2021-07-20 11:51:43.249] [jointLog] [info] Starting optimizer [2021-07-20 11:51:43.275] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2021-07-20 11:51:43.276] [jointLog] [info] iteration = 0 | max rel diff. = 234.179 [2021-07-20 11:51:43.402] [jointLog] [info] iteration = 100 | max rel diff. = 14.9698 [2021-07-20 11:51:43.527] [jointLog] [info] iteration = 200 | max rel diff. = 0.0473043 [2021-07-20 11:51:43.651] [jointLog] [info] iteration = 300 | max rel diff. = 0.047243 [2021-07-20 11:51:43.729] [jointLog] [info] iteration = 363 | max rel diff. = 0.00264651 [2021-07-20 11:51:43.730] [jointLog] [info] Finished optimizer [2021-07-20 11:51:43.730] [jointLog] [info] writing output CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl bleached_male_K5_01/quant.sf /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.gene_trans_map > bleached_male_K5_01/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P06-GCCAAT-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P06-GCCAAT-READ2-Sequences.txt.gz_val_2.fq.gz -o bleached_male_K5_02 -p 23 ### salmon (mapping-based) v0.12.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P06-GCCAAT-READ1-Sequences.txt.gz_val_1.fq.gz } ### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P06-GCCAAT-READ2-Sequences.txt.gz_val_2.fq.gz } ### [ output ] => { bleached_male_K5_02 } ### [ threads ] => { 23 } Logs will be written to bleached_male_K5_02/logs [2021-07-20 11:51:45.229] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2021-07-20 11:51:45.229] [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. [2021-07-20 11:51:45.229] [jointLog] [info] parsing read library format [2021-07-20 11:51:45.229] [jointLog] [info] There is 1 library. [2021-07-20 11:51:45.286] [jointLog] [info] Loading Quasi index [2021-07-20 11:51:45.286] [jointLog] [info] Loading 32-bit quasi index [2021-07-20 11:51:45.286] [stderrLog] [info] Loading Suffix Array [2021-07-20 11:51:45.331] [stderrLog] [info] Loading Transcript Info [2021-07-20 11:51:45.345] [stderrLog] [info] Loading Rank-Select Bit Array [2021-07-20 11:51:45.348] [stderrLog] [info] There were 42,425 set bits in the bit array [2021-07-20 11:51:45.350] [stderrLog] [info] Computing transcript lengths [2021-07-20 11:51:45.350] [stderrLog] [info] Waiting to finish loading hash [2021-07-20 11:51:46.008] [stderrLog] [info] Done loading index [2021-07-20 11:51:46.008] [jointLog] [info] done [2021-07-20 11:51:46.008] [jointLog] [info] Index contained 42,425 targets  processed 500,000 fragments hits: 117,099, hits per frag: 0.262298 processed 1,000,000 fragments hits: 234,559, hits per frag: 0.25926 processed 1,500,000 fragments hits: 351,755, hits per frag: 0.243699 processed 2,000,000 fragments hits: 469,817, hits per frag: 0.245276 processed 2,500,000 fragments hits: 588,033, hits per frag: 0.256673 processed 3,000,000 fragments hits: 705,931, hits per frag: 0.239429 processed 3,500,000 fragments hits: 823,532, hits per frag: 0.240183 processed 4,000,001 fragments hits: 941,098, hits per frag: 0.237935 processed 4,500,000 fragments hits: 1,057,737, hits per frag: 0.237009 processed 5,000,000 fragments hits: 1,175,573, hits per frag: 0.23697 processed 5,500,000 fragments hits: 1,293,334, hits per frag: 0.237581 processed 6,000,000 fragments hits: 1,410,891, hits per frag: 0.237842 processed 6,500,000 fragments hits: 1,527,704, hits per frag: 0.239015 processed 7,000,001 fragments hits: 1,643,612, hits per frag: 0.238765 processed 7,500,000 fragments hits: 1,761,959, hits per frag: 0.235616 processed 8,000,000 fragments hits: 1,878,474, hits per frag: 0.236516 processed 8,500,000 fragments hits: 1,995,044, hits per frag: 0.237082 processed 9,000,000 fragments hits: 2,112,425, hits per frag: 0.235676 processed 9,500,000 fragments hits: 2,230,142, hits per frag: 0.2364 processed 10,000,001 fragments hits: 2,347,096, hits per frag: 0.235547 processed 10,500,001 fragments hits: 2,463,834, hits per frag: 0.235995 processed 11,000,000 fragments hits: 2,580,336, hits per frag: 0.236187 processed 11,500,000 fragments hits: 2,697,723, hits per frag: 0.235115 processed 12,000,000 fragments hits: 2,814,874, hits per frag: 0.240337 processed 12,500,000 fragments hits: 2,932,373, hits per frag: 0.23552 processed 13,000,000 fragments hits: 3,049,748, hits per frag: 0.236463 processed 13,500,000 fragments hits: 3,166,303, hits per frag: 0.235845 processed 14,000,000 fragments hits: 3,284,547, hits per frag: 0.234905 processed 14,500,001 fragments hits: 3,401,014, hits per frag: 0.23605 processed 15,000,000 fragments hits: 3,517,743, hits per frag: 0.234707 processed 15,500,000 fragments hits: 3,636,608, hits per frag: 0.23535 processed 16,000,000 fragments hits: 3,753,000, hits per frag: 0.235276 processed 16,500,000 fragments hits: 3,869,450, hits per frag: 0.235102 processed 17,000,000 fragments hits: 3,986,852, hits per frag: 0.23558 processed 17,500,000 fragments hits: 4,104,296, hits per frag: 0.2359 processed 18,000,000 fragments hits: 4,221,154, hits per frag: 0.235297[2021-07-20 11:52:38.388] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments [2021-07-20 11:52:38.388] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments [2021-07-20 11:52:38.388] [jointLog] [info] Thread saw mini-batch with a maximum of 3.40% zero probability fragments [2021-07-20 11:52:38.388] [jointLog] [info] Thread saw mini-batch with a maximum of 3.62% zero probability fragments [2021-07-20 11:52:38.388] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments [2021-07-20 11:52:38.388] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments [2021-07-20 11:52:38.388] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments [2021-07-20 11:52:38.388] [jointLog] [info] Thread saw mini-batch with a maximum of 3.66% zero probability fragments [2021-07-20 11:52:38.388] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments [2021-07-20 11:52:38.388] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments [2021-07-20 11:52:38.388] [jointLog] [info] Thread saw mini-batch with a maximum of 3.60% zero probability fragments [2021-07-20 11:52:38.388] [jointLog] [info] Thread saw mini-batch with a maximum of 3.78% zero probability fragments [2021-07-20 11:52:38.388] [jointLog] [info] Thread saw mini-batch with a maximum of 3.50% zero probability fragments [2021-07-20 11:52:38.413] [jointLog] [info] Thread saw mini-batch with a maximum of 3.48% zero probability fragments [2021-07-20 11:52:38.428] [jointLog] [info] Thread saw mini-batch with a maximum of 3.70% zero probability fragments [2021-07-20 11:52:38.438] [jointLog] [info] Thread saw mini-batch with a maximum of 3.54% zero probability fragments [2021-07-20 11:52:38.449] [jointLog] [info] Thread saw mini-batch with a maximum of 3.76% zero probability fragments [2021-07-20 11:52:38.451] [jointLog] [info] Thread saw mini-batch with a maximum of 3.56% zero probability fragments [2021-07-20 11:52:38.454] [jointLog] [info] Thread saw mini-batch with a maximum of 3.44% zero probability fragments [2021-07-20 11:52:38.467] [jointLog] [info] Thread saw mini-batch with a maximum of 3.72% zero probability fragments [2021-07-20 11:52:38.505] [jointLog] [info] Thread saw mini-batch with a maximum of 3.52% zero probability fragments [2021-07-20 11:52:38.510] [jointLog] [info] Thread saw mini-batch with a maximum of 3.58% zero probability fragments [2021-07-20 11:52:38.520] [jointLog] [info] Thread saw mini-batch with a maximum of 3.64% zero probability fragments [2021-07-20 11:52:38.734] [jointLog] [info] Computed 41,799 rich equivalence classes for further processing [2021-07-20 11:52:38.734] [jointLog] [info] Counted 2,581,892 total reads in the equivalence classes [2021-07-20 11:52:38.770] [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. [2021-07-20 11:52:38.776] [jointLog] [warning] Only 2581892 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2021-07-20 11:52:38.776] [jointLog] [info] Mapping rate = 14.0573% [2021-07-20 11:52:38.776] [jointLog] [info] finished quantifyLibrary() [2021-07-20 11:52:38.776] [jointLog] [info] Starting optimizer [2021-07-20 11:52:38.797] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2021-07-20 11:52:38.798] [jointLog] [info] iteration = 0 | max rel diff. = 122.734 [2021-07-20 11:52:38.929] [jointLog] [info] iteration = 100 | max rel diff. = 13.4816 [2021-07-20 11:52:39.055] [jointLog] [info] iteration = 200 | max rel diff. = 0.0338604 [2021-07-20 11:52:39.116] [jointLog] [info] iteration = 249 | max rel diff. = 0.00774104 [2021-07-20 11:52:39.117] [jointLog] [info] Finished optimizer [2021-07-20 11:52:39.117] [jointLog] [info] writing output CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl bleached_male_K5_02/quant.sf /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.gene_trans_map > bleached_male_K5_02/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P07-AGTCAA-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P07-AGTCAA-READ2-Sequences.txt.gz_val_2.fq.gz -o bleached_male_K5_03 -p 23 ### salmon (mapping-based) v0.12.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P07-AGTCAA-READ1-Sequences.txt.gz_val_1.fq.gz } ### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P07-AGTCAA-READ2-Sequences.txt.gz_val_2.fq.gz } ### [ output ] => { bleached_male_K5_03 } ### [ threads ] => { 23 } Logs will be written to bleached_male_K5_03/logs [2021-07-20 11:52:40.652] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2021-07-20 11:52:40.652] [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. [2021-07-20 11:52:40.652] [jointLog] [info] parsing read library format [2021-07-20 11:52:40.652] [jointLog] [info] There is 1 library. [2021-07-20 11:52:40.711] [jointLog] [info] Loading Quasi index [2021-07-20 11:52:40.711] [jointLog] [info] Loading 32-bit quasi index [2021-07-20 11:52:40.711] [stderrLog] [info] Loading Suffix Array [2021-07-20 11:52:40.756] [stderrLog] [info] Loading Transcript Info [2021-07-20 11:52:40.770] [stderrLog] [info] Loading Rank-Select Bit Array [2021-07-20 11:52:40.773] [stderrLog] [info] There were 42,425 set bits in the bit array [2021-07-20 11:52:40.775] [stderrLog] [info] Computing transcript lengths [2021-07-20 11:52:40.775] [stderrLog] [info] Waiting to finish loading hash [2021-07-20 11:52:41.464] [stderrLog] [info] Done loading index [2021-07-20 11:52:41.464] [jointLog] [info] done [2021-07-20 11:52:41.464] [jointLog] [info] Index contained 42,425 targets  processed 500,001 fragments hits: 146,016, hits per frag: 0.346326 processed 1,000,000 fragments hits: 292,613, hits per frag: 0.414925 processed 1,500,000 fragments hits: 439,592, hits per frag: 0.311266 processed 2,000,000 fragments hits: 585,692, hits per frag: 0.355346 processed 2,500,001 fragments hits: 730,791, hits per frag: 0.297991 processed 3,000,000 fragments hits: 874,926, hits per frag: 0.310021 processed 3,500,002 fragments hits: 1,020,653, hits per frag: 0.295956 processed 4,000,002 fragments hits: 1,166,957, hits per frag: 0.297866 processed 4,500,000 fragments hits: 1,312,825, hits per frag: 0.294027 processed 5,000,001 fragments hits: 1,457,980, hits per frag: 0.298696 processed 5,500,001 fragments hits: 1,604,796, hits per frag: 0.294214 processed 6,000,001 fragments hits: 1,750,431, hits per frag: 0.304301 processed 6,500,000 fragments hits: 1,897,022, hits per frag: 0.297565 processed 7,000,000 fragments hits: 2,042,055, hits per frag: 0.294225 processed 7,500,000 fragments hits: 2,187,575, hits per frag: 0.295973 processed 8,000,000 fragments hits: 2,332,354, hits per frag: 0.293397 processed 8,500,000 fragments hits: 2,478,287, hits per frag: 0.295386 processed 9,000,000 fragments hits: 2,624,913, hits per frag: 0.296776 processed 9,500,000 fragments hits: 2,770,117, hits per frag: 0.293634 processed 10,000,000 fragments hits: 2,915,739, hits per frag: 0.294663 processed 10,500,000 fragments hits: 3,062,123, hits per frag: 0.294109 processed 11,000,000 fragments hits: 3,208,425, hits per frag: 0.294034 processed 11,500,000 fragments hits: 3,353,542, hits per frag: 0.292691 processed 12,000,001 fragments hits: 3,499,174, hits per frag: 0.292847 processed 12,500,001 fragments hits: 3,644,651, hits per frag: 0.293294 processed 13,000,000 fragments hits: 3,790,804, hits per frag: 0.292291 processed 13,500,000 fragments hits: 3,936,639, hits per frag: 0.294118 processed 14,000,001 fragments hits: 4,082,162, hits per frag: 0.293907 processed 14,500,000 fragments hits: 4,227,739, hits per frag: 0.292527 processed 15,000,000 fragments hits: 4,373,811, hits per frag: 0.292452 processed 15,500,002 fragments hits: 4,520,009, hits per frag: 0.293098 processed 16,000,000 fragments hits: 4,664,620, hits per frag: 0.292911 processed 16,500,000 fragments hits: 4,811,796, hits per frag: 0.294609 processed 17,000,001 fragments hits: 4,957,008, hits per frag: 0.292484 processed 17,500,000 fragments hits: 5,102,577, hits per frag: 0.291836 processed 18,000,000 fragments hits: 5,248,479, hits per frag: 0.293171 processed 18,500,000 fragments hits: 5,394,622, hits per frag: 0.292585 processed 19,000,000 fragments hits: 5,540,784, hits per frag: 0.293262 processed 19,500,000 fragments hits: 5,687,027, hits per frag: 0.292215 processed 20,000,000 fragments hits: 5,832,675, hits per frag: 0.293599 processed 20,500,001 fragments hits: 5,979,222, hits per frag: 0.292636 processed 21,000,002 fragments hits: 6,124,398, hits per frag: 0.293385 processed 21,500,000 fragments hits: 6,270,496, hits per frag: 0.293072 processed 22,000,000 fragments hits: 6,417,543, hits per frag: 0.292487 processed 22,500,001 fragments hits: 6,562,388, hits per frag: 0.292797 processed 23,000,000 fragments hits: 6,707,573, hits per frag: 0.291898 processed 23,500,000 fragments hits: 6,852,374, hits per frag: 0.292666 processed 24,000,000 fragments hits: 6,999,846, hits per frag: 0.291916 processed 24,500,000 fragments hits: 7,146,416, hits per frag: 0.29229 processed 25,000,001 fragments hits: 7,292,260, hits per frag: 0.292224 processed 25,500,000 fragments hits: 7,437,465, hits per frag: 0.293841[2021-07-20 11:53:52.566] [jointLog] [info] Thread saw mini-batch with a maximum of 1.64% zero probability fragments [2021-07-20 11:53:52.566] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 11:53:52.566] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 11:53:52.566] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 11:53:52.566] [jointLog] [info] Thread saw mini-batch with a maximum of 1.64% zero probability fragments [2021-07-20 11:53:52.566] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 11:53:52.566] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 11:53:52.566] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments [2021-07-20 11:53:52.566] [jointLog] [info] Thread saw mini-batch with a maximum of 1.78% zero probability fragments [2021-07-20 11:53:52.566] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 11:53:52.566] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 11:53:52.568] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments [2021-07-20 11:53:52.581] [jointLog] [info] Thread saw mini-batch with a maximum of 1.64% zero probability fragments [2021-07-20 11:53:52.593] [jointLog] [info] Thread saw mini-batch with a maximum of 1.66% zero probability fragments [2021-07-20 11:53:52.604] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 11:53:52.616] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments [2021-07-20 11:53:52.623] [jointLog] [info] Thread saw mini-batch with a maximum of 1.64% zero probability fragments [2021-07-20 11:53:52.629] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments [2021-07-20 11:53:52.646] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments [2021-07-20 11:53:52.646] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments [2021-07-20 11:53:52.664] [jointLog] [info] Thread saw mini-batch with a maximum of 1.64% zero probability fragments [2021-07-20 11:53:52.679] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments [2021-07-20 11:53:52.688] [jointLog] [info] Thread saw mini-batch with a maximum of 1.64% zero probability fragments [2021-07-20 11:53:52.872] [jointLog] [info] Computed 37,140 rich equivalence classes for further processing [2021-07-20 11:53:52.872] [jointLog] [info] Counted 5,180,205 total reads in the equivalence classes [2021-07-20 11:53:52.888] [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. [2021-07-20 11:53:52.888] [jointLog] [info] Mapping rate = 19.9957% [2021-07-20 11:53:52.888] [jointLog] [info] finished quantifyLibrary() [2021-07-20 11:53:52.888] [jointLog] [info] Starting optimizer [2021-07-20 11:53:52.919] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2021-07-20 11:53:52.921] [jointLog] [info] iteration = 0 | max rel diff. = 228.908 [2021-07-20 11:53:53.050] [jointLog] [info] iteration = 100 | max rel diff. = 3.09952 [2021-07-20 11:53:53.176] [jointLog] [info] iteration = 200 | max rel diff. = 0.0918124 [2021-07-20 11:53:53.301] [jointLog] [info] iteration = 300 | max rel diff. = 0.171985 [2021-07-20 11:53:53.427] [jointLog] [info] iteration = 400 | max rel diff. = 0.142528 [2021-07-20 11:53:53.438] [jointLog] [info] iteration = 410 | max rel diff. = 0.00111601 [2021-07-20 11:53:53.439] [jointLog] [info] Finished optimizer [2021-07-20 11:53:53.439] [jointLog] [info] writing output CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl bleached_male_K5_03/quant.sf /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.gene_trans_map > bleached_male_K5_03/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ2-Sequences.txt.gz_val_2.fq.gz -o bleached_female_K5_04 -p 23 ### salmon (mapping-based) v0.12.