CMD: salmon quant -i /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P01-AGTTCC-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P01-AGTTCC-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_K5_01 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_K5_01 } ### [ threads ] => { 23 } Logs will be written to bleached_K5_01/logs [2019-01-24 20:28:56.428] [jointLog] [info] parsing read library format [2019-01-24 20:28:56.428] [jointLog] [info] There is 1 library. [2019-01-24 20:28:56.487] [jointLog] [info] Loading Quasi index [2019-01-24 20:28:56.487] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:28:56.487] [stderrLog] [info] Loading Suffix Array [2019-01-24 20:28:56.720] [stderrLog] [info] Loading Transcript Info [2019-01-24 20:28:56.787] [stderrLog] [info] Loading Rank-Select Bit Array [2019-01-24 20:28:56.813] [stderrLog] [info] There were 49695 set bits in the bit array [2019-01-24 20:28:56.826] [stderrLog] [info] Computing transcript lengths [2019-01-24 20:28:56.826] [stderrLog] [info] Waiting to finish loading hash [2019-01-24 20:28:59.267] [jointLog] [info] done [2019-01-24 20:28:59.267] [jointLog] [info] Index contained 49695 targets [2019-01-24 20:28:59.267] [stderrLog] [info] Done loading index  processed 500001 fragments hits: 501403, hits per frag: 1.05569 processed 1000000 fragments hits: 4576937, hits per frag: 4.63446 processed 4570740 fragments hits: 4576968, hits per frag: 3.15937 processed 4571870 fragments hits: 4578129, hits per frag: 2.352 processed 4571881 fragments hits: 4578131, hits per frag: 1.87302 processed 4573511 fragments hits: 4579733, hits per frag: 1.53928 processed 4575391 fragments hits: 4581682, hits per frag: 1.31894 processed 4575418 fragments hits: 4581706, hits per frag: 1.16103 processed 4575439 fragments hits: 4581716, hits per frag: 1.02934 processed 5000000 fragments hits: 5006669, hits per frag: 1.00702 processed 5500000 fragments hits: 5507776, hits per frag: 1.00516 processed 6000000 fragments hits: 6008708, hits per frag: 1.01813 processed 6500000 fragments hits: 6510205, hits per frag: 1.00549 processed 7000000 fragments hits: 7011864, hits per frag: 1.01527 processed 7500000 fragments hits: 7512466, hits per frag: 1.01568 processed 8000000 fragments hits: 8013507, hits per frag: 1.00949 processed 8500000 fragments hits: 8512232, hits per frag: 1.01257 processed 9000000 fragments hits: 9012527, hits per frag: 1.00836 processed 9500000 fragments hits: 9511018, hits per frag: 1.00715 processed 10000000 fragments hits: 10010661, hits per frag: 1.01061 processed 10500000 fragments hits: 10512953, hits per frag: 1.01367 processed 11000001 fragments hits: 11012217, hits per frag: 1.01231 processed 11500000 fragments hits: 11514866, hits per frag: 1.00838 processed 12000000 fragments hits: 12014840, hits per frag: 1.00446 processed 12500000 fragments hits: 12514370, hits per frag: 1.01115 processed 13000001 fragments hits: 13014748, hits per frag: 1.00273 processed 13500000 fragments hits: 13514108, hits per frag: 1.00457 processed 14000000 fragments hits: 14015147, hits per frag: 1.00725 processed 14500000 fragments hits: 14516269, hits per frag: 1.00693 processed 15000000 fragments hits: 15019148, hits per frag: 1.00415 processed 15500002 fragments hits: 15517932, hits per frag: 1.00617 processed 16000000 fragments hits: 16018021, hits per frag: 1.00803 processed 16500000 fragments hits: 16517708, hits per frag: 1.00594 processed 17000000 fragments hits: 17019051, hits per frag: 1.00616 processed 17500000 fragments hits: 17520391, hits per frag: 1.00241 processed 18000000 fragments hits: 18020016, hits per frag: 1.00265 processed 18500000 fragments hits: 18518707, hits per frag: 1.00515 processed 19000000 fragments hits: 19018226, hits per frag: 1.00602 processed 19500000 fragments hits: 19517591, hits per frag: 1.00291 processed 20000000 fragments hits: 20018578, hits per frag: 1.00762 processed 20500001 fragments hits: 20521140, hits per frag: 1.00539 processed 21000000 fragments hits: 21021025, hits per frag: 1.00427 processed 21500000 fragments hits: 21522036, hits per frag: 1.00612 processed 22000000 fragments hits: 22022976, hits per frag: 1.00609 processed 22500001 fragments hits: 22522311, hits per frag: 1.00381 processed 23000000 fragments hits: 23022106, hits per frag: 1.00566 processed 23500000 fragments hits: 23525031, hits per frag: 1.00278 processed 24000000 fragments hits: 24026403, hits per frag: 1.00203 processed 24500001 fragments hits: 24530299, hits per frag: 1.00645 [2019-01-24 20:30:01.124] [jointLog] [info] Computed 64376 rich equivalence classes for further processing [2019-01-24 20:30:01.124] [jointLog] [info] Counted 11935577 total reads in the equivalence classes [2019-01-24 20:30:01.132] [jointLog] [warning] 0.00989258% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:30:01.132] [jointLog] [info] Mapping rate = 48.0364% [2019-01-24 20:30:01.132] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:30:01.132] [jointLog] [info] Starting optimizer [2019-01-24 20:30:01.176] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:30:01.178] [jointLog] [info] iteration = 0 | max rel diff. = 196.449 [2019-01-24 20:30:01.302] [jointLog] [info] iteration = 100 | max rel diff. = 0.111444 [2019-01-24 20:30:01.425] [jointLog] [info] iteration = 200 | max rel diff. = 0.0560557 [2019-01-24 20:30:01.547] [jointLog] [info] iteration = 300 | max rel diff. = 0.0372287 [2019-01-24 20:30:01.675] [jointLog] [info] iteration = 400 | max rel diff. = 0.0279104 [2019-01-24 20:30:01.799] [jointLog] [info] iteration = 500 | max rel diff. = 0.0217925 [2019-01-24 20:30:01.923] [jointLog] [info] iteration = 600 | max rel diff. = 0.0192097 [2019-01-24 20:30:02.047] [jointLog] [info] iteration = 700 | max rel diff. = 0.0172511 [2019-01-24 20:30:02.173] [jointLog] [info] iteration = 800 | max rel diff. = 0.0155193 [2019-01-24 20:30:02.298] [jointLog] [info] iteration = 900 | max rel diff. = 0.0130546 [2019-01-24 20:30:02.425] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0116435 [2019-01-24 20:30:02.551] [jointLog] [info] iteration = 1100 | max rel diff. = 0.01052 [2019-01-24 20:30:02.680] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0101162 [2019-01-24 20:30:02.685] [jointLog] [info] iteration = 1205 | max rel diff. = 0.009706 [2019-01-24 20:30:02.693] [jointLog] [info] Finished optimizer [2019-01-24 20:30:02.693] [jointLog] [info] writing output [2019-01-24 20:30:02.791] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_K5_01/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_K5_01/quant.sf /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.gene_trans_map > bleached_K5_01/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P06-GCCAAT-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P06-GCCAAT-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_K5_02 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_K5_02 } ### [ threads ] => { 23 } Logs will be written to bleached_K5_02/logs [2019-01-24 20:30:04.091] [jointLog] [info] parsing read library format [2019-01-24 20:30:04.091] [jointLog] [info] There is 1 library. [2019-01-24 20:30:04.154] [stderrLog] [info] Loading Suffix Array [2019-01-24 20:30:04.154] [jointLog] [info] Loading Quasi index [2019-01-24 20:30:04.154] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:30:04.430] [stderrLog] [info] Loading Transcript Info [2019-01-24 20:30:04.497] [stderrLog] [info] Loading Rank-Select Bit Array [2019-01-24 20:30:04.523] [stderrLog] [info] There were 49695 set bits in the bit array [2019-01-24 20:30:04.536] [stderrLog] [info] Computing transcript lengths [2019-01-24 20:30:04.536] [stderrLog] [info] Waiting to finish loading hash [2019-01-24 20:30:06.937] [stderrLog] [info] Done loading index [2019-01-24 20:30:06.937] [jointLog] [info] done [2019-01-24 20:30:06.937] [jointLog] [info] Index contained 49695 targets  processed 500000 fragments hits: 512442, hits per frag: 1.23509 processed 1000000 fragments hits: 1025533, hits per frag: 1.04488 processed 1500001 fragments hits: 1539930, hits per frag: 1.09141 processed 2000002 fragments hits: 2051302, hits per frag: 1.07776 processed 2500000 fragments hits: 2563623, hits per frag: 1.04528 processed 3000000 fragments hits: 3078422, hits per frag: 1.04092 processed 3500001 fragments hits: 3591597, hits per frag: 1.03469 processed 4000000 fragments hits: 4102653, hits per frag: 1.04964 processed 4500001 fragments hits: 4616168, hits per frag: 1.03645 processed 5000000 fragments hits: 5129291, hits per frag: 1.0422 processed 5500001 fragments hits: 5642540, hits per frag: 1.04651 processed 6000000 fragments hits: 6154489, hits per frag: 1.04292 processed 6500000 fragments hits: 6668128, hits per frag: 1.03595 processed 7000001 fragments hits: 7183977, hits per frag: 1.03466 processed 7500000 fragments hits: 7698891, hits per frag: 1.03295 processed 8000000 fragments hits: 8209952, hits per frag: 1.03853 processed 8500000 fragments hits: 8720091, hits per frag: 1.04439 processed 9000000 fragments hits: 9231111, hits per frag: 1.04314 processed 9500000 fragments hits: 9745101, hits per frag: 1.03974 processed 10000003 fragments hits: 10257728, hits per frag: 1.03312 processed 10500000 fragments hits: 10772486, hits per frag: 1.02805 processed 11000001 fragments hits: 11284763, hits per frag: 1.02841 processed 11500000 fragments hits: 11801290, hits per frag: 1.03037 processed 12000000 fragments hits: 12315468, hits per frag: 1.02832 processed 12500001 fragments hits: 12827362, hits per frag: 1.03185 processed 13000000 fragments hits: 13339314, hits per frag: 1.03401 processed 13500001 fragments hits: 13852787, hits per frag: 1.03031 processed 14000001 fragments hits: 14367048, hits per frag: 1.02827 processed 14500001 fragments hits: 14879973, hits per frag: 1.03204 processed 15000000 fragments hits: 15395169, hits per frag: 1.03352 processed 15500001 fragments hits: 15910222, hits per frag: 1.02727 processed 16000001 fragments hits: 16423779, hits per frag: 1.0313 processed 16500000 fragments hits: 16938569, hits per frag: 1.03033 processed 17000000 fragments hits: 17451436, hits per frag: 1.03169 processed 17500001 fragments hits: 17964856, hits per frag: 1.03134 processed 18000000 fragments hits: 18478587, hits per frag: 1.03208 [2019-01-24 20:30:50.998] [jointLog] [info] Computed 64760 rich equivalence classes for further processing [2019-01-24 20:30:50.998] [jointLog] [info] Counted 9296657 total reads in the equivalence classes [2019-01-24 20:30:51.007] [jointLog] [warning] 0.0114771% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:30:51.007] [jointLog] [info] Mapping rate = 50.6162% [2019-01-24 20:30:51.007] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:30:51.007] [jointLog] [info] Starting optimizer [2019-01-24 20:30:51.045] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:30:51.046] [jointLog] [info] iteration = 0 | max rel diff. = 170.931 [2019-01-24 20:30:51.169] [jointLog] [info] iteration = 100 | max rel diff. = 0.111748 [2019-01-24 20:30:51.290] [jointLog] [info] iteration = 200 | max rel diff. = 0.0558071 [2019-01-24 20:30:51.412] [jointLog] [info] iteration = 300 | max rel diff. = 0.0364306 [2019-01-24 20:30:51.536] [jointLog] [info] iteration = 400 | max rel diff. = 0.0280263 [2019-01-24 20:30:51.658] [jointLog] [info] iteration = 500 | max rel diff. = 0.0220556 [2019-01-24 20:30:51.779] [jointLog] [info] iteration = 600 | max rel diff. = 0.0187145 [2019-01-24 20:30:51.901] [jointLog] [info] iteration = 700 | max rel diff. = 0.0179586 [2019-01-24 20:30:52.027] [jointLog] [info] iteration = 800 | max rel diff. = 0.0141097 [2019-01-24 20:30:52.150] [jointLog] [info] iteration = 900 | max rel diff. = 0.0117583 [2019-01-24 20:30:52.273] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0110945 [2019-01-24 20:30:52.397] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0110354 [2019-01-24 20:30:52.486] [jointLog] [info] iteration = 1173 | max rel diff. = 0.00960069 [2019-01-24 20:30:52.491] [jointLog] [info] Finished optimizer [2019-01-24 20:30:52.491] [jointLog] [info] writing output [2019-01-24 20:30:52.583] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_K5_02/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_K5_02/quant.sf /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.gene_trans_map > bleached_K5_02/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P07-AGTCAA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P07-AGTCAA-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_K5_03 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_K5_03 } ### [ threads ] => { 23 } Logs will be written to bleached_K5_03/logs [2019-01-24 20:30:53.938] [jointLog] [info] parsing read library format [2019-01-24 20:30:53.938] [jointLog] [info] There is 1 library. [2019-01-24 20:30:54.000] [stderrLog] [info] Loading Suffix Array [2019-01-24 20:30:54.000] [jointLog] [info] Loading Quasi index [2019-01-24 20:30:54.000] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:30:54.267] [stderrLog] [info] Loading Transcript Info [2019-01-24 20:30:54.329] [stderrLog] [info] Loading Rank-Select Bit Array [2019-01-24 20:30:54.354] [stderrLog] [info] There were 49695 set bits in the bit array [2019-01-24 20:30:54.368] [stderrLog] [info] Computing transcript lengths [2019-01-24 20:30:54.368] [stderrLog] [info] Waiting to finish loading hash [2019-01-24 20:30:56.690] [stderrLog] [info] Done loading index [2019-01-24 20:30:56.690] [jointLog] [info] done [2019-01-24 20:30:56.690] [jointLog] [info] Index contained 49695 targets  processed 500000 fragments hits: 553303, hits per frag: 1.40077 processed 1000000 fragments hits: 1106856, hits per frag: 1.23508 processed 1500001 fragments hits: 1661074, hits per frag: 1.18135 processed 2000000 fragments hits: 2216581, hits per frag: 1.1263 processed 2500000 fragments hits: 2770131, hits per frag: 1.13409 processed 3000000 fragments hits: 3323803, hits per frag: 1.12462 processed 3500001 fragments hits: 3874281, hits per frag: 1.15017 processed 4000000 fragments hits: 4427309, hits per frag: 1.13014 processed 4500000 fragments hits: 4982593, hits per frag: 1.12847 processed 5000000 fragments hits: 5536141, hits per frag: 1.12062 processed 5500000 fragments hits: 6089632, hits per frag: 1.12778 processed 6000000 fragments hits: 6641629, hits per frag: 1.12843 processed 6500000 fragments hits: 7195563, hits per frag: 1.1221 processed 7000000 fragments hits: 7750044, hits per frag: 1.11987 processed 7500000 fragments hits: 8303191, hits per frag: 1.1235 processed 8000000 fragments hits: 8856284, hits per frag: 1.12398 processed 8500000 fragments hits: 9408730, hits per frag: 1.11744 processed 9000000 fragments hits: 9964185, hits per frag: 1.12491 processed 9500000 fragments hits: 10520409, hits per frag: 1.11048 processed 10000001 fragments hits: 11071727, hits per frag: 1.11532 processed 10500000 fragments hits: 11625719, hits per frag: 1.11812 processed 11000000 fragments hits: 12179481, hits per frag: 1.11749 processed 11500000 fragments hits: 12734060, hits per frag: 1.11376 processed 12000000 fragments hits: 13289391, hits per frag: 1.11133 processed 12500000 fragments hits: 13842070, hits per frag: 1.11528 processed 13000000 fragments hits: 14395309, hits per frag: 1.11029 processed 13500001 fragments hits: 14948413, hits per frag: 1.11066 processed 14000000 fragments hits: 15501640, hits per frag: 1.11053 processed 14500000 fragments hits: 16054433, hits per frag: 1.11644 processed 15000001 fragments hits: 16606166, hits per frag: 1.1126 processed 15500000 fragments hits: 17159958, hits per frag: 1.11535 processed 16000001 fragments hits: 17712199, hits per frag: 1.10986 processed 16500000 fragments hits: 18266004, hits per frag: 1.11139 processed 17000000 fragments hits: 18819016, hits per frag: 1.11247 processed 17500000 fragments hits: 19373008, hits per frag: 1.11232 processed 18000000 fragments hits: 19924338, hits per frag: 1.11071 processed 18500000 fragments hits: 20477039, hits per frag: 1.11097 processed 19000000 fragments hits: 21032069, hits per frag: 1.11146 processed 19500001 fragments hits: 21582975, hits per frag: 1.11133 processed 20000001 fragments hits: 22136590, hits per frag: 1.10985 processed 20500000 fragments hits: 22690585, hits per frag: 1.11117 processed 21000001 fragments hits: 23245826, hits per frag: 1.1115 processed 21500000 fragments hits: 23797884, hits per frag: 1.11444 processed 22000000 fragments hits: 24350413, hits per frag: 1.10907 processed 22500000 fragments hits: 24903630, hits per frag: 1.11104 processed 23000000 fragments hits: 25456803, hits per frag: 1.10827 processed 23500001 fragments hits: 26009607, hits per frag: 1.1111 processed 24000000 fragments hits: 26562783, hits per frag: 1.10903 processed 24500000 fragments hits: 27115871, hits per frag: 1.10836 processed 25000001 fragments hits: 27669950, hits per frag: 1.10905 processed 25500000 fragments hits: 28222633, hits per frag: 1.10727 processed 25500023 fragments hits: 28222645, hits per frag: 1.10885 [2019-01-24 20:31:56.386] [jointLog] [info] Computed 65922 rich equivalence classes for further processing [2019-01-24 20:31:56.386] [jointLog] [info] Counted 14021232 total reads in the equivalence classes [2019-01-24 20:31:56.395] [jointLog] [warning] 0.0136297% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:31:56.396] [jointLog] [info] Mapping rate = 54.1222% [2019-01-24 20:31:56.396] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:31:56.396] [jointLog] [info] Starting optimizer [2019-01-24 20:31:56.438] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:31:56.439] [jointLog] [info] iteration = 0 | max rel diff. = 213.842 [2019-01-24 20:31:56.569] [jointLog] [info] iteration = 100 | max rel diff. = 0.121097 [2019-01-24 20:31:56.694] [jointLog] [info] iteration = 200 | max rel diff. = 0.0551089 [2019-01-24 20:31:56.819] [jointLog] [info] iteration = 300 | max rel diff. = 0.0397445 [2019-01-24 20:31:56.947] [jointLog] [info] iteration = 400 | max rel diff. = 0.0284014 [2019-01-24 20:31:57.074] [jointLog] [info] iteration = 500 | max rel diff. = 0.0243248 [2019-01-24 20:31:57.202] [jointLog] [info] iteration = 600 | max rel diff. = 0.0191207 [2019-01-24 20:31:57.329] [jointLog] [info] iteration = 700 | max rel diff. = 0.0180264 [2019-01-24 20:31:57.455] [jointLog] [info] iteration = 800 | max rel diff. = 0.0135852 [2019-01-24 20:31:57.582] [jointLog] [info] iteration = 900 | max rel diff. = 0.0126782 [2019-01-24 20:31:57.709] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0126783 [2019-01-24 20:31:57.837] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0107923 [2019-01-24 20:31:57.966] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0101697 [2019-01-24 20:31:57.990] [jointLog] [info] iteration = 1220 | max rel diff. = 0.00874193 [2019-01-24 20:31:57.995] [jointLog] [info] Finished optimizer [2019-01-24 20:31:57.995] [jointLog] [info] writing output [2019-01-24 20:31:58.083] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_K5_03/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_K5_03/quant.sf /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.gene_trans_map > bleached_K5_03/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_K5_04 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_K5_04 } ### [ threads ] => { 23 } Logs will be written to bleached_K5_04/logs [2019-01-24 20:31:59.405] [jointLog] [info] parsing read library format [2019-01-24 20:31:59.405] [jointLog] [info] There is 1 library. [2019-01-24 20:31:59.466] [stderrLog] [info] Loading Suffix Array [2019-01-24 20:31:59.466] [jointLog] [info] Loading Quasi index [2019-01-24 20:31:59.466] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:31:59.715] [stderrLog] [info] Loading Transcript Info [2019-01-24 20:31:59.789] [stderrLog] [info] Loading Rank-Select Bit Array [2019-01-24 20:31:59.815] [stderrLog] [info] There were 49695 set bits in the bit array [2019-01-24 20:31:59.828] [stderrLog] [info] Computing transcript lengths [2019-01-24 20:31:59.828] [stderrLog] [info] Waiting to finish loading hash [2019-01-24 20:32:02.323] [stderrLog] [info] Done loading index [2019-01-24 20:32:02.323] [jointLog] [info] done [2019-01-24 20:32:02.323] [jointLog] [info] Index contained 49695 targets  processed 500000 fragments hits: 528203, hits per frag: 1.24023 processed 1000000 fragments hits: 1054885, hits per frag: 1.09068 processed 1500001 fragments hits: 1584203, hits per frag: 1.11877 processed 2000000 fragments hits: 2112938, hits per frag: 1.10445 processed 2500000 fragments hits: 2642309, hits per frag: 1.10707 processed 3000000 fragments hits: 3170393, hits per frag: 1.07343 processed 3500000 fragments hits: 3697360, hits per frag: 1.07845 processed 4000000 fragments hits: 4226875, hits per frag: 1.07569 processed 4500000 fragments hits: 4757023, hits per frag: 1.06466 processed 5000000 fragments hits: 5286209, hits per frag: 1.06974 processed 5500000 fragments hits: 5816236, hits per frag: 1.07356 processed 6000000 fragments hits: 6344537, hits per frag: 1.06354 processed 6500000 fragments hits: 6872618, hits per frag: 1.07849 processed 7000000 fragments hits: 7400991, hits per frag: 1.0595 processed 7500000 fragments hits: 7929432, hits per frag: 1.05949 processed 8000000 fragments hits: 8458786, hits per frag: 1.06018 processed 8500000 fragments hits: 8987629, hits per frag: 1.06583 processed 9000000 fragments hits: 9514427, hits per frag: 1.06716 processed 9500000 fragments hits: 10041718, hits per frag: 1.06772 processed 10000000 fragments hits: 10569980, hits per frag: 1.06935 processed 10500001 fragments hits: 11099016, hits per frag: 1.06235 processed 11000000 fragments hits: 11627320, hits per frag: 1.05836 processed 11500000 fragments hits: 12157436, hits per frag: 1.06 processed 12000000 fragments hits: 12685950, hits per frag: 1.06035 processed 12500000 fragments hits: 13212546, hits per frag: 1.06353 processed 13000001 fragments hits: 13740930, hits per frag: 1.05806 processed 13500000 fragments hits: 14268432, hits per frag: 1.06087 processed 14000000 fragments hits: 14796639, hits per frag: 1.06361 processed 14500001 fragments hits: 15324541, hits per frag: 1.06041 processed 15000000 fragments hits: 15852046, hits per frag: 1.06174 processed 15500001 fragments hits: 16380643, hits per frag: 1.05889 processed 16000000 fragments hits: 