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ1-Sequences.txt.gz_val_1.fq.gz } ### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ2-Sequences.txt.gz_val_2.fq.gz } ### [ output ] => { bleached_female_K5_04 } ### [ threads ] => { 23 } Logs will be written to bleached_female_K5_04/logs [2021-07-20 11:53:55.063] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2021-07-20 11:53:55.063] [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. [2021-07-20 11:53:55.063] [jointLog] [info] parsing read library format [2021-07-20 11:53:55.063] [jointLog] [info] There is 1 library. [2021-07-20 11:53:55.126] [stderrLog] [info] Loading Suffix Array [2021-07-20 11:53:55.126] [jointLog] [info] Loading Quasi index [2021-07-20 11:53:55.126] [jointLog] [info] Loading 32-bit quasi index [2021-07-20 11:53:55.169] [stderrLog] [info] Loading Transcript Info [2021-07-20 11:53:55.182] [stderrLog] [info] Loading Rank-Select Bit Array [2021-07-20 11:53:55.185] [stderrLog] [info] There were 42,425 set bits in the bit array [2021-07-20 11:53:55.187] [stderrLog] [info] Computing transcript lengths [2021-07-20 11:53:55.187] [stderrLog] [info] Waiting to finish loading hash [2021-07-20 11:53:55.837] [jointLog] [info] done [2021-07-20 11:53:55.837] [jointLog] [info] Index contained 42,425 targets [2021-07-20 11:53:55.837] [stderrLog] [info] Done loading index  processed 500,000 fragments hits: 138,999, hits per frag: 0.348905 processed 1,000,000 fragments hits: 277,546, hits per frag: 0.28704 processed 1,500,001 fragments hits: 415,278, hits per frag: 0.310964 processed 2,000,000 fragments hits: 552,832, hits per frag: 0.284011 processed 2,500,001 fragments hits: 690,031, hits per frag: 0.280306 processed 3,000,000 fragments hits: 827,898, hits per frag: 0.283711 processed 3,500,000 fragments hits: 965,972, hits per frag: 0.289635 processed 4,000,001 fragments hits: 1,105,768, hits per frag: 0.279007 processed 4,500,000 fragments hits: 1,245,151, hits per frag: 0.287146 processed 5,000,002 fragments hits: 1,384,335, hits per frag: 0.279708 processed 5,500,000 fragments hits: 1,522,904, hits per frag: 0.281944 processed 6,000,000 fragments hits: 1,661,333, hits per frag: 0.283552 processed 6,500,001 fragments hits: 1,800,797, hits per frag: 0.286364 processed 7,000,000 fragments hits: 1,939,708, hits per frag: 0.281328 processed 7,500,000 fragments hits: 2,077,150, hits per frag: 0.278533 processed 8,000,000 fragments hits: 2,215,275, hits per frag: 0.278151 processed 8,500,000 fragments hits: 2,352,550, hits per frag: 0.279704 processed 9,000,000 fragments hits: 2,490,352, hits per frag: 0.278044 processed 9,500,000 fragments hits: 2,626,649, hits per frag: 0.279006 processed 10,000,000 fragments hits: 2,761,968, hits per frag: 0.276811 processed 10,500,000 fragments hits: 2,898,338, hits per frag: 0.277643 processed 11,000,000 fragments hits: 3,035,925, hits per frag: 0.279271 processed 11,500,000 fragments hits: 3,173,582, hits per frag: 0.280692 processed 12,000,000 fragments hits: 3,311,143, hits per frag: 0.276199 processed 12,500,002 fragments hits: 3,449,966, hits per frag: 0.277631 processed 13,000,000 fragments hits: 3,587,670, hits per frag: 0.27771 processed 13,500,000 fragments hits: 3,725,204, hits per frag: 0.277621 processed 14,000,002 fragments hits: 3,863,303, hits per frag: 0.277619 processed 14,500,000 fragments hits: 4,001,919, hits per frag: 0.277609 processed 15,000,000 fragments hits: 4,140,369, hits per frag: 0.276718 processed 15,500,000 fragments hits: 4,278,752, hits per frag: 0.278021 processed 16,000,001 fragments hits: 4,416,790, hits per frag: 0.276994 processed 16,500,000 fragments hits: 4,554,983, hits per frag: 0.27717 processed 17,000,000 fragments hits: 4,693,712, hits per frag: 0.276817 processed 17,500,000 fragments hits: 4,832,954, hits per frag: 0.276583 processed 18,000,001 fragments hits: 4,972,220, hits per frag: 0.278049 processed 18,500,000 fragments hits: 5,109,779, hits per frag: 0.277409 processed 19,000,000 fragments hits: 5,247,545, hits per frag: 0.276605 processed 19,500,000 fragments hits: 5,386,752, hits per frag: 0.27823 processed 20,000,000 fragments hits: 5,523,977, hits per frag: 0.276834 processed 20,500,000 fragments hits: 5,662,702, hits per frag: 0.276377 processed 21,000,001 fragments hits: 5,803,019, hits per frag: 0.277952 processed 21,500,000 fragments hits: 5,941,136, hits per frag: 0.276573 processed 22,000,000 fragments hits: 6,078,589, hits per frag: 0.276364 processed 22,500,001 fragments hits: 6,216,336, hits per frag: 0.277956 processed 23,000,000 fragments hits: 6,353,581, hits per frag: 0.277993 processed 23,500,001 fragments hits: 6,493,436, hits per frag: 0.276485 processed 24,000,000 fragments hits: 6,631,631, hits per frag: 0.276608 processed 24,500,000 fragments hits: 6,767,351, hits per frag: 0.277197 processed 25,000,000 fragments hits: 6,904,713, hits per frag: 0.276693 processed 25,500,000 fragments hits: 7,042,615, hits per frag: 0.276441 processed 26,000,000 fragments hits: 7,180,109, hits per frag: 0.277037 processed 26,500,000 fragments hits: 7,318,407, hits per frag: 0.277189 processed 27,000,000 fragments hits: 7,456,379, hits per frag: 0.276847 processed 27,500,000 fragments hits: 7,593,773, hits per frag: 0.276951 processed 28,000,001 fragments hits: 7,731,532, hits per frag: 0.276368[2021-07-20 11:55:11.349] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments [2021-07-20 11:55:11.349] [jointLog] [info] Thread saw mini-batch with a maximum of 1.72% zero probability fragments [2021-07-20 11:55:11.349] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 11:55:11.349] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments [2021-07-20 11:55:11.349] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments [2021-07-20 11:55:11.349] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 11:55:11.349] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 11:55:11.349] [jointLog] [info] Thread saw mini-batch with a maximum of 1.76% zero probability fragments [2021-07-20 11:55:11.349] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments [2021-07-20 11:55:11.349] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 11:55:11.349] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments [2021-07-20 11:55:11.349] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 11:55:11.349] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments [2021-07-20 11:55:11.365] [jointLog] [info] Thread saw mini-batch with a maximum of 1.54% zero probability fragments [2021-07-20 11:55:11.381] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments [2021-07-20 11:55:11.396] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 11:55:11.400] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments [2021-07-20 11:55:11.416] [jointLog] [info] Thread saw mini-batch with a maximum of 1.90% zero probability fragments [2021-07-20 11:55:11.432] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 11:55:11.435] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 11:55:11.440] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 11:55:11.460] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 11:55:11.473] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments [2021-07-20 11:55:11.647] [jointLog] [info] Computed 35,555 rich equivalence classes for further processing [2021-07-20 11:55:11.647] [jointLog] [info] Counted 5,353,605 total reads in the equivalence classes [2021-07-20 11:55:11.672] [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. [2021-07-20 11:55:11.672] [jointLog] [info] Mapping rate = 18.9019% [2021-07-20 11:55:11.672] [jointLog] [info] finished quantifyLibrary() [2021-07-20 11:55:11.672] [jointLog] [info] Starting optimizer [2021-07-20 11:55:11.693] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2021-07-20 11:55:11.694] [jointLog] [info] iteration = 0 | max rel diff. = 254.312 [2021-07-20 11:55:11.828] [jointLog] [info] iteration = 100 | max rel diff. = 1.15307 [2021-07-20 11:55:11.953] [jointLog] [info] iteration = 200 | max rel diff. = 0.183332 [2021-07-20 11:55:12.079] [jointLog] [info] iteration = 300 | max rel diff. = 0.966041 [2021-07-20 11:55:12.112] [jointLog] [info] iteration = 327 | max rel diff. = 0.00582044 [2021-07-20 11:55:12.113] [jointLog] [info] Finished optimizer [2021-07-20 11:55:12.113] [jointLog] [info] writing output CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl bleached_female_K5_04/quant.sf /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.gene_trans_map > bleached_female_K5_04/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ2-Sequences.txt.gz_val_2.fq.gz -o bleached_female_K5_05 -p 23 ### salmon (mapping-based) v0.12.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ1-Sequences.txt.gz_val_1.fq.gz } ### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ2-Sequences.txt.gz_val_2.fq.gz } ### [ output ] => { bleached_female_K5_05 } ### [ threads ] => { 23 } Logs will be written to bleached_female_K5_05/logs [2021-07-20 11:55:13.477] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2021-07-20 11:55:13.477] [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. [2021-07-20 11:55:13.477] [jointLog] [info] parsing read library format [2021-07-20 11:55:13.477] [jointLog] [info] There is 1 library. [2021-07-20 11:55:13.535] [jointLog] [info] Loading Quasi index [2021-07-20 11:55:13.535] [jointLog] [info] Loading 32-bit quasi index [2021-07-20 11:55:13.536] [stderrLog] [info] Loading Suffix Array [2021-07-20 11:55:13.580] [stderrLog] [info] Loading Transcript Info [2021-07-20 11:55:13.592] [stderrLog] [info] Loading Rank-Select Bit Array [2021-07-20 11:55:13.595] [stderrLog] [info] There were 42,425 set bits in the bit array [2021-07-20 11:55:13.597] [stderrLog] [info] Computing transcript lengths [2021-07-20 11:55:13.597] [stderrLog] [info] Waiting to finish loading hash [2021-07-20 11:55:14.278] [stderrLog] [info] Done loading index [2021-07-20 11:55:14.278] [jointLog] [info] done [2021-07-20 11:55:14.278] [jointLog] [info] Index contained 42,425 targets  processed 500,000 fragments hits: 130,276, hits per frag: 0.289132 processed 1,000,000 fragments hits: 261,366, hits per frag: 0.285718 processed 1,500,000 fragments hits: 391,492, hits per frag: 0.282283 processed 2,000,000 fragments hits: 520,580, hits per frag: 0.286646 processed 2,500,000 fragments hits: 651,077, hits per frag: 0.262214 processed 3,000,000 fragments hits: 780,939, hits per frag: 0.265741 processed 3,500,000 fragments hits: 911,101, hits per frag: 0.277118 processed 4,000,000 fragments hits: 1,040,973, hits per frag: 0.263682 processed 4,500,000 fragments hits: 1,171,328, hits per frag: 0.267893 processed 5,000,000 fragments hits: 1,300,761, hits per frag: 0.265695 processed 5,500,000 fragments hits: 1,430,464, hits per frag: 0.264187 processed 6,000,000 fragments hits: 1,559,746, hits per frag: 0.262815 processed 6,500,000 fragments hits: 1,689,684, hits per frag: 0.260702 processed 7,000,001 fragments hits: 1,820,137, hits per frag: 0.268574 processed 7,500,000 fragments hits: 1,949,966, hits per frag: 0.260836 processed 8,000,000 fragments hits: 2,078,108, hits per frag: 0.260164 processed 8,500,000 fragments hits: 2,207,174, hits per frag: 0.261128 processed 9,000,000 fragments hits: 2,336,092, hits per frag: 0.261279 processed 9,500,000 fragments hits: 2,466,052, hits per frag: 0.260115 processed 10,000,000 fragments hits: 2,596,044, hits per frag: 0.263825 processed 10,500,000 fragments hits: 2,725,892, hits per frag: 0.261184 processed 11,000,001 fragments hits: 2,856,792, hits per frag: 0.261565 processed 11,500,000 fragments hits: 2,990,821, hits per frag: 0.262716 processed 12,000,000 fragments hits: 3,116,408, hits per frag: 0.260893 processed 12,500,001 fragments hits: 3,245,706, hits per frag: 0.263447 processed 13,000,000 fragments hits: 3,374,874, hits per frag: 0.261772 processed 13,500,000 fragments hits: 3,507,616, hits per frag: 0.266939 processed 14,000,002 fragments hits: 3,634,815, hits per frag: 0.261755 processed 14,500,000 fragments hits: 3,764,527, hits per frag: 0.261433 processed 15,000,000 fragments hits: 3,894,532, hits per frag: 0.260091 processed 15,500,001 fragments hits: 4,024,206, hits per frag: 0.261077 processed 16,000,000 fragments hits: 4,154,415, hits per frag: 0.259954 processed 16,500,001 fragments hits: 4,284,163, hits per frag: 0.259874 processed 17,000,001 fragments hits: 4,414,041, hits per frag: 0.261123 processed 17,500,001 fragments hits: 4,543,405, hits per frag: 0.260792 processed 18,000,000 fragments hits: 4,672,204, hits per frag: 0.260276 processed 18,500,000 fragments hits: 4,802,984, hits per frag: 0.259996 processed 19,000,000 fragments hits: 4,931,517, hits per frag: 0.260063 processed 19,500,001 fragments hits: 5,061,134, hits per frag: 0.260386 processed 20,000,000 fragments hits: 5,190,217, hits per frag: 0.259853 processed 20,500,000 fragments hits: 5,320,212, hits per frag: 0.261385 processed 21,000,000 fragments hits: 5,450,108, hits per frag: 0.263308 processed 21,500,000 fragments hits: 5,580,369, hits per frag: 0.26027 [2021-07-20 11:56:11.544] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 11:56:11.544] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 11:56:11.544] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 11:56:11.544] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 11:56:11.544] [jointLog] [info] Thread saw mini-batch with a maximum of 1.46% zero probability fragments [2021-07-20 11:56:11.545] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 11:56:11.545] [jointLog] [info] Thread saw mini-batch with a maximum of 1.54% zero probability fragments [2021-07-20 11:56:11.545] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 11:56:11.545] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 11:56:11.545] [jointLog] [info] Thread saw mini-batch with a maximum of 1.46% zero probability fragments [2021-07-20 11:56:11.548] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 11:56:11.552] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 11:56:11.570] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments [2021-07-20 11:56:11.578] [jointLog] [info] Thread saw mini-batch with a maximum of 1.66% zero probability fragments [2021-07-20 11:56:11.589] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments [2021-07-20 11:56:11.592] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 11:56:11.604] [jointLog] [info] Thread saw mini-batch with a maximum of 1.46% zero probability fragments [2021-07-20 11:56:11.611] [jointLog] [info] Thread saw mini-batch with a maximum of 1.72% zero probability fragments [2021-07-20 11:56:11.620] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 11:56:11.631] [jointLog] [info] Thread saw mini-batch with a maximum of 1.54% zero probability fragments [2021-07-20 11:56:11.632] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 11:56:11.653] [jointLog] [info] Thread saw mini-batch with a maximum of 1.38% zero probability fragments [2021-07-20 11:56:11.667] [jointLog] [info] Thread saw mini-batch with a maximum of 1.46% zero probability fragments [2021-07-20 11:56:11.849] [jointLog] [info] Computed 34,869 rich equivalence classes for further processing [2021-07-20 11:56:11.849] [jointLog] [info] Counted 3,921,460 total reads in the equivalence classes [2021-07-20 11:56:11.867] [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. [2021-07-20 11:56:11.871] [jointLog] [warning] Only 3921460 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2021-07-20 11:56:11.871] [jointLog] [info] Mapping rate = 17.9207% [2021-07-20 11:56:11.871] [jointLog] [info] finished quantifyLibrary() [2021-07-20 11:56:11.871] [jointLog] [info] Starting optimizer [2021-07-20 11:56:11.894] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2021-07-20 11:56:11.895] [jointLog] [info] iteration = 0 | max rel diff. = 138.15 [2021-07-20 11:56:12.024] [jointLog] [info] iteration = 100 | max rel diff. = 0.17429 [2021-07-20 11:56:12.148] [jointLog] [info] iteration = 200 | max rel diff. = 2.25838 [2021-07-20 11:56:12.273] [jointLog] [info] iteration = 300 | max rel diff. = 0.0348191 [2021-07-20 11:56:12.396] [jointLog] [info] iteration = 400 | max rel diff. = 0.080556 [2021-07-20 11:56:12.434] [jointLog] [info] iteration = 432 | max rel diff. = 0.00166393 [2021-07-20 11:56:12.436] [jointLog] [info] Finished optimizer [2021-07-20 11:56:12.436] [jointLog] [info] writing output CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl bleached_female_K5_05/quant.sf /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.gene_trans_map > bleached_female_K5_05/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ1-Sequences.txt.gz_val_1.fq.gz -2 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ2-Sequences.txt.gz_val_2.fq.gz -o bleached_female_K5_06 -p 23 ### salmon (mapping-based) v0.12.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ1-Sequences.txt.gz_val_1.fq.gz } ### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ2-Sequences.txt.gz_val_2.fq.gz } ### [ output ] => { bleached_female_K5_06 } ### [ threads ] => { 23 } Logs will be written to bleached_female_K5_06/logs [2021-07-20 11:56:13.890] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2021-07-20 11:56:13.890] [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. [2021-07-20 11:56:13.890] [jointLog] [info] parsing read library format [2021-07-20 11:56:13.890] [jointLog] [info] There is 1 library. [2021-07-20 11:56:13.948] [jointLog] [info] Loading Quasi index [2021-07-20 11:56:13.948] [jointLog] [info] Loading 32-bit quasi index [2021-07-20 11:56:13.948] [stderrLog] [info] Loading Suffix Array [2021-07-20 11:56:13.988] [stderrLog] [info] Loading Transcript Info [2021-07-20 11:56:14.000] [stderrLog] [info] Loading Rank-Select Bit Array [2021-07-20 11:56:14.002] [stderrLog] [info] There were 42,425 set bits in the bit array [2021-07-20 11:56:14.004] [stderrLog] [info] Computing transcript lengths [2021-07-20 11:56:14.004] [stderrLog] [info] Waiting to finish loading hash [2021-07-20 11:56:14.653] [stderrLog] [info] Done loading index [2021-07-20 11:56:14.653] [jointLog] [info] done [2021-07-20 11:56:14.653] [jointLog] [info] Index contained 42,425 targets  processed 500,001 fragments hits: 107,336, hits per frag: 0.259395 processed 1,000,000 fragments hits: 214,903, hits per frag: 0.215174 processed 1,500,000 fragments hits: 322,745, hits per frag: 0.233647 processed 2,000,000 fragments hits: 430,258, hits per frag: 0.22286 processed 2,500,000 fragments hits: 537,661, hits per frag: 0.228169 processed 3,000,000 fragments hits: 645,268, hits per frag: 0.217015 processed 3,500,000 fragments hits: 752,889, hits per frag: 0.221317 processed 4,000,000 fragments hits: 860,773, hits per frag: 0.216395 processed 4,500,002 fragments hits: 967,667, hits per frag: 0.223855 processed 5,000,000 fragments hits: 1,075,654, hits per frag: 0.217482 processed 5,500,000 fragments hits: 1,182,828, hits per frag: 0.216372 processed 6,000,000 fragments hits: 1,290,139, hits per frag: 0.215856 processed 6,500,000 fragments hits: 1,397,540, hits per frag: 0.215411 processed 7,000,000 fragments hits: 1,505,358, hits per frag: 0.217519 processed 7,500,000 fragments hits: 1,612,172, hits per frag: 0.21629 processed 8,000,000 fragments hits: 1,719,699, hits per frag: 0.216331 processed 8,500,000 fragments hits: 1,826,464, hits per frag: 0.21608 processed 9,000,000 fragments hits: 1,933,740, hits per frag: 0.220951 processed 9,500,000 fragments hits: 2,041,076, hits per frag: 0.215535 processed 10,000,000 fragments hits: 2,149,071, hits per frag: 0.21526 processed 10,500,000 fragments hits: 2,256,486, hits per frag: 0.21549 processed 11,000,000 fragments hits: 2,363,801, hits per frag: 0.219156 processed 11,500,000 fragments hits: 2,471,483, hits per frag: 0.216414 processed 12,000,000 fragments hits: 2,578,300, hits per frag: 0.215395 processed 12,500,000 fragments hits: 2,685,335, hits per frag: 0.216225 processed 13,000,000 fragments hits: 2,792,257, hits per frag: 0.214928 processed 13,500,002 fragments hits: 2,900,453, hits per frag: 0.216477 processed 14,000,000 fragments hits: 3,008,027, hits per frag: 0.216207 processed 14,500,000 fragments hits: 3,115,390, hits per frag: 0.217367 processed 15,000,001 fragments hits: 3,223,808, hits per frag: 0.215121 processed 15,500,000 fragments hits: 3,331,339, hits per frag: 0.216209 processed 16,000,000 fragments hits: 3,439,285, hits per frag: 0.219859 processed 16,500,000 fragments hits: 3,546,681, hits per frag: 0.21562 processed 17,000,001 fragments hits: 3,653,169, hits per frag: 0.215054 [2021-07-20 11:57:00.361] [jointLog] [info] Thread saw mini-batch with a maximum of 1.18% zero probability fragments [2021-07-20 11:57:00.361] [jointLog] [info] Thread saw mini-batch with a maximum of 1.12% zero probability fragments [2021-07-20 11:57:00.361] [jointLog] [info] Thread saw mini-batch with a maximum of 1.18% zero probability fragments [2021-07-20 11:57:00.361] [jointLog] [info] Thread saw mini-batch with a maximum of 1.32% zero probability fragments [2021-07-20 11:57:00.361] [jointLog] [info] Thread saw mini-batch with a maximum of 1.16% zero probability fragments [2021-07-20 11:57:00.361] [jointLog] [info] Thread saw mini-batch with a maximum of 1.30% zero probability fragments [2021-07-20 11:57:00.361] [jointLog] [info] Thread saw mini-batch with a maximum of 1.20% zero probability fragments [2021-07-20 11:57:00.361] [jointLog] [info] Thread saw mini-batch with a maximum of 1.18% zero probability fragments [2021-07-20 11:57:00.361] [jointLog] [info] Thread saw mini-batch with a maximum of 1.10% zero probability fragments [2021-07-20 11:57:00.361] [jointLog] [info] Thread saw mini-batch with a maximum of 1.14% zero probability fragments [2021-07-20 11:57:00.361] [jointLog] [info] Thread saw mini-batch with a maximum of 1.32% zero probability fragments [2021-07-20 11:57:00.361] [jointLog] [info] Thread saw mini-batch with a maximum of 1.12% zero probability fragments [2021-07-20 11:57:00.373] [jointLog] [info] Thread saw mini-batch with a maximum of 1.66% zero probability fragments [2021-07-20 11:57:00.381] [jointLog] [info] Thread saw mini-batch with a maximum of 1.18% zero probability fragments [2021-07-20 11:57:00.383] [jointLog] [info] Thread saw mini-batch with a maximum of 1.26% zero probability fragments [2021-07-20 11:57:00.383] [jointLog] [info] Thread saw mini-batch with a maximum of 1.14% zero probability fragments [2021-07-20 11:57:00.412] [jointLog] [info] Thread saw mini-batch with a maximum of 1.20% zero probability fragments [2021-07-20 11:57:00.422] [jointLog] [info] Thread saw mini-batch with a maximum of 1.08% zero probability fragments [2021-07-20 11:57:00.439] [jointLog] [info] Thread saw mini-batch with a maximum of 1.14% zero probability fragments [2021-07-20 11:57:00.443] [jointLog] [info] Thread saw mini-batch with a maximum of 1.24% zero probability fragments [2021-07-20 11:57:00.447] [jointLog] [info] Thread saw mini-batch with a maximum of 1.20% zero probability fragments [2021-07-20 11:57:00.456] [jointLog] [info] Thread saw mini-batch with a maximum of 1.24% zero probability fragments [2021-07-20 11:57:00.468] [jointLog] [info] Thread saw mini-batch with a maximum of 1.16% zero probability fragments [2021-07-20 11:57:00.672] [jointLog] [info] Computed 31,247 rich equivalence classes for further processing [2021-07-20 11:57:00.672] [jointLog] [info] Counted 2,687,775 total reads in the equivalence classes [2021-07-20 11:57:00.691] [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. [2021-07-20 11:57:00.694] [jointLog] [warning] Only 2687775 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2021-07-20 11:57:00.694] [jointLog] [info] Mapping rate = 15.5493% [2021-07-20 11:57:00.694] [jointLog] [info] finished quantifyLibrary() [2021-07-20 11:57:00.694] [jointLog] [info] Starting optimizer [2021-07-20 11:57:00.733] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2021-07-20 11:57:00.742] [jointLog] [info] iteration = 0 | max rel diff. = 242.594 [2021-07-20 11:57:00.875] [jointLog] [info] iteration = 100 | max rel diff. = 0.425729 [2021-07-20 11:57:00.997] [jointLog] [info] iteration = 200 | max rel diff. = 0.0451181 [2021-07-20 11:57:01.119] [jointLog] [info] iteration = 300 | max rel diff. = 0.120554 [2021-07-20 11:57:01.143] [jointLog] [info] iteration = 321 | max rel diff. = 0.00151507 [2021-07-20 11:57:01.144] [jointLog] [info] Finished optimizer [2021-07-20 11:57:01.144] [jointLog] [info] writing output CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl bleached_female_K5_06/quant.sf /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.gene_trans_map > bleached_female_K5_06/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.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 bleached_female_44_01 -p 23 ### salmon (mapping-based) v0.12.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.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 ] => { bleached_female_44_01 } ### [ threads ] => { 23 } Logs will be written to bleached_female_44_01/logs [2021-07-20 11:57:02.811] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2021-07-20 11:57:02.811] [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. [2021-07-20 11:57:02.811] [jointLog] [info] parsing read library format [2021-07-20 11:57:02.811] [jointLog] [info] There is 1 library. [2021-07-20 11:57:02.869] [jointLog] [info] Loading Quasi index [2021-07-20 11:57:02.869] [jointLog] [info] Loading 32-bit quasi index [2021-07-20 11:57:02.869] [stderrLog] [info] Loading Suffix Array [2021-07-20 11:57:02.913] [stderrLog] [info] Loading Transcript Info [2021-07-20 11:57:02.927] [stderrLog] [info] Loading Rank-Select Bit Array [2021-07-20 11:57:02.930] [stderrLog] [info] There were 42,425 set bits in the bit array [2021-07-20 11:57:02.932] [stderrLog] [info] Computing transcript lengths [2021-07-20 11:57:02.932] [stderrLog] [info] Waiting to finish loading hash [2021-07-20 11:57:03.618] [stderrLog] [info] Done loading index [2021-07-20 11:57:03.618] [jointLog] [info] done [2021-07-20 11:57:03.618] [jointLog] [info] Index contained 42,425 targets  processed 500,000 fragments hits: 126,995, hits per frag: 0.267784 processed 1,000,002 fragments hits: 253,511, hits per frag: 0.264624 processed 1,500,000 fragments hits: 380,244, hits per frag: 0.263054 processed 2,000,000 fragments hits: 506,146, hits per frag: 0.258497 processed 2,500,001 fragments hits: 632,898, hits per frag: 0.258706 processed 3,000,000 fragments hits: 760,671, hits per frag: 0.261907 processed 3,500,000 fragments hits: 887,893, hits per frag: 0.256035 processed 4,000,000 fragments hits: 1,013,615, hits per frag: 0.257335 processed 4,500,001 fragments hits: 1,140,547, hits per frag: 0.258262 processed 5,000,000 fragments hits: 1,267,559, hits per frag: 0.258267 processed 5,500,000 fragments hits: 1,394,682, hits per frag: 0.255022 processed 6,000,000 fragments hits: 1,522,150, hits per frag: 0.256111 processed 6,500,001 fragments hits: 1,648,345, hits per frag: 0.255812 processed 7,000,000 fragments hits: 1,774,292, hits per frag: 0.256666 processed 7,500,000 fragments hits: 1,899,117, hits per frag: 0.25366 processed 8,000,001 fragments hits: 2,023,677, hits per frag: 0.254315 processed 8,500,000 fragments hits: 2,149,855, hits per frag: 0.253405 processed 9,000,000 fragments hits: 2,275,165, hits per frag: 0.25436 processed 9,500,001 fragments hits: 2,400,824, hits per frag: 0.253845 processed 10,000,001 fragments hits: 2,526,658, hits per frag: 0.256113 processed 10,500,001 fragments hits: 2,652,667, hits per frag: 0.253426 processed 11,000,000 fragments hits: 2,779,456, hits per frag: 0.25332 processed 11,500,000 fragments hits: 2,906,449, hits per frag: 0.256079 processed 12,000,000 fragments hits: 3,033,148, hits per frag: 0.25406 processed 12,500,002 fragments hits: 3,160,534, hits per frag: 0.25303 processed 13,000,000 fragments hits: 3,286,155, hits per frag: 0.253678 processed 13,500,000 fragments hits: 3,412,448, hits per frag: 0.257265 processed 14,000,001 fragments hits: 3,538,945, hits per frag: 0.253154 processed 14,500,000 fragments hits: 3,665,758, hits per frag: 0.254071 processed 15,000,000 fragments hits: 3,792,241, hits per frag: 0.253131 processed 15,500,000 fragments hits: 3,919,352, hits per frag: 0.256974 processed 16,000,000 fragments hits: 4,046,169, hits per frag: 0.253295 processed 16,500,000 fragments hits: 4,172,503, hits per frag: 0.253968 processed 17,000,000 fragments hits: 4,299,945, hits per frag: 0.254363 processed 17,500,001 fragments