16907899, hits per frag: 1.05905 processed 16500002 fragments hits: 17437210, hits per frag: 1.06001 processed 17000000 fragments hits: 17965373, hits per frag: 1.06077 processed 17500000 fragments hits: 18494152, hits per frag: 1.0594 processed 18000000 fragments hits: 19024486, hits per frag: 1.05956 processed 18500000 fragments hits: 19551532, hits per frag: 1.06023 processed 19000000 fragments hits: 20079488, hits per frag: 1.06165 processed 19500000 fragments hits: 20608636, hits per frag: 1.06164 processed 20000000 fragments hits: 21136425, hits per frag: 1.06192 processed 20500000 fragments hits: 21665633, hits per frag: 1.05921 processed 21000000 fragments hits: 22194311, hits per frag: 1.05826 processed 21500000 fragments hits: 22724234, hits per frag: 1.0585 processed 22000001 fragments hits: 23250780, hits per frag: 1.06107 processed 22500001 fragments hits: 23779443, hits per frag: 1.0601 processed 23000000 fragments hits: 24312472, hits per frag: 1.06094 processed 23500000 fragments hits: 24841242, hits per frag: 1.05834 processed 24000000 fragments hits: 25369120, hits per frag: 1.06034 processed 24500000 fragments hits: 25898058, hits per frag: 1.05985 processed 25000001 fragments hits: 26425035, hits per frag: 1.05904 processed 25500001 fragments hits: 26954035, hits per frag: 1.06164 processed 26000000 fragments hits: 27482522, hits per frag: 1.05844 processed 26500001 fragments hits: 28013439, hits per frag: 1.05993 processed 27000000 fragments hits: 28542207, hits per frag: 1.06042 processed 27500000 fragments hits: 29070576, hits per frag: 1.05981 processed 28000000 fragments hits: 29598867, hits per frag: 1.0617 [2019-01-24 20:33:09.509] [jointLog] [info] Computed 65041 rich equivalence classes for further processing [2019-01-24 20:33:09.509] [jointLog] [info] Counted 15162807 total reads in the equivalence classes [2019-01-24 20:33:09.517] [jointLog] [warning] 0.0118102% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:33:09.517] [jointLog] [info] Mapping rate = 53.5352% [2019-01-24 20:33:09.517] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:33:09.517] [jointLog] [info] Starting optimizer [2019-01-24 20:33:09.546] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:33:09.547] [jointLog] [info] iteration = 0 | max rel diff. = 223.914 [2019-01-24 20:33:09.671] [jointLog] [info] iteration = 100 | max rel diff. = 0.113163 [2019-01-24 20:33:09.795] [jointLog] [info] iteration = 200 | max rel diff. = 0.0566745 [2019-01-24 20:33:09.919] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433007 [2019-01-24 20:33:10.044] [jointLog] [info] iteration = 400 | max rel diff. = 0.027911 [2019-01-24 20:33:10.169] [jointLog] [info] iteration = 500 | max rel diff. = 0.0229168 [2019-01-24 20:33:10.295] [jointLog] [info] iteration = 600 | max rel diff. = 0.019034 [2019-01-24 20:33:10.420] [jointLog] [info] iteration = 700 | max rel diff. = 0.0153454 [2019-01-24 20:33:10.549] [jointLog] [info] iteration = 800 | max rel diff. = 0.0149216 [2019-01-24 20:33:10.675] [jointLog] [info] iteration = 900 | max rel diff. = 0.0122229 [2019-01-24 20:33:10.802] [jointLog] [info] iteration = 1000 | max rel diff. = 0.012223 [2019-01-24 20:33:10.929] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0120077 [2019-01-24 20:33:11.057] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0101907 [2019-01-24 20:33:11.136] [jointLog] [info] iteration = 1263 | max rel diff. = 0.0089341 [2019-01-24 20:33:11.141] [jointLog] [info] Finished optimizer [2019-01-24 20:33:11.141] [jointLog] [info] writing output [2019-01-24 20:33:11.228] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_K5_04/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_K5_04/quant.sf /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.gene_trans_map > bleached_K5_04/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_K5_05 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_K5_05 } ### [ threads ] => { 23 } Logs will be written to bleached_K5_05/logs [2019-01-24 20:33:12.698] [jointLog] [info] parsing read library format [2019-01-24 20:33:12.698] [jointLog] [info] There is 1 library. [2019-01-24 20:33:12.758] [jointLog] [info] Loading Quasi index [2019-01-24 20:33:12.758] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:33:12.758] [stderrLog] [info] Loading Suffix Array [2019-01-24 20:33:13.016] [stderrLog] [info] Loading Transcript Info [2019-01-24 20:33:13.083] [stderrLog] [info] Loading Rank-Select Bit Array [2019-01-24 20:33:13.109] [stderrLog] [info] There were 49695 set bits in the bit array [2019-01-24 20:33:13.122] [stderrLog] [info] Computing transcript lengths [2019-01-24 20:33:13.123] [stderrLog] [info] Waiting to finish loading hash [2019-01-24 20:33:15.503] [jointLog] [info] done [2019-01-24 20:33:15.503] [jointLog] [info] Index contained 49695 targets [2019-01-24 20:33:15.503] [stderrLog] [info] Done loading index  processed 500001 fragments hits: 526149, hits per frag: 1.17374 processed 1000000 fragments hits: 1050594, hits per frag: 1.21214 processed 1500000 fragments hits: 1575636, hits per frag: 1.10485 processed 2000000 fragments hits: 2098406, hits per frag: 1.07012 processed 2500000 fragments hits: 2623160, hits per frag: 1.10893 processed 3000000 fragments hits: 3146885, hits per frag: 1.07147 processed 3500000 fragments hits: 3671274, hits per frag: 1.09407 processed 4000000 fragments hits: 4192451, hits per frag: 1.06696 processed 4500000 fragments hits: 4717586, hits per frag: 1.06792 processed 5000000 fragments hits: 5238152, hits per frag: 1.0591 processed 5500000 fragments hits: 5758568, hits per frag: 1.05472 processed 6000000 fragments hits: 6280320, hits per frag: 1.05566 processed 6500000 fragments hits: 6803340, hits per frag: 1.0576 processed 7000000 fragments hits: 7327211, hits per frag: 1.058 processed 7500001 fragments hits: 7850564, hits per frag: 1.05579 processed 8000000 fragments hits: 8375553, hits per frag: 1.05709 processed 8500000 fragments hits: 8900567, hits per frag: 1.05785 processed 9000000 fragments hits: 9423263, hits per frag: 1.05548 processed 9500001 fragments hits: 9948158, hits per frag: 1.05342 processed 10000000 fragments hits: 10469115, hits per frag: 1.05438 processed 10500000 fragments hits: 10991740, hits per frag: 1.0571 processed 11000000 fragments hits: 11511885, hits per frag: 1.05357 processed 11500000 fragments hits: 12035551, hits per frag: 1.05923 processed 12000000 fragments hits: 12558226, hits per frag: 1.05125 processed 12500001 fragments hits: 13082060, hits per frag: 1.05023 processed 13000000 fragments hits: 13604321, hits per frag: 1.04739 processed 13500000 fragments hits: 14126270, hits per frag: 1.04891 processed 14000000 fragments hits: 14648905, hits per frag: 1.05022 processed 14500000 fragments hits: 15170928, hits per frag: 1.04685 processed 15000000 fragments hits: 15691989, hits per frag: 1.0501 processed 15500000 fragments hits: 16212979, hits per frag: 1.0513 processed 16000000 fragments hits: 16733836, hits per frag: 1.05164 processed 16500000 fragments hits: 17257554, hits per frag: 1.04905 processed 17000000 fragments hits: 17780710, hits per frag: 1.05304 processed 17500000 fragments hits: 18304743, hits per frag: 1.05081 processed 18000000 fragments hits: 18826730, hits per frag: 1.04859 processed 18500000 fragments hits: 19350534, hits per frag: 1.05179 processed 19000000 fragments hits: 19876955, hits per frag: 1.05011 processed 19500000 fragments hits: 20399402, hits per frag: 1.04929 processed 20000000 fragments hits: 20920600, hits per frag: 1.04844 processed 20500002 fragments hits: 21443103, hits per frag: 1.04871 processed 21000000 fragments hits: 21966398, hits per frag: 1.0519 processed 21500000 fragments hits: 22491069, hits per frag: 1.05007 [2019-01-24 20:34:04.087] [jointLog] [info] Computed 61433 rich equivalence classes for further processing [2019-01-24 20:34:04.087] [jointLog] [info] Counted 11598043 total reads in the equivalence classes [2019-01-24 20:34:04.098] [jointLog] [warning] 0.0194906% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:34:04.098] [jointLog] [info] Mapping rate = 53.0019% [2019-01-24 20:34:04.098] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:34:04.098] [jointLog] [info] Starting optimizer [2019-01-24 20:34:04.127] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:34:04.129] [jointLog] [info] iteration = 0 | max rel diff. = 182.899 [2019-01-24 20:34:04.248] [jointLog] [info] iteration = 100 | max rel diff. = 0.113743 [2019-01-24 20:34:04.366] [jointLog] [info] iteration = 200 | max rel diff. = 0.0549201 [2019-01-24 20:34:04.487] [jointLog] [info] iteration = 300 | max rel diff. = 0.0381628 [2019-01-24 20:34:04.611] [jointLog] [info] iteration = 400 | max rel diff. = 0.0278757 [2019-01-24 20:34:04.735] [jointLog] [info] iteration = 500 | max rel diff. = 0.0217951 [2019-01-24 20:34:04.859] [jointLog] [info] iteration = 600 | max rel diff. = 0.020357 [2019-01-24 20:34:04.983] [jointLog] [info] iteration = 700 | max rel diff. = 0.0169519 [2019-01-24 20:34:05.107] [jointLog] [info] iteration = 800 | max rel diff. = 0.0150391 [2019-01-24 20:34:05.232] [jointLog] [info] iteration = 900 | max rel diff. = 0.0130591 [2019-01-24 20:34:05.374] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0110031 [2019-01-24 20:34:05.517] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0101259 [2019-01-24 20:34:05.645] [jointLog] [info] iteration = 1200 | max rel diff. = 0.010126 [2019-01-24 20:34:05.664] [jointLog] [info] iteration = 1216 | max rel diff. = 0.00989767 [2019-01-24 20:34:05.669] [jointLog] [info] Finished optimizer [2019-01-24 20:34:05.669] [jointLog] [info] writing output [2019-01-24 20:34:05.754] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_K5_05/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_K5_05/quant.sf /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.gene_trans_map > bleached_K5_05/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_K5_06 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_K5_06 } ### [ threads ] => { 23 } Logs will be written to bleached_K5_06/logs [2019-01-24 20:34:07.197] [jointLog] [info] parsing read library format [2019-01-24 20:34:07.197] [jointLog] [info] There is 1 library. [2019-01-24 20:34:07.259] [stderrLog] [info] Loading Suffix Array [2019-01-24 20:34:07.258] [jointLog] [info] Loading Quasi index [2019-01-24 20:34:07.258] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:34:07.521] [stderrLog] [info] Loading Transcript Info [2019-01-24 20:34:07.583] [stderrLog] [info] Loading Rank-Select Bit Array [2019-01-24 20:34:07.609] [stderrLog] [info] There were 49695 set bits in the bit array [2019-01-24 20:34:07.622] [stderrLog] [info] Computing transcript lengths [2019-01-24 20:34:07.622] [stderrLog] [info] Waiting to finish loading hash [2019-01-24 20:34:10.063] [stderrLog] [info] Done loading index [2019-01-24 20:34:10.063] [jointLog] [info] done [2019-01-24 20:34:10.063] [jointLog] [info] Index contained 49695 targets  processed 500001 fragments hits: 447091, hits per frag: 1.09183 processed 1000000 fragments hits: 892065, hits per frag: 1.00141 processed 1500000 fragments hits: 1340092, hits per frag: 