hits: 4,426,267, hits per frag: 0.255654 processed 18,000,000 fragments hits: 4,552,584, hits per frag: 0.255545 processed 18,500,000 fragments hits: 4,677,858, hits per frag: 0.253566 processed 19,000,000 fragments hits: 4,804,212, hits per frag: 0.253429 processed 19,500,000 fragments hits: 4,930,795, hits per frag: 0.253372 processed 20,000,000 fragments hits: 5,055,518, hits per frag: 0.253496 processed 20,500,001 fragments hits: 5,180,938, hits per frag: 0.253505 processed 21,000,001 fragments hits: 5,307,702, hits per frag: 0.254205 processed 21,500,001 fragments hits: 5,433,994, hits per frag: 0.253745 processed 22,000,000 fragments hits: 5,560,905, hits per frag: 0.25311 processed 22,500,000 fragments hits: 5,687,028, hits per frag: 0.253739 processed 23,000,000 fragments hits: 5,814,270, hits per frag: 0.253368 [2021-07-20 11:58:05.448] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 11:58:05.448] [jointLog] [info] Thread saw mini-batch with a maximum of 1.76% zero probability fragments [2021-07-20 11:58:05.448] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 11:58:05.448] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments [2021-07-20 11:58:05.448] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 11:58:05.448] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 11:58:05.448] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments [2021-07-20 11:58:05.448] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 11:58:05.448] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 11:58:05.448] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments [2021-07-20 11:58:05.448] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments [2021-07-20 11:58:05.462] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 11:58:05.472] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 11:58:05.484] [jointLog] [info] Thread saw mini-batch with a maximum of 1.88% zero probability fragments [2021-07-20 11:58:05.509] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 11:58:05.511] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments [2021-07-20 11:58:05.513] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 11:58:05.518] [jointLog] [info] Thread saw mini-batch with a maximum of 1.68% zero probability fragments [2021-07-20 11:58:05.543] [jointLog] [info] Thread saw mini-batch with a maximum of 1.66% zero probability fragments [2021-07-20 11:58:05.544] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 11:58:05.547] [jointLog] [info] Thread saw mini-batch with a maximum of 1.76% zero probability fragments [2021-07-20 11:58:05.569] [jointLog] [info] Thread saw mini-batch with a maximum of 1.64% zero probability fragments [2021-07-20 11:58:05.569] [jointLog] [info] Thread saw mini-batch with a maximum of 1.68% zero probability fragments [2021-07-20 11:58:05.726] [jointLog] [info] Computed 37,000 rich equivalence classes for further processing [2021-07-20 11:58:05.726] [jointLog] [info] Counted 3,894,898 total reads in the equivalence classes [2021-07-20 11:58:05.744] [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. [2021-07-20 11:58:05.747] [jointLog] [warning] Only 3894898 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2021-07-20 11:58:05.747] [jointLog] [info] Mapping rate = 16.916% [2021-07-20 11:58:05.747] [jointLog] [info] finished quantifyLibrary() [2021-07-20 11:58:05.747] [jointLog] [info] Starting optimizer [2021-07-20 11:58:05.780] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2021-07-20 11:58:05.781] [jointLog] [info] iteration = 0 | max rel diff. = 138.538 [2021-07-20 11:58:05.907] [jointLog] [info] iteration = 100 | max rel diff. = 0.867746 [2021-07-20 11:58:06.032] [jointLog] [info] iteration = 200 | max rel diff. = 7.40915 [2021-07-20 11:58:06.132] [jointLog] [info] iteration = 281 | max rel diff. = 0.00641646 [2021-07-20 11:58:06.133] [jointLog] [info] Finished optimizer [2021-07-20 11:58:06.133] [jointLog] [info] writing output CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl bleached_female_44_01/quant.sf /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.gene_trans_map > bleached_female_44_01/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.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 bleached_female_44_02 -p 23 ### salmon (mapping-based) v0.12.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.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 ] => { bleached_female_44_02 } ### [ threads ] => { 23 } Logs will be written to bleached_female_44_02/logs [2021-07-20 11:58:07.745] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2021-07-20 11:58:07.745] [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. [2021-07-20 11:58:07.745] [jointLog] [info] parsing read library format [2021-07-20 11:58:07.745] [jointLog] [info] There is 1 library. [2021-07-20 11:58:07.803] [jointLog] [info] Loading Quasi index [2021-07-20 11:58:07.803] [jointLog] [info] Loading 32-bit quasi index [2021-07-20 11:58:07.803] [stderrLog] [info] Loading Suffix Array [2021-07-20 11:58:07.847] [stderrLog] [info] Loading Transcript Info [2021-07-20 11:58:07.861] [stderrLog] [info] Loading Rank-Select Bit Array [2021-07-20 11:58:07.864] [stderrLog] [info] There were 42,425 set bits in the bit array [2021-07-20 11:58:07.866] [stderrLog] [info] Computing transcript lengths [2021-07-20 11:58:07.866] [stderrLog] [info] Waiting to finish loading hash [2021-07-20 11:58:08.561] [stderrLog] [info] Done loading index [2021-07-20 11:58:08.561] [jointLog] [info] done [2021-07-20 11:58:08.561] [jointLog] [info] Index contained 42,425 targets  processed 500,000 fragments hits: 137,629, hits per frag: 0.314333 processed 1,000,000 fragments hits: 274,959, hits per frag: 0.316842 processed 1,500,000 fragments hits: 411,842, hits per frag: 0.276342 processed 2,000,000 fragments hits: 549,134, hits per frag: 0.289965 processed 2,500,000 fragments hits: 686,357, hits per frag: 0.286596 processed 3,000,000 fragments hits: 824,083, hits per frag: 0.289661 processed 3,500,000 fragments hits: 961,613, hits per frag: 0.2765 processed 4,000,000 fragments hits: 1,101,163, hits per frag: 0.291559 processed 4,500,000 fragments hits: 1,240,216, hits per frag: 0.280069 processed 5,000,000 fragments hits: 1,378,275, hits per frag: 0.27864 processed 5,500,000 fragments hits: 1,516,180, hits per frag: 0.278397 processed 6,000,000 fragments hits: 1,653,880, hits per frag: 0.278859 processed 6,500,001 fragments hits: 1,790,959, hits per frag: 0.277494 processed 7,000,001 fragments hits: 1,927,862, hits per frag: 0.277502 processed 7,500,000 fragments hits: 2,064,348, hits per frag: 0.277564 processed 8,000,001 fragments hits: 2,200,764, hits per frag: 0.277427 processed 8,500,000 fragments hits: 2,337,197, hits per frag: 0.276285 processed 9,000,001 fragments hits: 2,474,055, hits per frag: 0.276029 processed 9,500,000 fragments hits: 2,610,504, hits per frag: 0.276707 processed 10,000,000 fragments hits: 2,748,621, hits per frag: 0.277334 processed 10,500,001 fragments hits: 2,885,811, hits per frag: 0.275663 processed 11,000,001 fragments hits: 3,023,839, hits per frag: 0.277757 processed 11,500,000 fragments hits: 3,161,717, hits per frag: 0.276063 processed 12,000,000 fragments hits: 3,299,680, hits per frag: 0.276934 processed 12,500,000 fragments hits: 3,438,113, hits per frag: 0.275598 processed 13,000,001 fragments hits: 3,576,200, hits per frag: 0.275933 processed 13,500,000 fragments hits: 3,713,732, hits per frag: 0.276423 processed 14,000,000 fragments hits: 3,852,100, hits per frag: 0.276685 processed 14,000,015 fragments hits: 3,852,104, hits per frag: 0.276251 processed 14,500,000 fragments hits: 3,989,750, hits per frag: 0.278302 processed 15,000,000 fragments hits: 4,127,554, hits per frag: 0.275436 processed 15,500,000 fragments hits: 4,265,691, hits per frag: 0.276212 processed 16,000,000 fragments hits: 4,404,002, hits per frag: 0.276464 processed 16,500,000 fragments hits: 4,542,559, hits per frag: 0.27596 processed 17,000,000 fragments hits: 4,679,002, hits per frag: 0.276154 processed 17,500,002 fragments hits: 4,815,518, hits per frag: 0.277583 processed 18,000,000 fragments hits: 4,952,664, hits per frag: 0.276045 processed 18,500,000 fragments hits: 5,090,189, hits per frag: 0.275644 processed 19,000,001 fragments hits: 5,226,540, hits per frag: 0.275193 processed 19,500,000 fragments hits: 5,363,383, hits per frag: 0.276137 processed 20,000,000 fragments hits: 5,499,832, hits per frag: 0.275522 processed 20,500,001 fragments hits: 5,638,472, hits per frag: 0.276483 processed 21,000,000 fragments hits: 5,775,423, hits per frag: 0.275308 processed 21,500,000 fragments hits: 5,914,039, hits per frag: 0.276352[2021-07-20 11:59:08.104] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 11:59:08.104] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments [2021-07-20 11:59:08.104] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments [2021-07-20 11:59:08.104] [jointLog] [info] Thread saw mini-batch with a maximum of 1.76% zero probability fragments [2021-07-20 11:59:08.104] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 11:59:08.104] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 11:59:08.104] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 11:59:08.104] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 11:59:08.107] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 11:59:08.110] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments [2021-07-20 11:59:08.110] [jointLog] [info] Thread saw mini-batch with a maximum of 1.54% zero probability fragments [2021-07-20 11:59:08.117] [jointLog] [info] Thread saw mini-batch with a maximum of 1.68% zero probability fragments [2021-07-20 11:59:08.125] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 11:59:08.126] [jointLog] [info] Thread saw mini-batch with a maximum of 1.54% zero probability fragments [2021-07-20 11:59:08.156] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 11:59:08.165] [jointLog] [info] Thread saw mini-batch with a maximum of 1.44% zero probability fragments [2021-07-20 11:59:08.167] [jointLog] [info] Thread saw mini-batch with a maximum of 1.68% zero probability fragments [2021-07-20 11:59:08.179] [jointLog] [info] Thread saw mini-batch with a maximum of 1.66% zero probability fragments [2021-07-20 11:59:08.197] [jointLog] [info] Thread saw mini-batch with a maximum of 1.76% zero probability fragments [2021-07-20 11:59:08.209] [jointLog] [info] Thread saw mini-batch with a maximum of 1.84% zero probability fragments [2021-07-20 11:59:08.210] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments [2021-07-20 11:59:08.229] [jointLog] [info] Thread saw mini-batch with a maximum of 1.66% zero probability fragments [2021-07-20 11:59:08.237] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 11:59:08.454] [jointLog] [info] Computed 36,112 rich equivalence classes for further processing [2021-07-20 11:59:08.454] [jointLog] [info] Counted 4,157,088 total reads in the equivalence classes [2021-07-20 11:59:08.478] [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. [2021-07-20 11:59:08.481] [jointLog] [warning] Only 4157088 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2021-07-20 11:59:08.481] [jointLog] [info] Mapping rate = 18.9482% [2021-07-20 11:59:08.481] [jointLog] [info] finished quantifyLibrary() [2021-07-20 11:59:08.482] [jointLog] [info] Starting optimizer [2021-07-20 11:59:08.502] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2021-07-20 11:59:08.504] [jointLog] [info] iteration = 0 | max rel diff. = 208.189 [2021-07-20 11:59:08.647] [jointLog] [info] iteration = 100 | max rel diff. = 1.5817 [2021-07-20 11:59:08.785] [jointLog] [info] iteration = 200 | max rel diff. = 0.216411 [2021-07-20 11:59:08.922] [jointLog] [info] iteration = 300 | max rel diff. = 0.104726 [2021-07-20 11:59:09.060] [jointLog] [info] iteration = 400 | max rel diff. = 0.00574586 [2021-07-20 11:59:09.060] [jointLog] [info] iteration = 401 | max rel diff. = 0.00574586 [2021-07-20 11:59:09.061] [jointLog] [info] Finished optimizer [2021-07-20 11:59:09.061] [jointLog] [info] writing output CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl bleached_female_44_02/quant.sf /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.gene_trans_map > bleached_female_44_02/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.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 bleached_female_44_03 -p 23 ### salmon (mapping-based) v0.12.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.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 ] => { bleached_female_44_03 } ### [ threads ] => { 23 } Logs will be written to bleached_female_44_03/logs [2021-07-20 11:59:10.655] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2021-07-20 11:59:10.655] [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. [2021-07-20 11:59:10.655] [jointLog] [info] parsing read library format [2021-07-20 11:59:10.655] [jointLog] [info] There is 1 library. [2021-07-20 11:59:10.713] [jointLog] [info] Loading Quasi index [2021-07-20 11:59:10.713] [jointLog] [info] Loading 32-bit quasi index [2021-07-20 11:59:10.713] [stderrLog] [info] Loading Suffix Array [2021-07-20 11:59:10.757] [stderrLog] [info] Loading Transcript Info [2021-07-20 11:59:10.768] [stderrLog] [info] Loading Rank-Select Bit Array [2021-07-20 11:59:10.771] [stderrLog] [info] There were 42,425 set bits in the bit array [2021-07-20 11:59:10.773] [stderrLog] [info] Computing transcript lengths [2021-07-20 11:59:10.773] [stderrLog] [info] Waiting to finish loading hash [2021-07-20 11:59:11.446] [stderrLog] [info] Done loading index [2021-07-20 11:59:11.446] [jointLog] [info] done [2021-07-20 11:59:11.446] [jointLog] [info] Index contained 42,425 targets  processed 500,000 fragments hits: 132,798, hits per frag: 0.343699 processed 1,000,000 fragments hits: 264,082, hits per frag: 0.284741 processed 1,500,000 fragments hits: 395,672, hits per frag: 0.287647 processed 2,000,000 fragments hits: 527,109, hits per frag: 0.266891 processed 2,500,001 fragments hits: 658,205, hits per frag: 0.2774 processed 3,000,000 fragments hits: 789,483, hits per frag: 0.269703 processed 3,500,000 fragments hits: 921,628, hits per frag: 0.267471 processed 4,000,000 fragments hits: 1,053,468, hits per frag: 0.26659 processed 4,500,000 fragments hits: 1,186,092, hits per frag: 0.264992 processed 5,000,001 fragments hits: 1,317,940, hits per frag: 0.273218 processed 5,500,000 fragments hits: 1,450,067, hits per frag: 0.265692 processed 6,000,000 fragments hits: 1,582,546, hits per frag: 0.268141 processed 6,500,000 fragments hits: 1,714,298, hits per frag: 0.264477 processed 7,000,000 fragments hits: 1,846,102, hits per frag: 0.266202 processed 7,500,000 fragments hits: 1,978,997, hits per frag: 0.265598 processed 8,000,000 fragments hits: 2,111,929, hits per frag: 0.265727 processed 8,500,000 fragments hits: 2,243,981, hits per frag: 0.266922 processed 9,000,000 fragments hits: 2,374,597, hits per frag: 0.270561 processed 9,500,000 fragments hits: 2,505,605, hits per frag: 0.266559 processed 10,000,000 fragments hits: 2,635,847, hits per frag: 0.266452 processed 10,500,000 fragments hits: 2,766,336, hits per frag: 0.266368 processed 11,000,001 fragments hits: 2,896,479, hits per frag: 0.266661 processed 11,500,000 fragments hits: 3,026,571, hits per frag: 0.266402 processed 12,000,000 fragments hits: 3,157,502, hits per frag: 0.266075 processed 12,500,000 fragments hits: 3,288,120, hits per frag: 0.264268 processed 13,000,000 fragments hits: 3,419,279, hits per frag: 0.26421 processed 13,500,000 fragments hits: 3,550,121, hits per frag: 0.263351 processed 14,000,000 fragments hits: 3,681,953, hits per frag: 0.263167 processed 14,500,000 fragments hits: 3,813,781, hits per frag: 0.263625 processed 15,000,000 fragments hits: 3,944,689, hits per frag: 0.263497 processed 15,500,002 fragments hits: 4,077,026, hits per frag: 0.26429 processed 16,000,000 fragments hits: 4,209,426, hits per frag: 0.263826 processed 16,500,000 fragments hits: 4,341,385, hits per frag: 0.265077 processed 17,000,000 fragments hits: 4,472,383, hits per frag: 0.264878 processed 17,500,000 fragments hits: 4,604,783, hits per frag: 0.263814 processed 18,000,000 fragments hits: 4,736,004, hits per frag: 0.264351 processed 18,500,000 fragments hits: 4,866,657, hits per frag: 0.264975 processed 19,000,000 fragments hits: 4,998,159, hits per frag: 0.264315 processed 19,500,000 fragments hits: 5,128,879, hits per frag: 0.263358 processed 20,000,000 fragments hits: 5,260,721, hits per frag: 0.264903 processed 20,500,000 fragments hits: 5,393,432, hits per frag: 0.264265 processed 21,000,001 fragments hits: 5,526,064, hits per frag: 0.26395 processed 21,500,001 fragments hits: 5,658,324, hits per frag: 0.264131 processed 22,000,000 fragments hits: 5,790,813, hits per frag: 0.264623 processed 22,500,000 fragments hits: 5,923,838, hits per frag: 0.264323 processed 23,000,000 fragments hits: 6,057,023, hits per frag: 0.26439 processed 23,500,001 fragments hits: 6,188,422, hits per frag: 0.263951 processed 24,000,000 fragments hits: 6,320,432, hits per frag: 0.264095 processed 24,500,001 fragments hits: 6,452,029, hits per frag: 0.26476 processed 25,000,000 fragments hits: 6,583,030, hits per frag: 0.265866 processed 25,500,000 fragments hits: 6,713,765, hits per frag: 0.266577 processed 26,500,000 fragments hits: 6,976,167, hits per frag: 0.263456 processed 27,000,000 fragments hits: 7,106,507, hits per frag: 0.263421 processed 27,500,000 fragments hits: 7,236,002, hits per frag: 0.264371 processed 28,000,000 fragments hits: 7,365,449, hits per frag: 0.263754 processed 28,500,001 fragments hits: 7,496,202, hits per frag: 0.26352 processed 29,000,001 fragments hits: 7,627,354, hits per frag: 0.264426 processed 29,500,000 fragments hits: 7,758,925, hits per frag: 0.263767 processed 30,000,000 fragments hits: 7,889,603, hits per frag: 0.264927 processed 30,500,001 fragments hits: 8,021,712, hits per frag: 0.263697 processed 31,000,000 fragments hits: 8,152,856, hits per frag: 0.263729 processed 31,500,001 fragments hits: 8,285,153, hits per frag: 0.263548[2021-07-20 12:00:36.606] [jointLog] [info] Thread saw mini-batch with a maximum of 1.34% zero probability fragments [2021-07-20 12:00:36.606] [jointLog] [info] Thread saw mini-batch with a maximum of 1.54% zero probability fragments [2021-07-20 12:00:36.606] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 12:00:36.606] [jointLog] [info] Thread saw mini-batch with a maximum of 1.42% zero probability fragments [2021-07-20 12:00:36.606] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:00:36.606] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 12:00:36.606] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 12:00:36.606] [jointLog] [info] Thread saw mini-batch with a maximum of 1.40% zero probability fragments [2021-07-20 12:00:36.606] [jointLog] [info] Thread saw mini-batch with a maximum of 1.44% zero probability fragments [2021-07-20 12:00:36.606] [jointLog] [info] Thread saw mini-batch with a maximum of 1.54% zero probability fragments [2021-07-20 12:00:36.613] [jointLog] [info] Thread saw mini-batch with a maximum of 1.62% zero probability fragments [2021-07-20 12:00:36.618] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 12:00:36.620] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:00:36.662] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 12:00:36.673] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:00:36.679] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 12:00:36.680] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 12:00:36.687] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:00:36.694] [jointLog] [info] Thread saw mini-batch with a maximum of 1.54% zero probability fragments [2021-07-20 12:00:36.698] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 12:00:36.710] [jointLog] [info] Thread saw mini-batch with a maximum of 1.40% zero probability fragments [2021-07-20 12:00:36.716] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:00:36.731] [jointLog] [info] Thread saw mini-batch with a maximum of 1.32% zero probability fragments [2021-07-20 12:00:36.915] [jointLog] [info] Computed 37,693 rich equivalence classes for further processing [2021-07-20 12:00:36.915] [jointLog] [info] Counted 5,527,616 total reads in the equivalence classes [2021-07-20 12:00:36.933] [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. [2021-07-20 12:00:36.933] [jointLog] [info] Mapping rate = 17.461% [2021-07-20 12:00:36.933] [jointLog] [info] finished quantifyLibrary() [2021-07-20 12:00:36.933] [jointLog] [info] Starting optimizer [2021-07-20 12:00:36.956] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2021-07-20 12:00:36.958] [jointLog] [info] iteration = 0 | max rel diff. = 148.896 [2021-07-20 12:00:37.093] [jointLog] [info] iteration = 100 | max rel diff. = 1.49672 [2021-07-20 12:00:37.219] [jointLog] [info] iteration = 200 | max rel diff. = 0.100456 [2021-07-20 12:00:37.287] [jointLog] [info] iteration = 255 | max rel diff. = 0.00346697 [2021-07-20 12:00:37.288] [jointLog] [info] Finished optimizer [2021-07-20 12:00:37.288] [jointLog] [info] writing output CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl bleached_female_44_03/quant.sf /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.gene_trans_map > bleached_female_44_03/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P02-ACAGTG-READ1-Sequences.txt.gz_val_1.fq.gz -2 /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_female_K5_01 -p 23 ### salmon (mapping-based) v0.12.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P02-ACAGTG-READ1-Sequences.txt.gz_val_1.fq.gz } ### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P02-ACAGTG-READ2-Sequences.txt.gz_val_2.fq.gz } ### [ output ] => { non-bleached_female_K5_01 } ### [ threads ] => { 23 } Logs will be written to non-bleached_female_K5_01/logs [2021-07-20 12:00:38.669] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2021-07-20 12:00:38.669] [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. [2021-07-20 12:00:38.669] [jointLog] [info] parsing read library format [2021-07-20 12:00:38.669] [jointLog] [info] There is 1 library. [2021-07-20 12:00:38.727] [jointLog] [info] Loading Quasi index [2021-07-20 12:00:38.727] [jointLog] [info] Loading 32-bit quasi index [2021-07-20 12:00:38.727] [stderrLog] [info] Loading Suffix Array [2021-07-20 12:00:38.768] [stderrLog] [info] Loading Transcript Info [2021-07-20 12:00:38.779] [stderrLog] [info] Loading Rank-Select Bit Array [2021-07-20 12:00:38.782] [stderrLog] [info] There were 42,425 set bits in the bit array [2021-07-20 12:00:38.784] [stderrLog] [info] Computing transcript lengths [2021-07-20 12:00:38.784] [stderrLog] [info] Waiting to finish loading hash [2021-07-20 12:00:39.469] [stderrLog] [info] Done loading index [2021-07-20 12:00:39.469] [jointLog] [info] done [2021-07-20 12:00:39.469] [jointLog] [info] Index contained 42,425 targets  processed 500,000 fragments hits: 140,772, hits per frag: 0.309079 processed 1,000,000 fragments hits: 282,475, hits per frag: 0.297962 processed 1,500,000 fragments hits: 423,009, hits per frag: 0.320387 processed 2,000,002 fragments hits: 564,018, hits per frag: 0.290874 processed 2,500,000 fragments hits: 705,779, hits per frag: 0.286659 processed 3,000,001 fragments hits: 847,250, hits per frag: 0.300397 processed 3,500,001 fragments hits: 988,351, hits per frag: 0.284144 processed 4,000,000 fragments hits: 1,128,778, hits per frag: 0.282673 processed 4,500,000 fragments hits: 1,269,833, hits per frag: 0.292555 processed 5,000,001 fragments hits: 1,410,751, hits per frag: 0.285815 processed 5,500,000 fragments hits: 1,551,443, hits per frag: 0.287691 processed 6,000,000 fragments hits: 1,692,199, hits per frag: 0.287571 processed 6,500,000 fragments hits: 1,832,408, hits per frag: 0.283632 processed 7,000,000 fragments hits: 1,973,891, hits per frag: 0.284827 processed 7,500,000 fragments hits: 2,114,575, hits per frag: 0.282995 processed 8,000,000 fragments hits: 2,255,922, hits per frag: 0.282266 processed 8,500,000 fragments hits: 2,396,001, hits per frag: 0.283745 processed 9,000,001 fragments hits: 2,535,547, hits per frag: 0.289272 processed 9,500,000 fragments hits: 2,675,444, hits per frag: 0.283721 processed 10,000,000 fragments hits: 2,815,879, hits per frag: 0.287077 processed 10,500,000 fragments hits: 2,956,072, hits per frag: 0.283972 processed 11,000,000 fragments hits: 3,096,359, hits per frag: 0.285423 processed 11,500,000 fragments hits: 3,236,299, hits per frag: 0.283091 processed 12,000,000 fragments hits: 3,377,100, hits per frag: 0.283676 processed 12,500,001 fragments hits: 3,517,697, hits per frag: 0.2831 processed 13,000,000 fragments hits: 3,659,045, hits per frag: 0.289227 processed 13,500,001 fragments hits: 3,799,172, hits per frag: 0.283711 processed 14,000,000 fragments hits: 3,940,023, hits per frag: 0.282417 processed 14,500,000 fragments hits: 4,080,778, hits per frag: 0.282388 processed 15,000,002 fragments hits: 4,221,174, hits per frag: 0.282171 processed 15,500,000 fragments hits: 4,362,188, hits per frag: 0.281621 processed 16,000,000 fragments hits: 4,502,917, hits per frag: 0.284723 processed 16,500,001 fragments hits: 4,642,744, hits per frag: 0.283247 processed 17,000,000 fragments hits: 4,782,428, hits per frag: 0.282382 processed 17,500,001 fragments hits: 4,922,755, hits per frag: 0.282447 processed 18,000,000 fragments hits: 5,063,758, hits per frag: 0.282292 processed 18,500,001 fragments hits: 5,204,632, hits per frag: 0.28484 processed 19,000,000 fragments hits: 5,345,131, hits per frag: 0.282554 processed 19,500,000 fragments hits: 5,485,626, hits per frag: 0.282568 processed 20,000,000 fragments hits: 5,627,351, hits per frag: 0.281723 processed 20,500,000 fragments hits: 5,767,246, hits per frag: 0.282238 processed 21,000,000 fragments hits: 5,908,187, hits per frag: 0.28215 processed 21,500,000 fragments hits: 6,048,294, hits per frag: 0.283571 processed 22,000,000 fragments hits: 6,189,008, hits per frag: 0.28249 processed 22,500,001 fragments hits: 6,329,510, hits per frag: 0.282998 processed 23,000,000 fragments hits: 6,470,597, hits per frag: 0.282468 processed 23,500,000 fragments hits: 6,610,019, hits per frag: 0.282015[2021-07-20 12:01:42.992] [jointLog] [info] Thread saw mini-batch with a maximum of 8.72% zero probability fragments [2021-07-20 12:01:42.992] [jointLog] [info] Thread saw mini-batch with a maximum of 8.78% zero probability fragments [2021-07-20 12:01:42.992] [jointLog] [info] Thread saw mini-batch with a maximum of 8.50% zero probability fragments [2021-07-20 12:01:42.992] [jointLog] [info] Thread saw mini-batch with a maximum of 8.92% zero probability fragments [2021-07-20 12:01:42.992] [jointLog] [info] Thread saw mini-batch with a maximum of 8.82% zero probability fragments [2021-07-20 12:01:42.992] [jointLog] [info] Thread saw mini-batch with a maximum of 8.52% zero probability fragments [2021-07-20 12:01:42.992] [jointLog] [info] Thread saw mini-batch with a maximum of 8.78% zero probability fragments [2021-07-20 12:01:42.992] [jointLog] [info] Thread saw mini-batch with a maximum of 8.76% zero probability fragments [2021-07-20 12:01:42.993] [jointLog] [info] Thread saw mini-batch with a maximum of 9.10% zero probability fragments [2021-07-20 12:01:42.993] [jointLog] [info] Thread saw mini-batch with a maximum of 8.74% zero probability fragments [2021-07-20 12:01:42.993] [jointLog] [info] Thread saw mini-batch with a maximum of 9.00% zero probability fragments [2021-07-20 12:01:43.001] [jointLog] [info] Thread saw mini-batch with a maximum of 9.16% zero probability fragments [2021-07-20 12:01:43.009] [jointLog] [info] Thread saw mini-batch with a maximum of 8.88% zero probability fragments [2021-07-20 12:01:43.022] [jointLog] [info] Thread saw mini-batch with a maximum of 8.62% zero probability fragments [2021-07-20 12:01:43.026] [jointLog] [info] Thread saw mini-batch with a maximum of 8.92% zero probability fragments [2021-07-20 12:01:43.053] [jointLog] [info] Thread saw mini-batch with a maximum of 8.86% zero probability fragments [2021-07-20 12:01:43.058] [jointLog] [info] Thread saw mini-batch with a maximum of 8.64% zero probability fragments [2021-07-20 12:01:43.060] [jointLog] [info] Thread saw mini-batch with a maximum of 8.74% zero probability fragments [2021-07-20 12:01:43.077] [jointLog] [info] Thread saw mini-batch with a maximum of 8.92% zero probability fragments [2021-07-20 12:01:43.086] [jointLog] [info] Thread saw mini-batch with a maximum of 8.72% zero probability fragments [2021-07-20 12:01:43.092] [jointLog] [info] Thread saw mini-batch with a maximum of 8.84% zero probability fragments [2021-07-20 12:01:43.102] [jointLog] [info] Thread saw mini-batch with a maximum of 8.82% zero probability fragments [2021-07-20 12:01:43.111] [jointLog] [info] Thread saw mini-batch with a maximum of 8.76% zero probability fragments [2021-07-20 12:01:43.317] [jointLog] [info] Computed 42,417 rich equivalence classes for further processing [2021-07-20 12:01:43.317] [jointLog] [info] Counted 2,970,177 total reads in the equivalence classes [2021-07-20 12:01:43.336] [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. [2021-07-20 12:01:43.339] [jointLog] [warning] Only 2970177 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2021-07-20 12:01:43.339] [jointLog] [info] Mapping rate = 12.4461% [2021-07-20 12:01:43.339] [jointLog] [info] finished quantifyLibrary() [2021-07-20 12:01:43.339] [jointLog] [info] Starting optimizer [2021-07-20 12:01:43.378] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2021-07-20 12:01:43.380] [jointLog] [info] iteration = 0 | max rel diff. = 187.582 [2021-07-20 12:01:43.513] [jointLog] [info] iteration = 100 | max rel diff. = 1.04324 [2021-07-20 12:01:43.639] [jointLog] [info] iteration = 200 | max rel diff. = 0.0226803 [2021-07-20 12:01:43.670] [jointLog] [info] iteration = 225 | max rel diff. = 0.00765156 [2021-07-20 12:01:43.672] [jointLog] [info] Finished optimizer [2021-07-20 12:01:43.672] [jointLog] [info] writing output CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_female_K5_01/quant.sf /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.gene_trans_map > non-bleached_female_K5_01/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P10-TAGCTT-READ1-Sequences.txt.gz_val_1.fq.gz -2 /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_female_K5_02 -p 23 ### salmon (mapping-based) v0.12.