0.944779 processed 2000000 fragments hits: 1787628, hits per frag: 0.913341 processed 2500000 fragments hits: 2234972, hits per frag: 0.929577 processed 3000002 fragments hits: 2680471, hits per frag: 0.941492 processed 3500000 fragments hits: 3125604, hits per frag: 0.910482 processed 4000000 fragments hits: 3569922, hits per frag: 0.901032 processed 4500000 fragments hits: 4014654, hits per frag: 0.893455 processed 5000000 fragments hits: 4461518, hits per frag: 0.904181 processed 5500000 fragments hits: 4909952, hits per frag: 0.918053 processed 6000000 fragments hits: 5357778, hits per frag: 0.910684 processed 6500000 fragments hits: 5805130, hits per frag: 0.899737 processed 7000001 fragments hits: 6251488, hits per frag: 0.906269 processed 7500000 fragments hits: 6696682, hits per frag: 0.902658 processed 8000000 fragments hits: 7144468, hits per frag: 0.897462 processed 8500002 fragments hits: 7589473, hits per frag: 0.902695 processed 9000000 fragments hits: 8036278, hits per frag: 0.905292 processed 9500000 fragments hits: 8483239, hits per frag: 0.89936 processed 10000000 fragments hits: 8927963, hits per frag: 0.901334 processed 10500000 fragments hits: 9373162, hits per frag: 0.89868 processed 11000000 fragments hits: 9818696, hits per frag: 0.896753 processed 11500001 fragments hits: 10265018, hits per frag: 0.903381 processed 12000002 fragments hits: 10709847, hits per frag: 0.900287 processed 12500000 fragments hits: 11154006, hits per frag: 0.898498 processed 13000000 fragments hits: 11597811, hits per frag: 0.894466 processed 13500001 fragments hits: 12046707, hits per frag: 0.894897 processed 14000000 fragments hits: 12494028, hits per frag: 0.8963 processed 14500001 fragments hits: 12942061, hits per frag: 0.898373 processed 15000000 fragments hits: 13390786, hits per frag: 0.898321 processed 15500001 fragments hits: 13839604, hits per frag: 0.898424 processed 16000000 fragments hits: 14286252, hits per frag: 0.896899 processed 16500000 fragments hits: 14731746, hits per frag: 0.897088 processed 17000000 fragments hits: 15176860, hits per frag: 0.897585 [2019-01-24 20:34:49.600] [jointLog] [info] Computed 57063 rich equivalence classes for further processing [2019-01-24 20:34:49.600] [jointLog] [info] Counted 8593018 total reads in the equivalence classes [2019-01-24 20:34:49.608] [jointLog] [warning] 0.0100547% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:34:49.608] [jointLog] [info] Mapping rate = 49.7123% [2019-01-24 20:34:49.608] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:34:49.608] [jointLog] [info] Starting optimizer [2019-01-24 20:34:49.637] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:34:49.638] [jointLog] [info] iteration = 0 | max rel diff. = 155.209 [2019-01-24 20:34:49.765] [jointLog] [info] iteration = 100 | max rel diff. = 0.109989 [2019-01-24 20:34:49.891] [jointLog] [info] iteration = 200 | max rel diff. = 0.0537113 [2019-01-24 20:34:50.013] [jointLog] [info] iteration = 300 | max rel diff. = 0.0432942 [2019-01-24 20:34:50.132] [jointLog] [info] iteration = 400 | max rel diff. = 0.0273283 [2019-01-24 20:34:50.252] [jointLog] [info] iteration = 500 | max rel diff. = 0.0235596 [2019-01-24 20:34:50.373] [jointLog] [info] iteration = 600 | max rel diff. = 0.0184223 [2019-01-24 20:34:50.493] [jointLog] [info] iteration = 700 | max rel diff. = 0.0158013 [2019-01-24 20:34:50.614] [jointLog] [info] iteration = 800 | max rel diff. = 0.0139032 [2019-01-24 20:34:50.735] [jointLog] [info] iteration = 900 | max rel diff. = 0.0120352 [2019-01-24 20:34:50.857] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0113604 [2019-01-24 20:34:50.979] [jointLog] [info] iteration = 1100 | max rel diff. = 0.010448 [2019-01-24 20:34:51.020] [jointLog] [info] iteration = 1134 | max rel diff. = 0.00905003 [2019-01-24 20:34:51.025] [jointLog] [info] Finished optimizer [2019-01-24 20:34:51.025] [jointLog] [info] writing output [2019-01-24 20:34:51.108] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_K5_06/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_K5_06/quant.sf /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.gene_trans_map > bleached_K5_06/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P03-ACTGAT-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P03-ACTGAT-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_44_01 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_44_01 } ### [ threads ] => { 23 } Logs will be written to bleached_44_01/logs [2019-01-24 20:34:52.452] [jointLog] [info] parsing read library format [2019-01-24 20:34:52.452] [jointLog] [info] There is 1 library. [2019-01-24 20:34:52.511] [jointLog] [info] Loading Quasi index [2019-01-24 20:34:52.512] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:34:52.512] [stderrLog] [info] Loading Suffix Array [2019-01-24 20:34:52.759] [stderrLog] [info] Loading Transcript Info [2019-01-24 20:34:52.826] [stderrLog] [info] Loading Rank-Select Bit Array [2019-01-24 20:34:52.851] [stderrLog] [info] There were 49695 set bits in the bit array [2019-01-24 20:34:52.865] [stderrLog] [info] Computing transcript lengths [2019-01-24 20:34:52.865] [stderrLog] [info] Waiting to finish loading hash [2019-01-24 20:34:55.358] [jointLog] [info] done [2019-01-24 20:34:55.358] [jointLog] [info] Index contained 49695 targets [2019-01-24 20:34:55.358] [stderrLog] [info] Done loading index  processed 500000 fragments hits: 487956, hits per frag: 1.03775 processed 1000000 fragments hits: 974723, hits per frag: 0.988035 processed 1500000 fragments hits: 1462713, hits per frag: 0.997435 processed 2000000 fragments hits: 1951416, hits per frag: 1.01178 processed 2500000 fragments hits: 2440602, hits per frag: 1.01864 processed 3000000 fragments hits: 2928212, hits per frag: 1.01097 processed 3500001 fragments hits: 3418352, hits per frag: 1.00134 processed 4000000 fragments hits: 3905508, hits per frag: 0.984949 processed 4500000 fragments hits: 4396145, hits per frag: 0.983667 processed 5000000 fragments hits: 4885504, hits per frag: 0.979067 processed 5500000 fragments hits: 5374308, hits per frag: 0.989442 processed 6000000 fragments hits: 5862661, hits per frag: 0.985226 processed 6500001 fragments hits: 6350375, hits per frag: 0.984067 processed 7000000 fragments hits: 6841479, hits per frag: 0.984248 processed 7500001 fragments hits: 7326450, hits per frag: 0.981507 processed 8000000 fragments hits: 7813334, hits per frag: 0.993788 processed 8500000 fragments hits: 8297268, hits per frag: 0.97971 processed 9000000 fragments hits: 8785188, hits per frag: 0.983841 processed 9500000 fragments hits: 9272748, hits per frag: 0.98469 processed 10000000 fragments hits: 9762879, hits per frag: 0.980597 processed 10500000 fragments hits: 10250700, hits per frag: 0.9807 processed 11000001 fragments hits: 10739230, hits per frag: 0.979399 processed 11500000 fragments hits: 11228712, hits per frag: 0.983281 processed 12000000 fragments hits: 11717201, hits per frag: 0.982582 processed 12500000 fragments hits: 12203727, hits per frag: 0.981978 processed 13000000 fragments hits: 12690879, hits per frag: 0.979505 processed 13500000 fragments hits: 13177891, hits per frag: 0.981496 processed 14000000 fragments hits: 13665359, hits per frag: 0.979247 processed 14500000 fragments hits: 14151536, hits per frag: 0.980978 processed 15000000 fragments hits: 14641132, hits per frag: 0.980772 processed 15500000 fragments hits: 15132935, hits per frag: 0.977443 processed 16000000 fragments hits: 15623901, hits per frag: 0.981758 processed 16500000 fragments hits: 16111830, hits per frag: 0.98173 processed 17500000 fragments hits: 17087161, hits per frag: 0.983349 processed 18000000 fragments hits: 17572904, hits per frag: 0.979186 processed 18500000 fragments hits: 18060972, hits per frag: 0.976984 processed 19000000 fragments hits: 18552808, hits per frag: 0.978993 processed 19500000 fragments hits: 19041823, hits per frag: 0.977232 processed 20000000 fragments hits: 19530760, hits per frag: 0.979215 processed 20500001 fragments hits: 20018709, hits per frag: 0.982043 processed 21000002 fragments hits: 20507148, hits per frag: 0.981414 processed 21500000 fragments hits: 20996044, hits per frag: 0.980247 processed 22000001 fragments hits: 21484756, hits per frag: 0.978392 processed 22500000 fragments hits: 21972305, hits per frag: 0.98106 processed 23000001 fragments hits: 22463344, hits per frag: 0.979933 [2019-01-24 20:35:49.734] [jointLog] [info] Computed 69834 rich equivalence classes for further processing [2019-01-24 20:35:49.734] [jointLog] [info] Counted 10972275 total reads in the equivalence classes [2019-01-24 20:35:49.742] [jointLog] [warning] 0.0188665% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:35:49.742] [jointLog] [info] Mapping rate = 47.6538% [2019-01-24 20:35:49.742] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:35:49.742] [jointLog] [info] Starting optimizer [2019-01-24 20:35:49.779] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:35:49.781] [jointLog] [info] iteration = 0 | max rel diff. = 194.902 [2019-01-24 20:35:49.909] [jointLog] [info] iteration = 100 | max rel diff. = 0.10837 [2019-01-24 20:35:50.038] [jointLog] [info] iteration = 200 | max rel diff. = 0.055573 [2019-01-24 20:35:50.168] [jointLog] [info] iteration = 300 | max rel diff. = 0.041752 [2019-01-24 20:35:50.298] [jointLog] [info] iteration = 400 | max rel diff. = 0.0294721 [2019-01-24 20:35:50.427] [jointLog] [info] iteration = 500 | max rel diff. = 0.0244157 [2019-01-24 20:35:50.557] [jointLog] [info] iteration = 600 | max rel diff. = 0.0187225 [2019-01-24 20:35:50.692] [jointLog] [info] iteration = 700 | max rel diff. = 0.0162498 [2019-01-24 20:35:50.824] [jointLog] [info] iteration = 800 | max rel diff. = 0.0142847 [2019-01-24 20:35:50.955] [jointLog] [info] iteration = 900 | max rel diff. = 0.0142847 [2019-01-24 20:35:51.087] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0116814 [2019-01-24 20:35:51.218] [jointLog] [info] iteration = 1100 | max rel diff. = 0.00973188 [2019-01-24 20:35:51.222] [jointLog] [info] Finished optimizer [2019-01-24 20:35:51.222] [jointLog] [info] writing output [2019-01-24 20:35:51.317] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_44_01/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_44_01/quant.sf /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.gene_trans_map > bleached_44_01/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P11-ACTTGA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P11-ACTTGA-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_44_02 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_44_02 } ### [ threads ] => { 23 } Logs will be written to bleached_44_02/logs [2019-01-24 20:35:52.718] [jointLog] [info] parsing read library format [2019-01-24 20:35:52.718] [jointLog] [info] There is 1 library. [2019-01-24 20:35:52.778] [jointLog] [info] Loading Quasi index [2019-01-24 20:35:52.778] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:35:52.778] [stderrLog] [info] Loading Suffix Array [2019-01-24 20:35:53.032] [stderrLog] [info] Loading Transcript Info [2019-01-24 20:35:53.099] [stderrLog] [info] Loading Rank-Select Bit Array [2019-01-24 20:35:53.125] [stderrLog] [info] There were 49695 set bits in the bit array [2019-01-24 20:35:53.138] [stderrLog] [info] Computing transcript lengths [2019-01-24 20:35:53.138] [stderrLog] [info] Waiting to finish loading hash [2019-01-24 20:35:55.630] [jointLog] [info] done [2019-01-24 20:35:55.630] [jointLog] [info] Index contained 49695 targets [2019-01-24 20:35:55.630] [stderrLog] [info] Done loading index  processed 500001 fragments hits: 515328, hits per frag: 1.19417 processed 1000000 fragments hits: 1031397, hits per frag: 1.16417 processed 1500000 fragments hits: 1548604, hits per frag: 1.07414 processed 2000001 fragments hits: 2067132, hits per frag: 1.04684 processed 2500000 fragments hits: 2582986, hits per frag: 1.05014 processed 3000004 fragments hits: 3101074, hits per frag: 1.05866 processed 3500000 fragments hits: 3616736, hits per frag: 1.05701 processed 4000000 fragments hits: 4133469, hits per frag: 1.04118 processed 4500000 fragments hits: 4648184, hits per frag: 1.04212 processed 5000000 fragments hits: 5164619, hits per frag: 1.05444 processed 5500000 fragments hits: 5683569, hits per frag: 1.04146 processed 6000001 fragments hits: 6200194, hits per frag: 1.0465 processed 6500000 fragments hits: 6715600, hits per frag: 1.04527 processed 7000000 fragments hits: 7232321, hits per frag: 1.05394 processed 7500000 fragments hits: 7745908, hits per frag: 1.03978 processed 8000000 fragments hits: 8259995, hits per frag: 1.04016 processed 8500000 fragments hits: 8772500, hits per frag: 1.03489 processed 9000000 fragments hits: 9286163, hits per frag: 1.03901 processed 9500001 fragments hits: 9800087, hits per frag: 1.03802 processed 10000000 fragments hits: 10312367, hits per frag: 1.0365 processed 10500000 fragments hits: 10826853, hits per frag: 1.0354 processed 11000000 fragments hits: 11342894, hits per frag: 1.03439 processed 11500000 fragments hits: 11858990, hits per frag: 1.03979 processed 12000001 fragments hits: 12374198, hits per frag: 1.04281 processed 12500000 fragments hits: 12889571, hits per frag: 1.04386 processed 13000000 fragments hits: 13407504, hits per frag: 1.03563 processed 13500000 fragments hits: 13924673, hits per frag: 1.03965 processed 14000000 fragments hits: 14440747, hits per frag: 1.03827 processed 14500000 fragments hits: 14955824, hits per frag: 1.03347 processed 15000000 fragments hits: 15470987, hits per frag: 1.0346 processed 15500000 fragments hits: 15988335, hits per frag: 1.03777 processed 16000001 fragments hits: 16504183, hits per frag: 1.03366 processed 16500000 fragments hits: 17020290, hits per frag: 1.03236 processed 17000000 fragments hits: 17535491, hits per frag: 1.03746 processed 17500001 fragments hits: 18052133, hits per frag: 1.03496 processed 18000000 fragments hits: 18564623, hits per frag: 1.03712 processed 19000000 fragments hits: 19593484, hits per frag: 1.03921 processed 19500000 fragments hits: 20107703, hits per frag: 1.03428 processed 20000000 fragments hits: 20620762, hits per frag: 1.03255 processed 20500000 fragments hits: 21135253, hits per frag: 1.03251 processed 21000000 fragments hits: 21650052, hits per frag: 1.03449 processed 21500000 fragments hits: 22164567, hits per frag: 1.0338 [2019-01-24 20:36:46.426] [jointLog] [info] Computed 67767 rich equivalence classes for further processing [2019-01-24 20:36:46.426] [jointLog] [info] Counted 11293046 total reads in the equivalence classes [2019-01-24 20:36:46.434] [jointLog] [warning] 0.0142576% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:36:46.435] [jointLog] [info] Mapping rate = 51.4744% [2019-01-24 20:36:46.435] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:36:46.435] [jointLog] [info] Starting optimizer [2019-01-24 20:36:46.469] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:36:46.471] [jointLog] [info] iteration = 0 | max rel diff. = 181.99 [2019-01-24 20:36:46.603] [jointLog] [info] iteration = 100 | max rel diff. = 0.111053 [2019-01-24 20:36:46.728] [jointLog] [info] iteration = 200 | max rel diff. = 0.0549641 [2019-01-24 20:36:46.853] [jointLog] [info] iteration = 300 | max rel diff. = 0.0384646 [2019-01-24 20:36:46.979] [jointLog] [info] iteration = 400 | max rel diff. = 0.0282863 [2019-01-24 20:36:47.104] [jointLog] [info] iteration = 500 | max rel diff. = 0.0218018 [2019-01-24 20:36:47.230] [jointLog] [info] iteration = 600 | max rel diff. = 0.0220224 [2019-01-24 20:36:47.356] [jointLog] [info] iteration = 700 | max rel diff. = 0.0160771 [2019-01-24 20:36:47.481] [jointLog] [info] iteration = 800 | max rel diff. = 0.0145656 [2019-01-24 20:36:47.608] [jointLog] [info] iteration = 900 | max rel diff. = 0.012139 [2019-01-24 20:36:47.734] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0116756 [2019-01-24 20:36:47.861] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0103384 [2019-01-24 20:36:47.991] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0103384 [2019-01-24 20:36:48.026] [jointLog] [info] iteration = 1228 | max rel diff. = 0.00876464 [2019-01-24 20:36:48.030] [jointLog] [info] Finished optimizer [2019-01-24 20:36:48.030] [jointLog] [info] writing output [2019-01-24 20:36:48.118] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_44_02/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_44_02/quant.sf /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.gene_trans_map > bleached_44_02/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P14-GTGGCC-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P14-GTGGCC-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_44_03 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_44_03 } ### [ threads ] => { 23 } Logs will be written to bleached_44_03/logs [2019-01-24 20:36:49.576] [jointLog] [info] parsing read library format [2019-01-24 20:36:49.576] [jointLog] [info] There is 1 library. [2019-01-24 20:36:49.638] [stderrLog] [info] Loading Suffix Array [2019-01-24 20:36:49.638] [jointLog] [info] Loading Quasi index [2019-01-24 20:36:49.638] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:36:49.881] [stderrLog] [info] Loading Transcript Info [2019-01-24 20:36:49.948] [stderrLog] [info] Loading Rank-Select Bit Array [2019-01-24 20:36:49.974] [stderrLog] [info] There were 49695 set bits in the bit array [2019-01-24 20:36:49.987] [stderrLog] [info] Computing transcript lengths [2019-01-24 20:36:49.988] [stderrLog] [info] Waiting to finish loading hash [2019-01-24 20:36:52.362] [stderrLog] [info] Done loading index [2019-01-24 20:36:52.362] [jointLog] [info] done [2019-01-24 20:36:52.362] [jointLog] [info] Index contained 49695 targets  processed 500000 fragments hits: 513053, hits per frag: 1.19067 processed 1000000 fragments hits: 1025105, hits per frag: 1.13914 processed 1500000 fragments hits: 1536843, hits per frag: 1.09192 processed 2000000 fragments hits: 2051537, hits per frag: 1.03629 processed 2500000 fragments hits: 2564433, hits per frag: 1.06235 processed 3000000 fragments hits: 3079310, hits per frag: 1.04853 processed 3500000 fragments hits: 3591867, hits per frag: 1.03282 processed 4000001 fragments hits: 4106440, hits per frag: 1.04924 processed 4500000 fragments hits: 4619124, hits per frag: 1.05386 processed 5000000 fragments hits: 5132193, hits per frag: 1.03452 processed 5500000 fragments hits: 5647756, hits per frag: 1.03723 processed 6000001 fragments hits: 6162016, hits per frag: 1.03465 processed 6500000 fragments hits: 6676596, hits per frag: 1.04253 processed 7000000 fragments hits: 7188747, hits per frag: 1.03189 processed 7500000 fragments hits: 7702716, hits per frag: 1.02991 processed 8000001 fragments hits: 8215301, hits per frag: 1.04033 processed 8500000 fragments hits: 8727562, hits per frag: 1.03212 processed 9000000 fragments hits: 9239011, hits per frag: 1.03314 processed 9500000 fragments hits: 9753463, hits per frag: 1.03919 processed 10000001 fragments hits: 10264572, hits per frag: 1.0366 processed 10500000 fragments hits: 10776755, hits per frag: 1.03411 processed 11000000 fragments hits: 11288680, hits per frag: 1.03211 processed 11500000 fragments hits: 11802657, hits per frag: 1.033 processed 12000000 fragments hits: 12315798, hits per frag: 1.03197 processed 12500000 fragments hits: 12828305, hits per frag: 1.0293 processed 13000000 fragments hits: 13339907, hits per frag: 1.02966 processed 13500000 fragments hits: 13851787, hits per frag: 1.02881 processed 14000001 fragments hits: 14364621, hits per frag: 1.02919 processed 14500000 fragments hits: 14877979, hits per frag: 1.03002 processed 15000000 fragments hits: 15390545, hits per frag: 1.03478 processed 15500000 fragments hits: 15903848, hits per frag: 1.03082 processed 16000000 fragments hits: 16417003, hits per frag: 1.03241 processed 16500001 fragments hits: 16933030, hits per frag: 1.02933 processed 17000000 fragments hits: 17445880, hits per frag: 1.03375 processed 17500000 fragments hits: 17957429, hits per frag: 1.02946 processed 18000000 fragments hits: 18471826, hits per frag: 1.02943 processed 18500000 fragments hits: 18984510, hits per frag: 1.03038 processed 19000000 fragments hits: 19498679, hits per frag: 1.03491 processed 19500000 fragments hits: 20011544, hits per frag: 1.02782 processed 20000000 fragments hits: 20524944, hits per frag: 1.02927 processed 20500000 fragments hits: 21037824, hits per frag: 1.02995 processed 21000000 fragments hits: 21551865, hits per frag: 1.02777 processed 21500001 fragments hits: 22065726, hits per frag: 1.02792 processed 22000000 fragments hits: 22579804, hits per frag: 1.03098 processed 22500000 fragments hits: 23094168, hits per frag: 1.02784 processed 23000000 fragments hits: 23607603, hits per frag: 1.02689 processed 23500001 fragments hits: 24121576, hits per frag: 1.02951 processed 24000000 fragments hits: 24635511, hits per frag: 1.02762 processed 24500001 fragments hits: 25149304, hits per frag: 1.03035 processed 25000000 fragments hits: 25661966, hits per frag: 1.0276 processed 25500000 fragments hits: 26175653, hits per frag: 1.02803 processed 26000000 fragments hits: 26689218, hits per frag: 1.03063 processed 26500000 fragments hits: 27202643, hits per frag: 1.02813 processed 27000000 fragments hits: 27714625, hits per frag: 1.02939 processed 27500000 fragments hits: 28227081, hits per frag: 1.02845 processed 28000000 fragments hits: 28738642, hits per frag: 1.03186 processed 28500000 fragments hits: 29252603, hits per frag: 1.03225 processed 29000000 fragments hits: 29760314, hits per frag: 1.02914 processed 29500001 fragments hits: 30272160, hits per frag: 1.02919 processed 30000000 fragments hits: 30783652, hits per frag: 1.02914 processed 30500000 fragments hits: 31296515, hits per frag: 1.02924 processed 31000000 fragments hits: 31809957, hits per frag: 1.03092 processed 31500000 fragments hits: 32324065, hits per frag: 1.02716 [2019-01-24 20:38:10.531] [jointLog] [info] Computed 72303 rich equivalence classes for further processing [2019-01-24 20:38:10.531] [jointLog] [info] Counted 15490301 total reads in the equivalence classes [2019-01-24 20:38:10.541] [jointLog] [warning] 0.0123607% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:38:10.541] [jointLog] [info] Mapping rate = 