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P10-TAGCTT-READ1-Sequences.txt.gz_val_1.fq.gz } ### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P10-TAGCTT-READ2-Sequences.txt.gz_val_2.fq.gz } ### [ output ] => { non-bleached_female_K5_02 } ### [ threads ] => { 23 } Logs will be written to non-bleached_female_K5_02/logs [2021-07-20 12:01:45.097] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2021-07-20 12:01:45.097] [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. [2021-07-20 12:01:45.097] [jointLog] [info] parsing read library format [2021-07-20 12:01:45.097] [jointLog] [info] There is 1 library. [2021-07-20 12:01:45.154] [jointLog] [info] Loading Quasi index [2021-07-20 12:01:45.155] [jointLog] [info] Loading 32-bit quasi index [2021-07-20 12:01:45.155] [stderrLog] [info] Loading Suffix Array [2021-07-20 12:01:45.200] [stderrLog] [info] Loading Transcript Info [2021-07-20 12:01:45.214] [stderrLog] [info] Loading Rank-Select Bit Array [2021-07-20 12:01:45.217] [stderrLog] [info] There were 42,425 set bits in the bit array [2021-07-20 12:01:45.219] [stderrLog] [info] Computing transcript lengths [2021-07-20 12:01:45.219] [stderrLog] [info] Waiting to finish loading hash [2021-07-20 12:01:45.880] [stderrLog] [info] Done loading index [2021-07-20 12:01:45.880] [jointLog] [info] done [2021-07-20 12:01:45.880] [jointLog] [info] Index contained 42,425 targets  processed 500,000 fragments hits: 122,162, hits per frag: 0.263211 processed 1,000,001 fragments hits: 244,923, hits per frag: 0.277964 processed 1,500,000 fragments hits: 367,542, hits per frag: 0.256898 processed 2,000,000 fragments hits: 489,124, hits per frag: 0.250522 processed 2,500,000 fragments hits: 611,874, hits per frag: 0.245936 processed 3,000,000 fragments hits: 733,659, hits per frag: 0.251958 processed 3,500,000 fragments hits: 856,051, hits per frag: 0.247501 processed 4,000,000 fragments hits: 978,164, hits per frag: 0.250907 processed 4,500,000 fragments hits: 1,100,813, hits per frag: 0.248658 processed 5,000,000 fragments hits: 1,223,825, hits per frag: 0.253405 processed 5,500,000 fragments hits: 1,347,307, hits per frag: 0.25202 processed 6,000,000 fragments hits: 1,470,495, hits per frag: 0.248397 processed 6,500,001 fragments hits: 1,593,204, hits per frag: 0.246765 processed 7,000,000 fragments hits: 1,715,954, hits per frag: 0.251112 processed 7,500,001 fragments hits: 1,839,131, hits per frag: 0.247565 processed 8,000,000 fragments hits: 1,961,832, hits per frag: 0.248482 processed 8,500,000 fragments hits: 2,084,368, hits per frag: 0.245783 processed 9,000,000 fragments hits: 2,207,072, hits per frag: 0.247086 processed 9,500,000 fragments hits: 2,329,427, hits per frag: 0.246818 processed 10,000,001 fragments hits: 2,451,612, hits per frag: 0.245956 processed 10,500,000 fragments hits: 2,573,495, hits per frag: 0.248148 processed 11,000,002 fragments hits: 2,693,795, hits per frag: 0.245842 processed 11,500,000 fragments hits: 2,814,935, hits per frag: 0.24649 processed 12,000,000 fragments hits: 2,935,981, hits per frag: 0.245465 processed 12,500,001 fragments hits: 3,057,536, hits per frag: 0.247188 processed 13,000,001 fragments hits: 3,178,688, hits per frag: 0.245127 processed 13,500,001 fragments hits: 3,300,512, hits per frag: 0.245588 processed 14,000,000 fragments hits: 3,420,963, hits per frag: 0.2465 processed 14,500,000 fragments hits: 3,543,026, hits per frag: 0.247668 processed 15,000,000 fragments hits: 3,664,610, hits per frag: 0.244675 processed 15,500,000 fragments hits: 3,786,364, hits per frag: 0.245196 processed 16,000,001 fragments hits: 3,908,203, hits per frag: 0.244528 processed 16,500,000 fragments hits: 4,031,073, hits per frag: 0.246741 processed 17,000,001 fragments hits: 4,154,229, hits per frag: 0.246421 processed 17,500,000 fragments hits: 4,276,791, hits per frag: 0.245341 processed 18,000,000 fragments hits: 4,399,299, hits per frag: 0.247001 processed 18,500,000 fragments hits: 4,522,028, hits per frag: 0.246589 processed 19,000,000 fragments hits: 4,644,797, hits per frag: 0.246142 processed 19,500,000 fragments hits: 4,767,142, hits per frag: 0.246381 processed 20,000,000 fragments hits: 4,889,674, hits per frag: 0.244711 processed 20,500,001 fragments hits: 5,011,961, hits per frag: 0.244614 processed 21,000,000 fragments hits: 5,135,631, hits per frag: 0.244956 processed 21,500,000 fragments hits: 5,259,750, hits per frag: 0.245458 processed 22,500,002 fragments hits: 5,504,690, hits per frag: 0.24526 processed 23,000,000 fragments hits: 5,627,015, hits per frag: 0.244987 processed 23,500,001 fragments hits: 5,749,686, hits per frag: 0.245096 processed 24,000,000 fragments hits: 5,872,969, hits per frag: 0.245367 processed 24,500,000 fragments hits: 5,996,813, hits per frag: 0.246451 processed 25,000,000 fragments hits: 6,119,891, hits per frag: 0.24554 processed 25,500,000 fragments hits: 6,242,030, hits per frag: 0.246752 processed 26,000,000 fragments hits: 6,363,694, hits per frag: 0.245277 processed 26,500,000 fragments hits: 6,484,145, hits per frag: 0.247707 processed 27,000,001 fragments hits: 6,605,963, hits per frag: 0.245349 processed 27,500,001 fragments hits: 6,727,956, hits per frag: 0.245518 processed 28,000,001 fragments hits: 6,849,955, hits per frag: 0.245179 processed 28,500,000 fragments hits: 6,971,793, hits per frag: 0.245728 processed 29,000,000 fragments hits: 7,093,161, hits per frag: 0.244801 processed 29,500,000 fragments hits: 7,215,291, hits per frag: 0.245107 processed 30,000,001 fragments hits: 7,337,156, hits per frag: 0.245895 processed 30,500,000 fragments hits: 7,459,687, hits per frag: 0.244957 processed 31,000,001 fragments hits: 7,581,702, hits per frag: 0.244759 processed 31,500,000 fragments hits: 7,703,442, hits per frag: 0.245674 processed 32,000,000 fragments hits: 7,824,352, hits per frag: 0.244749 processed 32,500,000 fragments hits: 7,946,029, hits per frag: 0.244899 processed 33,000,000 fragments hits: 8,069,406, hits per frag: 0.245579[2021-07-20 12:03:11.372] [jointLog] [info] Thread saw mini-batch with a maximum of 1.40% zero probability fragments [2021-07-20 12:03:11.372] [jointLog] [info] Thread saw mini-batch with a maximum of 1.54% zero probability fragments [2021-07-20 12:03:11.372] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:03:11.372] [jointLog] [info] Thread saw mini-batch with a maximum of 1.40% zero probability fragments [2021-07-20 12:03:11.372] [jointLog] [info] Thread saw mini-batch with a maximum of 1.42% zero probability fragments [2021-07-20 12:03:11.372] [jointLog] [info] Thread saw mini-batch with a maximum of 1.38% zero probability fragments [2021-07-20 12:03:11.372] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 12:03:11.372] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 12:03:11.374] [jointLog] [info] Thread saw mini-batch with a maximum of 1.32% zero probability fragments [2021-07-20 12:03:11.376] [jointLog] [info] Thread saw mini-batch with a maximum of 1.42% zero probability fragments [2021-07-20 12:03:11.376] [jointLog] [info] Thread saw mini-batch with a maximum of 1.46% zero probability fragments [2021-07-20 12:03:11.384] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:03:11.402] [jointLog] [info] Thread saw mini-batch with a maximum of 1.44% zero probability fragments [2021-07-20 12:03:11.408] [jointLog] [info] Thread saw mini-batch with a maximum of 1.46% zero probability fragments [2021-07-20 12:03:11.417] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 12:03:11.431] [jointLog] [info] Thread saw mini-batch with a maximum of 1.60% zero probability fragments [2021-07-20 12:03:11.434] [jointLog] [info] Thread saw mini-batch with a maximum of 1.54% zero probability fragments [2021-07-20 12:03:11.442] [jointLog] [info] Thread saw mini-batch with a maximum of 1.42% zero probability fragments [2021-07-20 12:03:11.470] [jointLog] [info] Thread saw mini-batch with a maximum of 1.40% zero probability fragments [2021-07-20 12:03:11.472] [jointLog] [info] Thread saw mini-batch with a maximum of 1.36% zero probability fragments [2021-07-20 12:03:11.477] [jointLog] [info] Thread saw mini-batch with a maximum of 1.36% zero probability fragments [2021-07-20 12:03:11.486] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:03:11.494] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 12:03:11.654] [jointLog] [info] Computed 37,674 rich equivalence classes for further processing [2021-07-20 12:03:11.654] [jointLog] [info] Counted 5,437,497 total reads in the equivalence classes [2021-07-20 12:03:11.671] [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. [2021-07-20 12:03:11.671] [jointLog] [info] Mapping rate = 16.4485% [2021-07-20 12:03:11.671] [jointLog] [info] finished quantifyLibrary() [2021-07-20 12:03:11.671] [jointLog] [info] Starting optimizer [2021-07-20 12:03:11.693] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2021-07-20 12:03:11.695] [jointLog] [info] iteration = 0 | max rel diff. = 171.119 [2021-07-20 12:03:11.826] [jointLog] [info] iteration = 100 | max rel diff. = 15.0486 [2021-07-20 12:03:11.953] [jointLog] [info] iteration = 200 | max rel diff. = 0.0167249 [2021-07-20 12:03:12.084] [jointLog] [info] iteration = 300 | max rel diff. = 0.0442374 [2021-07-20 12:03:12.211] [jointLog] [info] iteration = 400 | max rel diff. = 0.0317334 [2021-07-20 12:03:12.328] [jointLog] [info] iteration = 493 | max rel diff. = 0.0079792 [2021-07-20 12:03:12.329] [jointLog] [info] Finished optimizer [2021-07-20 12:03:12.329] [jointLog] [info] writing output CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_female_K5_02/quant.sf /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.gene_trans_map > non-bleached_female_K5_02/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx -l ISR -1 /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P15-GTTTCG-READ1-Sequences.txt.gz_val_1.fq.gz -2 /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_female_K5_03 -p 23 ### salmon (mapping-based) v0.12.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P15-GTTTCG-READ1-Sequences.txt.gz_val_1.fq.gz } ### [ mates2 ] => { /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P15-GTTTCG-READ2-Sequences.txt.gz_val_2.fq.gz } ### [ output ] => { non-bleached_female_K5_03 } ### [ threads ] => { 23 } Logs will be written to non-bleached_female_K5_03/logs [2021-07-20 12:03:13.529] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2021-07-20 12:03:13.529] [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. [2021-07-20 12:03:13.529] [jointLog] [info] parsing read library format [2021-07-20 12:03:13.529] [jointLog] [info] There is 1 library. [2021-07-20 12:03:13.585] [jointLog] [info] Loading Quasi index [2021-07-20 12:03:13.585] [jointLog] [info] Loading 32-bit quasi index [2021-07-20 12:03:13.586] [stderrLog] [info] Loading Suffix Array [2021-07-20 12:03:13.626] [stderrLog] [info] Loading Transcript Info [2021-07-20 12:03:13.637] [stderrLog] [info] Loading Rank-Select Bit Array [2021-07-20 12:03:13.640] [stderrLog] [info] There were 42,425 set bits in the bit array [2021-07-20 12:03:13.642] [stderrLog] [info] Computing transcript lengths [2021-07-20 12:03:13.642] [stderrLog] [info] Waiting to finish loading hash [2021-07-20 12:03:14.396] [jointLog] [info] done [2021-07-20 12:03:14.396] [jointLog] [info] Index contained 42,425 targets [2021-07-20 12:03:14.396] [stderrLog] [info] Done loading index  processed 500,000 fragments hits: 129,089, hits per frag: 0.283472 processed 1,000,000 fragments hits: 259,284, hits per frag: 0.295193 processed 1,500,000 fragments hits: 388,178, hits per frag: 0.268114 processed 2,000,000 fragments hits: 516,197, hits per frag: 0.288325 processed 2,500,001 fragments hits: 645,356, hits per frag: 0.266326 processed 3,000,000 fragments hits: 774,802, hits per frag: 0.261614 processed 3,500,000 fragments hits: 904,238, hits per frag: 0.260954 processed 4,000,000 fragments hits: 1,032,619, hits per frag: 0.260582 processed 4,500,002 fragments hits: 1,162,311, hits per frag: 0.263092 processed 5,000,001 fragments hits: 1,291,054, hits per frag: 0.262004 processed 5,500,000 fragments hits: 1,419,389, hits per frag: 0.258943 processed 6,000,000 fragments hits: 1,548,458, hits per frag: 0.261141 processed 6,500,000 fragments hits: 1,676,852, hits per frag: 0.261804 processed 7,000,002 fragments hits: 1,806,845, hits per frag: 0.261144 processed 7,500,000 fragments hits: 1,935,727, hits per frag: 0.260886 processed 8,000,000 fragments hits: 2,065,231, hits per frag: 0.264042 processed 8,500,000 fragments hits: 2,194,538, hits per frag: 0.259189 processed 9,000,000 fragments hits: 2,323,385, hits per frag: 0.259701 processed 9,500,001 fragments hits: 2,451,978, hits per frag: 0.259328 processed 10,000,000 fragments hits: 2,580,871, hits per frag: 0.2596 processed 10,500,002 fragments hits: 2,710,121, hits per frag: 0.258541 processed 11,000,000 fragments hits: 2,838,831, hits per frag: 0.258922 processed 11,500,000 fragments hits: 2,966,878, hits per frag: 0.25812 processed 12,000,000 fragments hits: 3,095,690, hits per frag: 0.259634 processed 12,500,000 fragments hits: 3,223,020, hits per frag: 0.259004 processed 13,000,000 fragments hits: 3,351,611, hits per frag: 0.258552 processed 13,500,000 fragments hits: 3,479,387, hits per frag: 0.259925 processed 14,000,000 fragments hits: 3,607,690, hits per frag: 0.259457 processed 14,500,001 fragments hits: 3,736,926, hits per frag: 0.258663 processed 15,000,001 fragments hits: 3,865,413, hits per frag: 0.259012 processed 15,500,000 fragments hits: 3,994,913, hits per frag: 0.259994 processed 16,000,000 fragments hits: 4,123,249, hits per frag: 0.259651 processed 16,500,001 fragments hits: 4,252,454, hits per frag: 0.258483 processed 17,000,000 fragments hits: 4,381,669, hits per frag: 0.261296 processed 17,500,000 fragments hits: 4,510,462, hits per frag: 0.258209 processed 18,000,000 fragments hits: 4,640,041, hits per frag: 0.25843 processed 18,500,000 fragments hits: 4,768,920, hits per frag: 0.258582 processed 19,000,001 fragments hits: 4,898,368, hits per frag: 0.259039 processed 19,500,000 fragments hits: 5,028,546, hits per frag: 0.258772 processed 20,000,000 fragments hits: 5,157,770, hits per frag: 0.26032 processed 20,500,000 fragments hits: 5,287,241, hits per frag: 0.258495 processed 21,000,000 fragments hits: 5,416,961, hits per frag: 0.258687 processed 21,500,000 fragments hits: 5,546,335, hits per frag: 0.258628 processed 22,000,001 fragments hits: 5,674,964, hits per frag: 0.258253 processed 22,500,000 fragments hits: 5,803,946, hits per frag: 0.259073 processed 23,000,002 fragments hits: 5,933,678, hits per frag: 0.258356 processed 23,500,000 fragments hits: 6,062,645, hits per frag: 0.26044 processed 24,000,000 fragments hits: 6,190,702, hits per frag: 0.258477 processed 24,500,001 fragments hits: 6,319,270, hits per frag: 0.258574 processed 25,000,000 fragments hits: 6,448,799, hits per frag: 0.258167 processed 25,500,000 fragments hits: 6,578,218, hits per frag: 0.258821 processed 26,000,001 fragments hits: 6,708,183, hits per frag: 0.258525 processed 26,500,000 fragments hits: 6,837,505, hits per frag: 0.259816 processed 27,000,000 fragments hits: 6,965,706, hits per frag: 0.259321 processed 27,500,000 fragments hits: 7,095,030, hits per frag: 0.259136 processed 28,000,000 fragments hits: 7,223,187, hits per frag: 0.258363 processed 28,500,000 fragments hits: 7,352,341, hits per frag: 0.258303 processed 29,000,000 fragments hits: 7,481,724, hits per frag: 0.260395 processed 29,500,000 fragments hits: 7,610,628, hits per frag: 0.258452 processed 30,000,000 fragments hits: 