48.9319% [2019-01-24 20:38:10.541] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:38:10.541] [jointLog] [info] Starting optimizer [2019-01-24 20:38:10.586] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:38:10.589] [jointLog] [info] iteration = 0 | max rel diff. = 240.467 [2019-01-24 20:38:10.724] [jointLog] [info] iteration = 100 | max rel diff. = 0.121879 [2019-01-24 20:38:10.858] [jointLog] [info] iteration = 200 | max rel diff. = 0.0554258 [2019-01-24 20:38:10.989] [jointLog] [info] iteration = 300 | max rel diff. = 0.0367977 [2019-01-24 20:38:11.122] [jointLog] [info] iteration = 400 | max rel diff. = 0.0264665 [2019-01-24 20:38:11.256] [jointLog] [info] iteration = 500 | max rel diff. = 0.0232654 [2019-01-24 20:38:11.387] [jointLog] [info] iteration = 600 | max rel diff. = 0.0203682 [2019-01-24 20:38:11.515] [jointLog] [info] iteration = 700 | max rel diff. = 0.0151962 [2019-01-24 20:38:11.643] [jointLog] [info] iteration = 800 | max rel diff. = 0.0132154 [2019-01-24 20:38:11.771] [jointLog] [info] iteration = 900 | max rel diff. = 0.0126242 [2019-01-24 20:38:11.901] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0111944 [2019-01-24 20:38:12.032] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0108682 [2019-01-24 20:38:12.162] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0100707 [2019-01-24 20:38:12.291] [jointLog] [info] iteration = 1300 | max rel diff. = 0.0100707 [2019-01-24 20:38:12.335] [jointLog] [info] iteration = 1335 | max rel diff. = 0.00897824 [2019-01-24 20:38:12.339] [jointLog] [info] Finished optimizer [2019-01-24 20:38:12.339] [jointLog] [info] writing output [2019-01-24 20:38:12.429] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_44_03/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_44_03/quant.sf /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.gene_trans_map > bleached_44_03/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P02-ACAGTG-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P02-ACAGTG-READ2-Sequences.txt.gz_val_2.fq.gz) -o non-bleached_K5_01 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { non-bleached_K5_01 } ### [ threads ] => { 23 } Logs will be written to non-bleached_K5_01/logs [2019-01-24 20:38:14.053] [jointLog] [info] parsing read library format [2019-01-24 20:38:14.053] [jointLog] [info] There is 1 library. [2019-01-24 20:38:14.115] [stderrLog] [info] Loading Suffix Array [2019-01-24 20:38:14.115] [jointLog] [info] Loading Quasi index [2019-01-24 20:38:14.115] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:38:14.389] [stderrLog] [info] Loading Transcript Info [2019-01-24 20:38:14.452] [stderrLog] [info] Loading Rank-Select Bit Array [2019-01-24 20:38:14.478] [stderrLog] [info] There were 49695 set bits in the bit array [2019-01-24 20:38:14.491] [stderrLog] [info] Computing transcript lengths [2019-01-24 20:38:14.491] [stderrLog] [info] Waiting to finish loading hash [2019-01-24 20:38:16.889] [stderrLog] [info] Done loading index [2019-01-24 20:38:16.889] [jointLog] [info] done [2019-01-24 20:38:16.889] [jointLog] [info] Index contained 49695 targets  processed 500000 fragments hits: 526085, hits per frag: 1.30407 processed 1000000 fragments hits: 1053224, hits per frag: 1.11218 processed 1500000 fragments hits: 1578723, hits per frag: 1.09779 processed 2000000 fragments hits: 2107304, hits per frag: 1.06605 processed 2500001 fragments hits: 2635901, hits per frag: 1.07523 processed 3000000 fragments hits: 3164227, hits per frag: 1.06355 processed 3500000 fragments hits: 3692309, hits per frag: 1.07277 processed 4000001 fragments hits: 4218581, hits per frag: 1.07385 processed 4500001 fragments hits: 4746059, hits per frag: 1.06965 processed 5000000 fragments hits: 5273387, hits per frag: 1.06546 processed 5500000 fragments hits: 5799401, hits per frag: 1.06993 processed 6000000 fragments hits: 6325975, hits per frag: 1.06917 processed 6500000 fragments hits: 6853636, hits per frag: 1.06966 processed 7000000 fragments hits: 7379583, hits per frag: 1.06823 processed 7500000 fragments hits: 7906854, hits per frag: 1.06966 processed 8000000 fragments hits: 8434057, hits per frag: 1.05901 processed 8500000 fragments hits: 8962063, hits per frag: 1.06367 processed 9000000 fragments hits: 9490205, hits per frag: 1.07143 processed 9500000 fragments hits: 10015129, hits per frag: 1.06481 processed 10000000 fragments hits: 10544712, hits per frag: 1.06051 processed 10500000 fragments hits: 11070355, hits per frag: 1.06451 processed 11000000 fragments hits: 11598679, hits per frag: 1.06188 processed 11500000 fragments hits: 12126187, hits per frag: 1.05826 processed 12000001 fragments hits: 12654396, hits per frag: 1.0666 processed 12500000 fragments hits: 13181547, hits per frag: 1.05711 processed 13000000 fragments hits: 13708376, hits per frag: 1.06055 processed 13500000 fragments hits: 14234782, hits per frag: 1.06207 processed 14000000 fragments hits: 14761697, hits per frag: 1.06019 processed 14500000 fragments hits: 15288389, hits per frag: 1.06194 processed 15000000 fragments hits: 15813818, hits per frag: 1.06287 processed 15500000 fragments hits: 16341189, hits per frag: 1.05934 processed 16000001 fragments hits: 16871153, hits per frag: 1.06025 processed 16500000 fragments hits: 17399177, hits per frag: 1.05684 processed 17000000 fragments hits: 17926411, hits per frag: 1.05674 processed 17500001 fragments hits: 18452547, hits per frag: 1.05551 processed 18000000 fragments hits: 18979066, hits per frag: 1.05654 processed 18500001 fragments hits: 19506223, hits per frag: 1.05508 processed 19000000 fragments hits: 20034475, hits per frag: 1.05915 processed 19500000 fragments hits: 20563865, hits per frag: 1.05709 processed 20000000 fragments hits: 21091989, hits per frag: 1.05689 processed 20500000 fragments hits: 21618879, hits per frag: 1.05809 processed 21000000 fragments hits: 22146177, hits per frag: 1.05645 processed 21500000 fragments hits: 22671990, hits per frag: 1.05986 processed 22000000 fragments hits: 23198376, hits per frag: 1.0581 processed 22500000 fragments hits: 23726310, hits per frag: 1.05759 processed 23000000 fragments hits: 24255920, hits per frag: 1.05967 processed 23500000 fragments hits: 24780941, hits per frag: 1.06096 [2019-01-24 20:39:13.242] [jointLog] [info] Computed 62169 rich equivalence classes for further processing [2019-01-24 20:39:13.242] [jointLog] [info] Counted 12605879 total reads in the equivalence classes [2019-01-24 20:39:13.251] [jointLog] [warning] 0.0207925% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:39:13.251] [jointLog] [info] Mapping rate = 52.823% [2019-01-24 20:39:13.251] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:39:13.251] [jointLog] [info] Starting optimizer [2019-01-24 20:39:13.291] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:39:13.292] [jointLog] [info] iteration = 0 | max rel diff. = 200.725 [2019-01-24 20:39:13.415] [jointLog] [info] iteration = 100 | max rel diff. = 0.116693 [2019-01-24 20:39:13.536] [jointLog] [info] iteration = 200 | max rel diff. = 0.0544396 [2019-01-24 20:39:13.657] [jointLog] [info] iteration = 300 | max rel diff. = 0.0363253 [2019-01-24 20:39:13.781] [jointLog] [info] iteration = 400 | max rel diff. = 0.0283504 [2019-01-24 20:39:13.907] [jointLog] [info] iteration = 500 | max rel diff. = 0.0225882 [2019-01-24 20:39:14.030] [jointLog] [info] iteration = 600 | max rel diff. = 0.0197365 [2019-01-24 20:39:14.153] [jointLog] [info] iteration = 700 | max rel diff. = 0.0166923 [2019-01-24 20:39:14.276] [jointLog] [info] iteration = 800 | max rel diff. = 0.0145051 [2019-01-24 20:39:14.399] [jointLog] [info] iteration = 900 | max rel diff. = 0.0126437 [2019-01-24 20:39:14.523] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0122782 [2019-01-24 20:39:14.647] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0122782 [2019-01-24 20:39:14.771] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0103527 [2019-01-24 20:39:14.788] [jointLog] [info] iteration = 1214 | max rel diff. = 0.00901315 [2019-01-24 20:39:14.792] [jointLog] [info] Finished optimizer [2019-01-24 20:39:14.792] [jointLog] [info] writing output [2019-01-24 20:39:14.883] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: non-bleached_K5_01/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_K5_01/quant.sf /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.gene_trans_map > non-bleached_K5_01/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P10-TAGCTT-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P10-TAGCTT-READ2-Sequences.txt.gz_val_2.fq.gz) -o non-bleached_K5_02 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { non-bleached_K5_02 } ### [ threads ] => { 23 } Logs will be written to non-bleached_K5_02/logs [2019-01-24 20:39:16.408] [jointLog] [info] parsing read library format [2019-01-24 20:39:16.408] [jointLog] [info] There is 1 library. [2019-01-24 20:39:16.468] [jointLog] [info] Loading Quasi index [2019-01-24 20:39:16.468] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:39:16.468] [stderrLog] [info] Loading Suffix Array [2019-01-24 20:39:16.723] [stderrLog] [info] Loading Transcript Info [2019-01-24 20:39:16.793] [stderrLog] [info] Loading Rank-Select Bit Array [2019-01-24 20:39:16.818] [stderrLog] [info] There were 49695 set bits in the bit array [2019-01-24 20:39:16.832] [stderrLog] [info] Computing transcript lengths [2019-01-24 20:39:16.832] [stderrLog] [info] Waiting to finish loading hash [2019-01-24 20:39:19.196] [jointLog] [info] done [2019-01-24 20:39:19.196] [jointLog] [info] Index contained 49695 targets [2019-01-24 20:39:19.196] [stderrLog] [info] Done loading index  processed 500000 fragments hits: 485933, hits per frag: 1.13788 processed 1000000 fragments hits: 972496, hits per frag: 1.09013 processed 1500000 fragments hits: 1460404, hits per frag: 0.990284 processed 2000000 fragments hits: 1946490, hits per frag: 1.01307 processed 2500000 fragments hits: 2435663, hits per frag: 1.00501 processed 3000000 fragments hits: 2921249, hits per frag: 0.984164 processed 3500000 fragments hits: 3412661, hits per frag: 0.989288 processed 4000000 fragments hits: 3900467, hits per frag: 0.978001 processed 4500000 fragments hits: 4389069, hits per frag: 0.982397 processed 5000000 fragments hits: 4875708, hits per frag: 0.987308 processed 5500000 fragments hits: 5364272, hits per frag: 0.981273 processed 6000000 fragments hits: 5853202, hits per frag: 0.984106 processed 7000000 fragments hits: 6828605, hits per frag: 0.990469 processed 7500000 fragments hits: 7317064, hits per frag: 0.986749 processed 8000001 fragments hits: 7806176, hits per frag: 0.977059 processed 8500000 fragments hits: 8291451, hits per frag: 0.985178 processed 9000000 fragments hits: 8776574, hits per frag: 0.98638 processed 9500001 fragments hits: 9263944, hits per frag: 0.983275 processed 10000000 fragments hits: 9748622, hits per frag: 0.975656 processed 10500000 fragments hits: 10236277, hits per frag: 0.977382 processed 11000000 fragments hits: 10723475, hits per frag: 0.979773 processed 11500001 fragments hits: 11209855, hits per frag: 0.981603 processed 12000000 fragments hits: 11694918, hits per frag: 0.975539 