7,739,641, hits per frag: 0.258628 processed 30,500,000 fragments hits: 7,868,941, hits per frag: 0.258763 processed 31,000,000 fragments hits: 7,997,349, hits per frag: 0.25859 processed 31,500,001 fragments hits: 8,125,836, hits per frag: 0.259799 processed 32,000,000 fragments hits: 8,255,340, hits per frag: 0.258757 processed 32,500,000 fragments hits: 8,385,168, hits per frag: 0.258815 processed 33,000,000 fragments hits: 8,515,167, hits per frag: 0.258451 processed 33,500,000 fragments hits: 8,644,014, hits per frag: 0.258298 processed 34,000,000 fragments hits: 8,772,654, hits per frag: 0.258661 processed 34,500,000 fragments hits: 8,902,204, hits per frag: 0.258635[2021-07-20 12:04:46.354] [jointLog] [info] Thread saw mini-batch with a maximum of 1.42% zero probability fragments [2021-07-20 12:04:46.354] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 12:04:46.354] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 12:04:46.354] [jointLog] [info] Thread saw mini-batch with a maximum of 1.38% zero probability fragments [2021-07-20 12:04:46.354] [jointLog] [info] Thread saw mini-batch with a maximum of 1.66% zero probability fragments [2021-07-20 12:04:46.354] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:04:46.354] [jointLog] [info] Thread saw mini-batch with a maximum of 1.42% zero probability fragments [2021-07-20 12:04:46.354] [jointLog] [info] Thread saw mini-batch with a maximum of 1.40% zero probability fragments [2021-07-20 12:04:46.354] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:04:46.354] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 12:04:46.358] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 12:04:46.362] [jointLog] [info] Thread saw mini-batch with a maximum of 1.40% zero probability fragments [2021-07-20 12:04:46.369] [jointLog] [info] Thread saw mini-batch with a maximum of 1.54% zero probability fragments [2021-07-20 12:04:46.394] [jointLog] [info] Thread saw mini-batch with a maximum of 1.46% zero probability fragments [2021-07-20 12:04:46.404] [jointLog] [info] Thread saw mini-batch with a maximum of 1.46% zero probability fragments [2021-07-20 12:04:46.423] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:04:46.430] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 12:04:46.435] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 12:04:46.458] [jointLog] [info] Thread saw mini-batch with a maximum of 1.44% zero probability fragments [2021-07-20 12:04:46.460] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 12:04:46.469] [jointLog] [info] Thread saw mini-batch with a maximum of 1.44% zero probability fragments [2021-07-20 12:04:46.474] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 12:04:46.495] [jointLog] [info] Thread saw mini-batch with a maximum of 1.44% zero probability fragments [2021-07-20 12:04:46.674] [jointLog] [info] Computed 36,387 rich equivalence classes for further processing [2021-07-20 12:04:46.674] [jointLog] [info] Counted 6,134,418 total reads in the equivalence classes [2021-07-20 12:04:46.692] [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. [2021-07-20 12:04:46.692] [jointLog] [info] Mapping rate = 17.7643% [2021-07-20 12:04:46.692] [jointLog] [info] finished quantifyLibrary() [2021-07-20 12:04:46.692] [jointLog] [info] Starting optimizer [2021-07-20 12:04:46.724] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2021-07-20 12:04:46.726] [jointLog] [info] iteration = 0 | max rel diff. = 234.238 [2021-07-20 12:04:46.855] [jointLog] [info] iteration = 100 | max rel diff. = 0.166962 [2021-07-20 12:04:46.981] [jointLog] [info] iteration = 200 | max rel diff. = 0.0594658 [2021-07-20 12:04:47.075] [jointLog] [info] iteration = 276 | max rel diff. = 0.0035865 [2021-07-20 12:04:47.076] [jointLog] [info] Finished optimizer [2021-07-20 12:04:47.076] [jointLog] [info] writing output CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_female_K5_03/quant.sf /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.gene_trans_map > non-bleached_female_K5_03/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.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 non-bleached_female_44_01 -p 23 ### salmon (mapping-based) v0.12.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.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 ] => { non-bleached_female_44_01 } ### [ threads ] => { 23 } Logs will be written to non-bleached_female_44_01/logs [2021-07-20 12:04:48.441] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2021-07-20 12:04:48.441] [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. [2021-07-20 12:04:48.441] [jointLog] [info] parsing read library format [2021-07-20 12:04:48.441] [jointLog] [info] There is 1 library. [2021-07-20 12:04:48.499] [jointLog] [info] Loading Quasi index [2021-07-20 12:04:48.499] [jointLog] [info] Loading 32-bit quasi index [2021-07-20 12:04:48.499] [stderrLog] [info] Loading Suffix Array [2021-07-20 12:04:48.543] [stderrLog] [info] Loading Transcript Info [2021-07-20 12:04:48.554] [stderrLog] [info] Loading Rank-Select Bit Array [2021-07-20 12:04:48.556] [stderrLog] [info] There were 42,425 set bits in the bit array [2021-07-20 12:04:48.559] [stderrLog] [info] Computing transcript lengths [2021-07-20 12:04:48.559] [stderrLog] [info] Waiting to finish loading hash [2021-07-20 12:04:49.250] [stderrLog] [info] Done loading index [2021-07-20 12:04:49.250] [jointLog] [info] done [2021-07-20 12:04:49.250] [jointLog] [info] Index contained 42,425 targets  processed 500,000 fragments hits: 132,972, hits per frag: 0.379442 processed 1,000,001 fragments hits: 265,862, hits per frag: 0.283177 processed 1,500,000 fragments hits: 398,103, hits per frag: 0.268452 processed 2,000,000 fragments hits: 530,632, hits per frag: 0.268823 processed 2,500,000 fragments hits: 662,739, hits per frag: 0.272541 processed 3,000,000 fragments hits: 795,250, hits per frag: 0.279754 processed 3,500,000 fragments hits: 927,656, hits per frag: 0.266896 processed 4,000,000 fragments hits: 1,058,840, hits per frag: 0.271656 processed 4,500,000 fragments hits: 1,190,953, hits per frag: 0.277215 processed 5,000,001 fragments hits: 1,322,155, hits per frag: 0.265588 processed 5,500,000 fragments hits: 1,453,900, hits per frag: 0.265314 processed 6,000,000 fragments hits: 1,586,511, hits per frag: 0.269693 processed 6,500,001 fragments hits: 1,718,386, hits per frag: 0.267161 processed 7,000,000 fragments hits: 1,850,990, hits per frag: 0.267509 processed 7,500,000 fragments hits: 1,982,614, hits per frag: 0.266378 processed 8,000,000 fragments hits: 2,114,211, hits per frag: 0.265496 processed 8,500,000 fragments hits: 2,245,525, hits per frag: 0.265502 processed 9,000,000 fragments hits: 2,377,322, hits per frag: 0.265196 processed 9,500,000 fragments hits: 2,509,638, hits per frag: 0.26515 processed 10,000,000 fragments hits: 2,642,139, hits per frag: 0.265769 processed 10,500,000 fragments hits: 2,774,438, hits per frag: 0.267522 processed 11,000,001 fragments hits: 2,907,550, hits per frag: 0.265342 processed 11,500,000 fragments hits: 3,039,246, hits per frag: 0.26634 processed 12,000,000 fragments hits: 3,171,895, hits per frag: 0.265708 processed 12,500,000 fragments hits: 3,302,682, hits per frag: 0.266147 processed 13,000,001 fragments hits: 3,434,182, hits per frag: 0.26509 processed 13,500,000 fragments hits: 3,566,435, hits per frag: 0.266788 processed 14,000,000 fragments hits: 3,697,948, hits per frag: 0.265117 processed 14,500,000 fragments hits: 3,830,196, hits per frag: 0.265043 processed 15,000,000 fragments hits: 3,962,436, hits per frag: 0.265226 processed 15,500,001 fragments hits: 4,095,125, hits per frag: 0.265851 processed 16,000,000 fragments hits: 4,226,728, hits per frag: 0.264799 processed 16,500,000 fragments hits: 4,359,064, hits per frag: 0.266623 processed 17,000,000 fragments hits: 4,491,395, hits per frag: 0.265273 processed 17,500,000 fragments hits: 4,622,875, hits per frag: 0.264892 processed 18,000,000 fragments hits: 4,754,615, hits per frag: 0.265289 processed 18,500,000 fragments hits: 4,886,560, hits per frag: 0.264701 processed 19,000,001 fragments hits: 5,019,634, hits per frag: 0.264656 processed 19,000,042 fragments hits: 5,019,644, hits per frag: 0.265492 processed 19,500,000 fragments hits: 5,150,964, hits per frag: 0.265173 processed 20,000,000 fragments hits: 5,282,686, hits per frag: 0.264569 processed 20,500,001 fragments hits: 5,414,217, hits per frag: 0.266047 processed 21,000,000 fragments hits: 5,546,215, hits per frag: 0.264874 processed 21,500,000 fragments hits: 5,678,344, hits per frag: 0.265224 processed 22,000,000 fragments hits: 5,810,531, hits per frag: 0.264909[2021-07-20 12:05:50.195] [jointLog] [info] Thread saw mini-batch with a maximum of 2.28% zero probability fragments [2021-07-20 12:05:50.195] [jointLog] [info] Thread saw mini-batch with a maximum of 2.28% zero probability fragments [2021-07-20 12:05:50.195] [jointLog] [info] Thread saw mini-batch with a maximum of 2.26% zero probability fragments [2021-07-20 12:05:50.195] [jointLog] [info] Thread saw mini-batch with a maximum of 2.38% zero probability fragments [2021-07-20 12:05:50.195] [jointLog] [info] Thread saw mini-batch with a maximum of 2.28% zero probability fragments [2021-07-20 12:05:50.195] [jointLog] [info] Thread saw mini-batch with a maximum of 2.46% zero probability fragments [2021-07-20 12:05:50.195] [jointLog] [info] Thread saw mini-batch with a maximum of 2.24% zero probability fragments [2021-07-20 12:05:50.195] [jointLog] [info] Thread saw mini-batch with a maximum of 2.30% zero probability fragments [2021-07-20 12:05:50.195] [jointLog] [info] Thread saw mini-batch with a maximum of 2.20% zero probability fragments [2021-07-20 12:05:50.195] [jointLog] [info] Thread saw mini-batch with a maximum of 2.26% zero probability fragments [2021-07-20 12:05:50.195] [jointLog] [info] Thread saw mini-batch with a maximum of 2.30% zero probability fragments [2021-07-20 12:05:50.195] [jointLog] [info] Thread saw mini-batch with a maximum of 2.22% zero probability fragments [2021-07-20 12:05:50.204] [jointLog] [info] Thread saw mini-batch with a maximum of 2.22% zero probability fragments [2021-07-20 12:05:50.217] [jointLog] [info] Thread saw mini-batch with a maximum of 2.38% zero probability fragments [2021-07-20 12:05:50.230] [jointLog] [info] Thread saw mini-batch with a maximum of 2.42% zero probability fragments [2021-07-20 12:05:50.240] [jointLog] [info] Thread saw mini-batch with a maximum of 2.22% zero probability fragments [2021-07-20 12:05:50.252] [jointLog] [info] Thread saw mini-batch with a maximum of 2.26% zero probability fragments [2021-07-20 12:05:50.256] [jointLog] [info] Thread saw mini-batch with a maximum of 2.28% zero probability fragments [2021-07-20 12:05:50.278] [jointLog] [info] Thread saw mini-batch with a maximum of 2.38% zero probability fragments [2021-07-20 12:05:50.284] [jointLog] [info] Thread saw mini-batch with a maximum of 2.26% zero probability fragments [2021-07-20 12:05:50.299] [jointLog] [info] Thread saw mini-batch with a maximum of 2.36% zero probability fragments [2021-07-20 12:05:50.304] [jointLog] [info] Thread saw mini-batch with a maximum of 2.26% zero probability fragments [2021-07-20 12:05:50.314] [jointLog] [info] Thread saw mini-batch with a maximum of 2.28% zero probability fragments [2021-07-20 12:05:50.570] [jointLog] [info] Computed 40,916 rich equivalence classes for further processing [2021-07-20 12:05:50.570] [jointLog] [info] Counted 3,850,315 total reads in the equivalence classes [2021-07-20 12:05:50.588] [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. [2021-07-20 12:05:50.591] [jointLog] [warning] Only 3850315 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2021-07-20 12:05:50.591] [jointLog] [info] Mapping rate = 17.1149% [2021-07-20 12:05:50.591] [jointLog] [info] finished quantifyLibrary() [2021-07-20 12:05:50.591] [jointLog] [info] Starting optimizer [2021-07-20 12:05:50.640] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2021-07-20 12:05:50.642] [jointLog] [info] iteration = 0 | max rel diff. = 182.944 [2021-07-20 12:05:50.772] [jointLog] [info] iteration = 100 | max rel diff. = 0.34924 [2021-07-20 12:05:50.898] [jointLog] [info] iteration = 200 | max rel diff. = 0.0935445 [2021-07-20 12:05:51.025] [jointLog] [info] iteration = 300 | max rel diff. = 0.2391 [2021-07-20 12:05:51.145] [jointLog] [info] iteration = 396 | max rel diff. = 0.00222743 [2021-07-20 12:05:51.149] [jointLog] [info] Finished optimizer [2021-07-20 12:05:51.149] [jointLog] [info] writing output CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_female_44_01/quant.sf /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.gene_trans_map > non-bleached_female_44_01/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.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 non-bleached_female_44_02 -p 23 ### salmon (mapping-based) v0.12.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.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 ] => { non-bleached_female_44_02 } ### [ threads ] => { 23 } Logs will be written to non-bleached_female_44_02/logs [2021-07-20 12:05:52.368] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2021-07-20 12:05:52.368] [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. [2021-07-20 12:05:52.368] [jointLog] [info] parsing read library format [2021-07-20 12:05:52.368] [jointLog] [info] There is 1 library. [2021-07-20 12:05:52.426] [jointLog] [info] Loading Quasi index [2021-07-20 12:05:52.426] [jointLog] [info] Loading 32-bit quasi index [2021-07-20 12:05:52.426] [stderrLog] [info] Loading Suffix Array [2021-07-20 12:05:52.470] [stderrLog] [info] Loading Transcript Info [2021-07-20 12:05:52.482] [stderrLog] [info] Loading Rank-Select Bit Array [2021-07-20 12:05:52.485] [stderrLog] [info] There were 42,425 set bits in the bit array [2021-07-20 12:05:52.487] [stderrLog] [info] Computing transcript lengths [2021-07-20 12:05:52.487] [stderrLog] [info] Waiting to finish loading hash [2021-07-20 12:05:53.159] [stderrLog] [info] Done loading index [2021-07-20 12:05:53.159] [jointLog] [info] done [2021-07-20 12:05:53.159] [jointLog] [info] Index contained 42,425 targets  processed 500,003 fragments hits: 132,973, hits per frag: 0.288932 processed 1,000,000 fragments hits: 265,446, hits per frag: 0.288746 processed 1,500,000 fragments hits: 397,427, hits per frag: 0.28225 processed 2,000,000 fragments hits: 529,031, hits per frag: 0.26688 processed 2,500,000 fragments hits: 660,727, hits per frag: 0.272998 processed 3,000,000 fragments hits: 791,751, hits per frag: 0.26847 processed 3,500,000 fragments hits: 924,172, hits per frag: 0.267358 processed 4,000,000 fragments hits: 1,056,389, hits per frag: 0.272415 processed 4,500,000 fragments hits: 1,188,535, hits per frag: 0.267645 processed 5,000,001 fragments hits: 1,320,666, hits per frag: 0.264233 processed 5,500,000 fragments hits: 1,453,413, hits per frag: 0.271152 processed 6,000,000 fragments hits: 1,585,304, hits per frag: 0.270691 processed 6,500,000 fragments hits: 1,718,173, hits per frag: 0.268551 processed 7,000,000 fragments hits: 1,849,883, hits per frag: 0.266536 processed 7,500,000 fragments hits: 1,980,990, hits per frag: 0.26996 processed 8,000,000 fragments hits: 2,112,972, hits per frag: 0.266952 processed 8,500,002 fragments hits: 2,244,149, hits per frag: 0.26559 processed 9,000,000 fragments hits: 2,375,987, hits per frag: 0.265795 processed 9,500,000 fragments hits: 2,507,051, hits per frag: 0.264761 processed 10,000,000 fragments hits: 2,637,744, hits per frag: 0.264245 processed 10,500,000 fragments hits: 2,768,949, hits per frag: 0.26503 processed 11,000,001 fragments hits: 2,900,110, hits per frag: 0.266182 processed 11,500,000 fragments hits: 3,031,916, hits per frag: 0.265024 processed 12,000,001 fragments hits: 3,162,254, hits per frag: 0.265004 processed 12,500,000 fragments hits: 3,293,709, hits per frag: 0.267237 processed 13,000,002 fragments hits: 3,425,912, hits per frag: 0.264231 processed 13,500,001 fragments hits: 3,557,273, hits per frag: 0.263823 processed 14,000,000 fragments hits: 3,689,170, hits per frag: 0.264675 processed 14,500,001 fragments hits: 3,821,301, hits per frag: 0.263985 processed 15,000,001 fragments hits: 3,952,881, hits per frag: 0.264637 processed 15,500,000 fragments hits: 4,085,362, hits per frag: 0.264606 processed 16,000,000 fragments hits: 4,217,557, hits per frag: 0.264787 processed 16,500,000 fragments hits: 4,349,697, hits per frag: 0.265216 processed 16,500,023 fragments hits: 4,349,708, hits per frag: 0.264228 processed 17,000,000 fragments hits: 4,481,047, hits per frag: 0.264752 processed 17,500,001 fragments hits: 4,612,825, hits per frag: 0.264053 processed 18,000,000 fragments hits: 4,746,150, hits per frag: 0.267097 processed 18,500,000 fragments hits: 4,878,143, hits per frag: 0.264554 processed 19,000,000 fragments hits: 5,010,520, hits per frag: 0.264641 processed 19,500,001 fragments hits: 5,142,694, hits per frag: 0.264061 processed 20,000,000 fragments hits: 5,274,832, hits per frag: 0.265015 processed 20,500,000 fragments hits: 5,407,347, hits per frag: 0.264255 processed 21,000,000 fragments hits: 5,538,811, hits per frag: 0.265261 processed 21,500,001 fragments hits: 5,670,805, hits per frag: 0.264386 processed 22,000,000 fragments hits: 5,803,193, hits per frag: 0.263985 processed 22,500,000 fragments hits: 5,934,731, hits per frag: 0.264109 processed 23,000,000 fragments hits: 6,067,420, hits per frag: 0.265025 processed 23,500,000 fragments hits: 6,199,013, hits per frag: 0.264069 processed 24,000,000 fragments hits: 6,331,243, hits per frag: 0.264867 processed 24,500,001 fragments hits: 6,462,856, hits per frag: 0.264756 processed 25,000,001 fragments hits: 6,595,201, hits per frag: 0.265537 processed 25,500,000 fragments hits: 6,728,143, hits per frag: 0.264909 processed 26,000,000 fragments hits: 6,859,392, hits per frag: 0.264423[2021-07-20 12:07:00.556] [jointLog] [info] Thread saw mini-batch with a maximum of 4.26% zero probability fragments [2021-07-20 12:07:00.556] [jointLog] [info] Thread saw mini-batch with a maximum of 4.32% zero probability fragments [2021-07-20 12:07:00.556] [jointLog] [info] Thread saw mini-batch with a maximum of 4.04% zero probability fragments [2021-07-20 12:07:00.557] [jointLog] [info] Thread saw mini-batch with a maximum of 3.90% zero probability fragments [2021-07-20 12:07:00.557] [jointLog] [info] Thread saw mini-batch with a maximum of 4.08% zero probability fragments [2021-07-20 12:07:00.557] [jointLog] [info] Thread saw mini-batch with a maximum of 4.14% zero probability fragments [2021-07-20 12:07:00.557] [jointLog] [info] Thread saw mini-batch with a maximum of 4.18% zero probability fragments [2021-07-20 12:07:00.557] [jointLog] [info] Thread saw mini-batch with a maximum of 4.58% zero probability fragments [2021-07-20 12:07:00.557] [jointLog] [info] Thread saw mini-batch with a maximum of 3.98% zero probability fragments [2021-07-20 12:07:00.557] [jointLog] [info] Thread saw mini-batch with a maximum of 4.08% zero probability fragments [2021-07-20 12:07:00.560] [jointLog] [info] Thread saw mini-batch with a maximum of 4.46% zero probability fragments [2021-07-20 12:07:00.563] [jointLog] [info] Thread saw mini-batch with a maximum of 3.98% zero probability fragments [2021-07-20 12:07:00.564] [jointLog] [info] Thread saw mini-batch with a maximum of 4.22% zero probability fragments [2021-07-20 12:07:00.577] [jointLog] [info] Thread saw mini-batch with a maximum of 4.00% zero probability fragments [2021-07-20 12:07:00.602] [jointLog] [info] Thread saw mini-batch with a maximum of 4.16% zero probability fragments [2021-07-20 12:07:00.621] [jointLog] [info] Thread saw mini-batch with a maximum of 4.14% zero probability fragments [2021-07-20 12:07:00.622] [jointLog] [info] Thread saw mini-batch with a maximum of 4.06% zero probability fragments [2021-07-20 12:07:00.626] [jointLog] [info] Thread saw mini-batch with a maximum of 4.16% zero probability fragments [2021-07-20 12:07:00.638] [jointLog] [info] Thread saw mini-batch with a maximum of 4.08% zero probability fragments [2021-07-20 12:07:00.659] [jointLog] [info] Thread saw mini-batch with a maximum of 4.08% zero probability fragments [2021-07-20 12:07:00.664] [jointLog] [info] Thread saw mini-batch with a maximum of 4.26% zero probability fragments [2021-07-20 12:07:00.664] [jointLog] [info] Thread saw mini-batch with a maximum of 4.20% zero probability fragments [2021-07-20 12:07:00.691] [jointLog] [info] Thread saw mini-batch with a maximum of 4.16% zero probability fragments [2021-07-20 12:07:00.909] [jointLog] [info] Computed 44,074 rich equivalence classes for further processing [2021-07-20 12:07:00.909] [jointLog] [info] Counted 4,028,510 total reads in the equivalence classes [2021-07-20 12:07:00.924] [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. [2021-07-20 12:07:00.927] [jointLog] [warning] Only 4028510 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2021-07-20 12:07:00.927] [jointLog] [info] Mapping rate = 15.4404% [2021-07-20 12:07:00.927] [jointLog] [info] finished quantifyLibrary() [2021-07-20 12:07:00.927] [jointLog] [info] Starting optimizer [2021-07-20 12:07:00.950] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2021-07-20 12:07:00.952] [jointLog] [info] iteration = 0 | max rel diff. = 153.974 [2021-07-20 12:07:01.081] [jointLog] [info] iteration = 100 | max rel diff. = 0.151829 [2021-07-20 12:07:01.206] [jointLog] [info] iteration = 200 | max rel diff. = 0.0568259 [2021-07-20 12:07:01.272] [jointLog] [info] iteration = 254 | max rel diff. = 0.00476842 [2021-07-20 12:07:01.273] [jointLog] [info] Finished optimizer [2021-07-20 12:07:01.273] [jointLog] [info] writing output CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_female_44_02/quant.sf /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.gene_trans_map > non-bleached_female_44_02/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.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 non-bleached_female_44_03 -p 23 ### salmon (mapping-based) v0.12.0 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.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 ] => { non-bleached_female_44_03 } ### [ threads ] => { 23 } Logs will be written to non-bleached_female_44_03/logs [2021-07-20 12:07:02.785] [jointLog] [info] Fragment incompatibility prior below threshold. Incompatible fragments will be ignored. [2021-07-20 12:07:02.785] [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. [2021-07-20 12:07:02.785] [jointLog] [info] parsing read library format [2021-07-20 12:07:02.785] [jointLog] [info] There is 1 library. [2021-07-20 12:07:02.848] [stderrLog] [info] Loading Suffix Array [2021-07-20 12:07:02.848] [jointLog] [info] Loading Quasi index [2021-07-20 12:07:02.848] [jointLog] [info] Loading 32-bit quasi index [2021-07-20 12:07:02.893] [stderrLog] [info] Loading Transcript Info [2021-07-20 12:07:02.905] [stderrLog] [info] Loading Rank-Select Bit Array [2021-07-20 12:07:02.907] [stderrLog] [info] There were 42,425 set bits in the bit array [2021-07-20 12:07:02.910] [stderrLog] [info] Computing transcript lengths [2021-07-20 12:07:02.910] [stderrLog] [info] Waiting to finish loading hash [2021-07-20 12:07:03.664] [jointLog] [info] done [2021-07-20 12:07:03.664] [jointLog] [info] Index contained 42,425 targets [2021-07-20 12:07:03.663] [stderrLog] [info] Done loading index  processed 500,001 fragments hits: 128,398, hits per frag: 0.365813 processed 1,000,001 fragments hits: 256,096, hits per frag: 0.294203 processed 1,500,000 fragments hits: 384,419, hits per frag: 0.266189 processed 2,000,000 fragments hits: 511,406, hits per frag: 0.263246 processed 2,500,000 fragments hits: 637,662, hits per frag: 0.272134 processed 3,000,000 fragments hits: 765,348, hits per frag: 0.264421 processed 3,500,001 fragments hits: 892,917, hits per frag: 0.264721 processed 4,000,000 fragments hits: 1,020,155, hits per frag: 0.25679 processed 4,500,000 fragments hits: 1,147,292, hits per frag: 0.256233 processed 5,000,000 fragments hits: 1,273,870, hits per frag: 0.258527 processed 5,500,000 fragments hits: 1,401,186, hits per frag: 0.262971 processed 6,000,000 fragments hits: 1,527,591, hits per frag: 0.25706 processed 6,500,000 fragments hits: 1,655,459, hits per frag: 0.258981 processed 7,000,000 fragments hits: 1,781,769, hits per frag: 0.256611 processed 7,500,001 fragments hits: 1,908,793, hits per frag: 0.255272 processed 8,000,001 fragments hits: 2,035,801, hits per frag: 0.258045 processed 8,500,000 fragments hits: 2,161,863, hits per frag: 0.255616 processed 9,000,000 fragments hits: 2,287,945, hits per frag: 0.2556 processed 9,500,000 fragments hits: 2,414,465, hits per frag: 0.25568 processed 10,000,000 fragments hits: 2,541,138, hits per frag: 0.256221 processed 10,500,001 fragments hits: 2,666,988, hits per frag: 0.259982 processed 11,000,001 fragments hits: 2,793,580, hits per frag: 0.256249 processed 11,500,000 fragments hits: 2,920,269, hits per frag: 0.254143 processed 12,000,000 fragments hits: 3,047,090, hits per frag: 0.255108 processed 12,500,000 fragments hits: 3,173,775, hits per frag: 0.258621 processed 13,000,002 fragments hits: 3,301,140, hits per frag: 0.254866 processed 13,500,000 fragments hits: 3,428,775, hits per frag: 0.255032 processed 14,000,001 fragments hits: 3,556,949, hits per frag: 0.255883 processed 14,500,000 fragments hits: 3,684,182, hits per frag: 0.254238 processed 15,000,000 fragments hits: 3,811,605, hits per frag: 0.255111 processed 15,500,000 fragments hits: 3,938,338, hits per frag: 0.254821 processed 16,000,000 fragments hits: 4,065,367, hits per frag: 0.255454 processed 16,500,000 fragments hits: 4,191,991, hits per frag: 0.254975 processed 17,000,000 fragments hits: 4,319,832, hits per frag: 0.254614 processed 17,500,000 fragments hits: 4,448,386, hits per frag: 0.254346 processed 18,000,000 fragments hits: 4,576,526, hits per frag: 0.256015 processed 18,500,001 fragments hits: 4,704,169, hits per frag: 0.25556 processed 19,000,000 fragments hits: 4,832,036, hits per frag: 0.255128 processed 19,500,000 fragments hits: 4,958,606, hits per frag: 0.254902 processed 20,000,000 fragments hits: 5,085,757, hits per frag: 0.254939 processed 20,500,000 fragments hits: 5,212,770, hits per frag: 0.254813 processed 21,000,000 fragments hits: 5,340,166, hits per frag: 0.255301 processed 21,500,000 fragments hits: 5,467,013, hits per frag: 0.255088 processed 22,000,000 fragments hits: 5,594,562, hits per frag: 0.256439 processed 22,500,000 fragments hits: 5,720,856, hits per frag: 0.255228 processed 23,000,000 fragments hits: 5,847,161, hits per frag: 0.256397 processed 23,500,000 fragments hits: 5,973,620, hits per frag: 0.25543 processed 24,000,001 fragments hits: 6,099,706, hits per frag: 0.254255 processed 24,500,000 fragments hits: 6,226,489, hits per frag: 0.254881 processed 25,000,000 fragments hits: 6,354,392, hits per frag: 0.255698 processed 25,500,000 fragments hits: 6,481,599, hits per frag: 0.254568 processed 26,000,000 fragments hits: 6,608,844, hits per frag: 0.254991 [2021-07-20 12:08:15.452] [jointLog] [info] Thread saw mini-batch with a maximum of 1.68% zero probability fragments [2021-07-20 12:08:15.452] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 12:08:15.452] [jointLog] [info] Thread saw mini-batch with a maximum of 1.64% zero probability fragments [2021-07-20 12:08:15.452] [jointLog] [info] Thread saw mini-batch with a maximum of 1.56% zero probability fragments [2021-07-20 12:08:15.452] [jointLog] [info] Thread saw mini-batch with a maximum of 1.44% zero probability fragments [2021-07-20 12:08:15.452] [jointLog] [info] Thread saw mini-batch with a maximum of 1.78% zero probability fragments [2021-07-20 12:08:15.452] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 12:08:15.452] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:08:15.452] [jointLog] [info] Thread saw mini-batch with a maximum of 1.48% zero probability fragments [2021-07-20 12:08:15.452] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:08:15.453] [jointLog] [info] Thread saw mini-batch with a maximum of 1.68% zero probability fragments [2021-07-20 12:08:15.464] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:08:15.464] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 12:08:15.489] [jointLog] [info] Thread saw mini-batch with a maximum of 1.66% zero probability fragments [2021-07-20 12:08:15.492] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 12:08:15.501] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 12:08:15.524] [jointLog] [info] Thread saw mini-batch with a maximum of 1.70% zero probability fragments [2021-07-20 12:08:15.530] [jointLog] [info] Thread saw mini-batch with a maximum of 1.50% zero probability fragments [2021-07-20 12:08:15.537] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 12:08:15.541] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:08:15.559] [jointLog] [info] Thread saw mini-batch with a maximum of 1.52% zero probability fragments [2021-07-20 12:08:15.574] [jointLog] [info] Thread saw mini-batch with a maximum of 1.44% zero probability fragments [2021-07-20 12:08:15.580] [jointLog] [info] Thread saw mini-batch with a maximum of 1.58% zero probability fragments [2021-07-20 12:08:15.766] [jointLog] [info] Computed 36,590 rich equivalence classes for further processing [2021-07-20 12:08:15.766] [jointLog] [info] Counted 4,594,829 total reads in the equivalence classes [2021-07-20 12:08:15.785] [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. [2021-07-20 12:08:15.789] [jointLog] [warning] Only 4594829 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2021-07-20 12:08:15.789] [jointLog] [info] Mapping rate = 17.3621% [2021-07-20 12:08:15.789] [jointLog] [info] finished quantifyLibrary() [2021-07-20 12:08:15.789] [jointLog] [info] Starting optimizer [2021-07-20 12:08:15.810] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2021-07-20 12:08:15.812] [jointLog] [info] iteration = 0 | max rel diff. = 303.264 [2021-07-20 12:08:15.943] [jointLog] [info] iteration = 100 | max rel diff. = 0.789669 [2021-07-20 12:08:16.071] [jointLog] [info] iteration = 200 | max rel diff. = 0.612909 [2021-07-20 12:08:16.147] [jointLog] [info] iteration = 261 | max rel diff. = 0.00330405 [2021-07-20 12:08:16.148] [jointLog] [info] Finished optimizer [2021-07-20 12:08:16.148] [jointLog] [info] writing output CMD: /home/shared/Trinityrnaseq-v2.8.5/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_female_44_03/quant.sf /media/sam/4TB_toshiba/porites/20210720_pcom_trinity_cnidaria_RNAseq/pcom_cnidaria_transcriptome_v1.0.fasta.gene_trans_map > non-bleached_female_44_03/quant.sf.genes