processed 12500000 fragments hits: 12181784, hits per frag: 0.981321 processed 13000000 fragments hits: 12668206, hits per frag: 0.982521 processed 13500000 fragments hits: 13152676, hits per frag: 0.980627 processed 14000000 fragments hits: 13637792, hits per frag: 0.977236 processed 14500001 fragments hits: 14125569, hits per frag: 0.979077 processed 15000000 fragments hits: 14612449, hits per frag: 0.97826 processed 15500000 fragments hits: 15101195, hits per frag: 0.977301 processed 16000000 fragments hits: 15588073, hits per frag: 0.980307 processed 16500000 fragments hits: 16074529, hits per frag: 0.980255 processed 17000000 fragments hits: 16564710, hits per frag: 0.979733 processed 17500000 fragments hits: 17052905, hits per frag: 0.975635 processed 18000000 fragments hits: 17538645, hits per frag: 0.977653 processed 18500000 fragments hits: 18025153, hits per frag: 0.979747 processed 19000000 fragments hits: 18511951, hits per frag: 0.97498 processed 19500001 fragments hits: 18999174, hits per frag: 0.977436 processed 20000000 fragments hits: 19485366, hits per frag: 0.977754 processed 20500000 fragments hits: 19973076, hits per frag: 0.976904 processed 21000000 fragments hits: 20460538, hits per frag: 0.97602 processed 21500001 fragments hits: 20950102, hits per frag: 0.97614 processed 22000001 fragments hits: 21438593, hits per frag: 0.978408 processed 22500000 fragments hits: 21926937, hits per frag: 0.975197 processed 23000000 fragments hits: 22414257, hits per frag: 0.979335 processed 23500000 fragments hits: 22900933, hits per frag: 0.976038 processed 24000000 fragments hits: 23389728, hits per frag: 0.976865 processed 24500000 fragments hits: 23878568, hits per frag: 0.978482 processed 25000000 fragments hits: 24365918, hits per frag: 0.978581 processed 25500001 fragments hits: 24854436, hits per frag: 0.975344 processed 26000000 fragments hits: 25343709, hits per frag: 0.975738 processed 26500000 fragments hits: 25827970, hits per frag: 0.977047 processed 27000001 fragments hits: 26313709, hits per frag: 0.975491 processed 27500000 fragments hits: 26800306, hits per frag: 0.97788 processed 28000001 fragments hits: 27288184, hits per frag: 0.975983 processed 28500000 fragments hits: 27773123, hits per frag: 0.977078 processed 29000000 fragments hits: 28258271, hits per frag: 0.97543 processed 29500000 fragments hits: 28748249, hits per frag: 0.976963 processed 30000001 fragments hits: 29235099, hits per frag: 0.977175 processed 30500000 fragments hits: 29722864, hits per frag: 0.979208 processed 31000000 fragments hits: 30210886, hits per frag: 0.976557 processed 31500001 fragments hits: 30698844, hits per frag: 0.974861 processed 32000000 fragments hits: 31185387, hits per frag: 0.974869 processed 32500000 fragments hits: 31671100, hits per frag: 0.974605 processed 33000000 fragments hits: 32158824, hits per frag: 0.975309 [2019-01-24 20:40:37.157] [jointLog] [info] Computed 73055 rich equivalence classes for further processing [2019-01-24 20:40:37.157] [jointLog] [info] Counted 15867401 total reads in the equivalence classes [2019-01-24 20:40:37.167] [jointLog] [warning] 0.0111532% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:40:37.167] [jointLog] [info] Mapping rate = 47.9991% [2019-01-24 20:40:37.167] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:40:37.167] [jointLog] [info] Starting optimizer [2019-01-24 20:40:37.207] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:40:37.209] [jointLog] [info] iteration = 0 | max rel diff. = 236.959 [2019-01-24 20:40:37.343] [jointLog] [info] iteration = 100 | max rel diff. = 0.111357 [2019-01-24 20:40:37.474] [jointLog] [info] iteration = 200 | max rel diff. = 0.0601673 [2019-01-24 20:40:37.605] [jointLog] [info] iteration = 300 | max rel diff. = 0.0399289 [2019-01-24 20:40:37.739] [jointLog] [info] iteration = 400 | max rel diff. = 0.0272458 [2019-01-24 20:40:37.872] [jointLog] [info] iteration = 500 | max rel diff. = 0.0228421 [2019-01-24 20:40:38.006] [jointLog] [info] iteration = 600 | max rel diff. = 0.0184071 [2019-01-24 20:40:38.139] [jointLog] [info] iteration = 700 | max rel diff. = 0.0173163 [2019-01-24 20:40:38.273] [jointLog] [info] iteration = 800 | max rel diff. = 0.0146934 [2019-01-24 20:40:38.406] [jointLog] [info] iteration = 900 | max rel diff. = 0.0132414 [2019-01-24 20:40:38.540] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0119551 [2019-01-24 20:40:38.674] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0106357 [2019-01-24 20:40:38.810] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0106357 [2019-01-24 20:40:38.852] [jointLog] [info] iteration = 1232 | max rel diff. = 0.00903994 [2019-01-24 20:40:38.857] [jointLog] [info] Finished optimizer [2019-01-24 20:40:38.857] [jointLog] [info] writing output [2019-01-24 20:40:38.952] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: non-bleached_K5_02/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_K5_02/quant.sf /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.gene_trans_map > non-bleached_K5_02/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P15-GTTTCG-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P15-GTTTCG-READ2-Sequences.txt.gz_val_2.fq.gz) -o non-bleached_K5_03 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { non-bleached_K5_03 } ### [ threads ] => { 23 } Logs will be written to non-bleached_K5_03/logs [2019-01-24 20:40:40.281] [jointLog] [info] parsing read library format [2019-01-24 20:40:40.281] [jointLog] [info] There is 1 library. [2019-01-24 20:40:40.343] [stderrLog] [info] Loading Suffix Array [2019-01-24 20:40:40.343] [jointLog] [info] Loading Quasi index [2019-01-24 20:40:40.343] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:40:40.613] [stderrLog] [info] Loading Transcript Info [2019-01-24 20:40:40.675] [stderrLog] [info] Loading Rank-Select Bit Array [2019-01-24 20:40:40.700] [stderrLog] [info] There were 49695 set bits in the bit array [2019-01-24 20:40:40.714] [stderrLog] [info] Computing transcript lengths [2019-01-24 20:40:40.714] [stderrLog] [info] Waiting to finish loading hash [2019-01-24 20:40:43.346] [stderrLog] [info] Done loading index [2019-01-24 20:40:43.347] [jointLog] [info] done [2019-01-24 20:40:43.347] [jointLog] [info] Index contained 49695 targets  processed 500000 fragments hits: 506123, hits per frag: 1.02558 processed 1000001 fragments hits: 1011409, hits per frag: 1.13216 processed 1500000 fragments hits: 1517939, hits per frag: 1.09485 processed 2000001 fragments hits: 2026949, hits per frag: 1.05247 processed 2500000 fragments hits: 2533024, hits per frag: 1.03557 processed 3000001 fragments hits: 3040091, hits per frag: 1.02569 processed 3500000 fragments hits: 3547167, hits per frag: 1.02465 processed 4000000 fragments hits: 4055057, hits per frag: 1.03736 processed 4500000 fragments hits: 4562112, hits per frag: 1.03751 processed 5000000 fragments hits: 5068748, hits per frag: 1.02295 processed 5500000 fragments hits: 5574705, hits per frag: 1.02932 processed 6000000 fragments hits: 6079021, hits per frag: 1.02206 processed 6500001 fragments hits: 6585451, hits per frag: 1.02946 processed 7000000 fragments hits: 7091115, hits per frag: 1.01572 processed 7500000 fragments hits: 7596115, hits per frag: 1.02731 processed 8000000 fragments hits: 8103697, hits per frag: 1.03061 processed 8500000 fragments hits: 8611397, hits per frag: 1.02273 processed 9000000 fragments hits: 9118450, hits per frag: 1.02337 processed 9500000 fragments hits: 9627472, hits per frag: 1.02212 processed 10000000 fragments hits: 10134388, hits per frag: 1.02365 processed 10500000 fragments hits: 10642796, hits per frag: 1.02218 processed 11000001 fragments hits: 11150462, hits per frag: 1.01907 processed 11500000 fragments hits: 11657371, hits per frag: 1.02114 processed 12000000 fragments hits: 12167843, hits per frag: 1.02134 processed 12500000 fragments hits: 12673921, hits per frag: 1.01873 processed 13000000 fragments hits: 13182057, hits per frag: 1.01509 processed 13500000 fragments hits: 13689222, hits per frag: 1.01571 processed 14000000 fragments hits: 14196863, hits per frag: 1.015 processed 14500002 fragments hits: 14704379, hits per frag: 1.01711 processed 15000001 fragments hits: 15211419, hits per frag: 1.02082 processed 15500001 fragments hits: 15717702, hits per frag: 1.01482 processed 16000000 fragments hits: 16222170, hits per frag: 1.0185 processed 16500000 fragments hits: 16729465, hits per frag: 1.02032 processed 17000001 fragments hits: 17238456, hits per frag: 1.01766 processed 17500000 fragments hits: 17745742, hits per frag: 1.01494 processed 18000001 fragments hits: 18253042, hits per frag: 1.01642 processed 18500000 fragments hits: 18760103, hits per frag: 1.01531 processed 19000000 fragments hits: 19267212, hits per frag: 1.01769 processed 19500000 fragments hits: 19774530, hits per frag: 1.01999 processed 20000001 fragments hits: 20281328, hits per frag: 1.01926 processed 20500000 fragments hits: 20786674, hits per frag: 1.01823 processed 21000000 fragments hits: 21293353, hits per frag: 1.01845 processed 21500000 fragments hits: 21798219, hits per frag: 1.02004 processed 22000000 fragments hits: 22304410, hits per frag: 1.01647 processed 22500000 fragments hits: 22810742, hits per frag: 1.0171 processed 23000001 fragments hits: 23317829, hits per frag: 1.02078 processed 23500001 fragments hits: 23822721, hits per frag: 1.01521 processed 24000000 fragments hits: 24329113, hits per frag: 1.01515 processed 24500000 fragments hits: 24835721, hits per frag: 1.01533 processed 25000001 fragments hits: 25341155, hits per frag: 1.01725 processed 25500000 fragments hits: 25845099, hits per frag: 1.01576 processed 26000001 fragments hits: 26351226, hits per frag: 1.01765 processed 26500001 fragments hits: 26860451, hits per frag: 1.0166 processed 27000000 fragments hits: 27367230, hits per frag: 1.01547 processed 27500001 fragments hits: 27875369, hits per frag: 1.01635 processed 28000000 fragments hits: 28384737, hits per frag: 1.01702 processed 28500001 fragments hits: 28893111, hits per frag: 1.01696 processed 29000000 fragments hits: 29399322, hits per frag: 1.01848 processed 29500000 fragments hits: 29906336, hits per frag: 1.01437 processed 30000000 fragments hits: 30413547, hits per frag: 1.01651 processed 30500001 fragments hits: 30919840, hits per frag: 1.01585 processed 31000000 fragments hits: 31427913, hits per frag: 1.0166 processed 31500000 fragments hits: 31933925, hits per frag: 1.01567 processed 32000000 fragments hits: 32440878, hits per frag: 1.01601 processed 32500000 fragments hits: 32950315, hits per frag: 1.01615 processed 33000000 fragments hits: 33459002, hits per frag: 1.01687 processed 33500000 fragments hits: 33966122, hits per frag: 1.01579 processed 34000000 fragments hits: 34471977, hits per frag: 1.01693 processed 34500000 fragments hits: 34977623, hits per frag: 1.01666 [2019-01-24 20:42:04.903] [jointLog] [info] Computed 68550 rich equivalence classes for further processing [2019-01-24 20:42:04.903] [jointLog] [info] Counted 17762650 total reads in the equivalence classes [2019-01-24 20:42:04.913] [jointLog] [warning] 0.0188954% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:42:04.913] [jointLog] [info] Mapping rate = 51.4379% [2019-01-24 20:42:04.913] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:42:04.913] [jointLog] [info] Starting optimizer [2019-01-24 20:42:04.952] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:42:04.953] [jointLog] [info] iteration = 0 | max rel diff. = 244.632 [2019-01-24 20:42:05.084] [jointLog] [info] iteration = 100 | max rel diff. = 0.112384 [2019-01-24 20:42:05.214] [jointLog] [info] iteration = 200 | max rel diff. = 0.05385 [2019-01-24 20:42:05.346] [jointLog] [info] iteration = 300 | max rel diff. = 0.0394625 [2019-01-24 20:42:05.478] [jointLog] [info] iteration = 400 | max rel diff. = 0.0283208 [2019-01-24 20:42:05.610] [jointLog] [info] iteration = 500 | max rel diff. = 0.0226103 [2019-01-24 20:42:05.740] [jointLog] [info] iteration = 600 | max rel diff. = 0.0188708 [2019-01-24 20:42:05.870] [jointLog] [info] iteration = 700 | max rel diff. = 0.018486 [2019-01-24 20:42:06.003] [jointLog] [info] iteration = 800 | max rel diff. = 0.0151063 [2019-01-24 20:42:06.135] [jointLog] [info] iteration = 900 | max rel diff. = 0.0134778 [2019-01-24 20:42:06.268] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0117462 [2019-01-24 20:42:06.400] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0107751 [2019-01-24 20:42:06.459] [jointLog] [info] iteration = 1145 | max rel diff. = 0.00949558 [2019-01-24 20:42:06.464] [jointLog] [info] Finished optimizer [2019-01-24 20:42:06.464] [jointLog] [info] writing output [2019-01-24 20:42:06.559] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: non-bleached_K5_03/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_K5_03/quant.sf /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.gene_trans_map > non-bleached_K5_03/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P04-GTCCGC-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P04-GTCCGC-READ2-Sequences.txt.gz_val_2.fq.gz) -o non-bleached_44_01 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { non-bleached_44_01 } ### [ threads ] => { 23 } Logs will be written to non-bleached_44_01/logs [2019-01-24 20:42:07.963] [jointLog] [info] parsing read library format [2019-01-24 20:42:07.963] [jointLog] [info] There is 1 library. [2019-01-24 20:42:08.024] [stderrLog] [info] Loading Suffix Array [2019-01-24 20:42:08.024] [jointLog] [info] Loading Quasi index [2019-01-24 20:42:08.024] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:42:08.301] [stderrLog] [info] Loading Transcript Info [2019-01-24 20:42:08.363] [stderrLog] [info] Loading Rank-Select Bit Array [2019-01-24 20:42:08.389] [stderrLog] [info] There were 49695 set bits in the bit array [2019-01-24 20:42:08.402] [stderrLog] [info] Computing transcript lengths [2019-01-24 20:42:08.402] [stderrLog] [info] Waiting to finish loading hash [2019-01-24 20:42:10.751] [stderrLog] [info] Done loading index [2019-01-24 20:42:10.751] [jointLog] [info] done [2019-01-24 20:42:10.751] [jointLog] [info] Index contained 49695 targets  processed 500000 fragments hits: 513823, hits per frag: 1.35768 processed 1000000 fragments hits: 1027596, hits per frag: 1.05435 processed 1500002 fragments hits: 1543127, hits per frag: 1.07365 processed 2000000 fragments hits: 2058999, hits per frag: 1.09412 processed 2500001 fragments hits: 2573065, hits per frag: 1.05207 processed 3000002 fragments hits: 3088579, hits per frag: 1.04361 processed 3500000 fragments hits: 3600359, hits per frag: 1.05107 processed 4000000 fragments hits: 4115793, hits per frag: 1.05509 processed 4500000 fragments hits: 4628318, hits per frag: 1.03435 processed 5000001 fragments hits: 5141745, hits per frag: 1.03944 processed 5500000 fragments hits: 5655809, hits per frag: 1.06333 processed 6000000 fragments hits: 6170781, hits per frag: 1.03428 processed 6500000 fragments hits: 6685510, hits per frag: 1.04309 processed 7000000 fragments hits: 7200032, hits per frag: 1.04662 processed 7500000 fragments hits: 7717477, hits per frag: 1.04007 processed 8000001 fragments hits: 8232880, hits per frag: 1.03346 processed 8500001 fragments hits: 8749763, hits per frag: 1.03375 processed 9000000 fragments hits: 9263714, hits per frag: 1.04305 processed 9500000 fragments hits: 9779743, hits per frag: 1.03383 processed 10000000 fragments hits: 10292917, hits per frag: 1.04593 processed 10500000 fragments hits: 10806156, hits per frag: 1.03265 processed 11000000 fragments hits: 11321966, hits per frag: 1.03474 processed 11500000 fragments hits: 11835130, hits per frag: 1.03178 processed 12000001 fragments hits: 12349415, hits per frag: 1.03772 processed 12500000 fragments hits: 12863597, hits per frag: 1.03022 processed 13000000 fragments hits: 13376526, hits per frag: 1.0305 processed 13500000 fragments hits: 13889215, hits per frag: 1.03437 processed 14000001 fragments hits: 14402779, hits per frag: 1.03445 processed 14500000 fragments hits: 14917495, hits per frag: 1.031 processed 15000000 fragments hits: 15430796, hits per frag: 1.03352 processed 15500000 fragments hits: 15945304, hits per frag: 1.03406 processed 16000000 fragments hits: 16455986, hits per frag: 1.03105 processed 16500000 fragments hits: 16967788, hits per frag: 1.03156 processed 17000000 fragments hits: 17481896, hits per frag: 1.03319 processed 17500000 fragments hits: 17996518, hits per frag: 1.03334 processed 18000000 fragments hits: 18509066, hits per frag: 1.03317 processed 18500000 fragments hits: 19022243, hits per frag: 1.03318 processed 19000000 fragments hits: 19537957, hits per frag: 1.03207 processed 19500000 fragments hits: 20052473, hits per frag: 1.03198 processed 20000000 fragments hits: 20568570, hits per frag: 1.03191 processed 20500000 fragments hits: 21082197, hits per frag: 1.03574 processed 21000001 fragments hits: 21597342, hits per frag: 1.0296 processed 21500000 fragments hits: 22113307, hits per frag: 1.03212 processed 22000000 fragments hits: 22630377, hits per frag: 1.03809 [2019-01-24 20:43:04.582] [jointLog] [info] Computed 65318 rich equivalence classes for further processing [2019-01-24 20:43:04.582] [jointLog] [info] Counted 11317076 total reads in the equivalence classes [2019-01-24 20:43:04.590] [jointLog] [warning] 0.0315555% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:43:04.591] [jointLog] [info] Mapping rate = 50.3052% [2019-01-24 20:43:04.591] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:43:04.591] [jointLog] [info] Starting optimizer [2019-01-24 20:43:04.628] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:43:04.629] [jointLog] [info] iteration = 0 | max rel diff. = 197.278 [2019-01-24 20:43:04.753] [jointLog] [info] iteration = 100 | max rel diff. = 0.111824 [2019-01-24 20:43:04.876] [jointLog] [info] iteration = 200 | max rel diff. = 0.0552807 [2019-01-24 20:43:04.999] [jointLog] [info] iteration = 300 | max rel diff. = 0.0417485 [2019-01-24 20:43:05.125] [jointLog] [info] iteration = 400 | max rel diff. = 0.0278165 [2019-01-24 20:43:05.250] [jointLog] [info] iteration = 500 | max rel diff. = 0.021356 [2019-01-24 20:43:05.378] [jointLog] [info] iteration = 600 | max rel diff. = 0.0192814 [2019-01-24 20:43:05.504] [jointLog] [info] iteration = 700 | max rel diff. = 0.015984 [2019-01-24 20:43:05.630] [jointLog] [info] iteration = 800 | max rel diff. = 0.0140516 [2019-01-24 20:43:05.755] [jointLog] [info] iteration = 900 | max rel diff. = 0.0126681 [2019-01-24 20:43:05.882] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0110663 [2019-01-24 20:43:06.010] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0107412 [2019-01-24 20:43:06.138] [jointLog] [info] iteration = 1200 | max rel diff. = 0.010121 [2019-01-24 20:43:06.144] [jointLog] [info] iteration = 1206 | max rel diff. = 0.00938457 [2019-01-24 20:43:06.149] [jointLog] [info] Finished optimizer [2019-01-24 20:43:06.149] [jointLog] [info] writing output [2019-01-24 20:43:06.244] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: non-bleached_44_01/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_44_01/quant.sf /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.gene_trans_map > non-bleached_44_01/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P05-GAGTGG-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P05-GAGTGG-READ2-Sequences.txt.gz_val_2.fq.gz) -o non-bleached_44_02 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { non-bleached_44_02 } ### [ threads ] => { 23 } Logs will be written to non-bleached_44_02/logs [2019-01-24 20:43:07.633] [jointLog] [info] parsing read library format [2019-01-24 20:43:07.633] [jointLog] [info] There is 1 library. [2019-01-24 20:43:07.694] [stderrLog] [info] Loading Suffix Array [2019-01-24 20:43:07.694] [jointLog] [info] Loading Quasi index [2019-01-24 20:43:07.694] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:43:07.944] [stderrLog] [info] Loading Transcript Info [2019-01-24 20:43:08.011] [stderrLog] [info] Loading Rank-Select Bit Array [2019-01-24 20:43:08.036] [stderrLog] [info] There were 49695 set bits in the bit array [2019-01-24 20:43:08.050] [stderrLog] [info] Computing transcript lengths [2019-01-24 20:43:08.050] [stderrLog] [info] Waiting to finish loading hash [2019-01-24 20:43:10.518] [jointLog] [info] done [2019-01-24 20:43:10.518] [jointLog] [info] Index contained 49695 targets [2019-01-24 20:43:10.518] [stderrLog] [info] Done loading index  processed 500000 fragments hits: 534536, hits per frag: 1.45284 processed 1000000 fragments hits: 1066726, hits per frag: 1.09588 processed 1500000 fragments hits: 1600018, hits per frag: 1.11501 processed 2000000 fragments hits: 2134023, hits per frag: 1.13032 processed 2500000 fragments hits: 2668269, hits per frag: 1.09777 processed 3000000 fragments hits: 3198717, hits per frag: 1.09428 processed 3500001 fragments hits: 3731655, hits per frag: 1.07506 processed 4000000 fragments hits: 4264114, hits per frag: 1.09412 processed 4500000 fragments hits: 4796409, hits per frag: 1.08156 processed 5000000 fragments hits: 5330176, hits per frag: 1.08777 processed 5500000 fragments hits: 5861145, hits per frag: 1.08519 processed 6000001 fragments hits: 6393321, hits per frag: 1.07838 processed 6500000 fragments hits: 6926100, hits per frag: 1.07768 processed 7000001 fragments hits: 7459096, hits per frag: 1.07164 processed 7500000 fragments hits: 7990769, hits per frag: 1.07518 processed 8000000 fragments hits: 8525522, hits per frag: 1.07392 processed 8500000 fragments hits: 9059102, hits per frag: 1.07417 processed 9000000 fragments hits: 9592042, hits per frag: 1.06732 processed 9500001 fragments hits: 10125349, hits per frag: 1.07474 processed 10000000 fragments hits: 10659290, hits per frag: 1.0703 processed 10500000 fragments hits: 11193186, hits per frag: 1.08071 processed 11000000 fragments hits: 11727761, hits per frag: 1.07764 processed 11500000 fragments hits: 12260924, hits per frag: 1.07062 processed 12000000 fragments hits: 12792170, hits per frag: 1.07681 processed 12500000 fragments hits: 13326165, hits per frag: 1.06948 processed 13000000 fragments hits: 13860760, hits per frag: 1.06999 processed 13500000 fragments hits: 14394520, hits per frag: 1.07617 processed 14000001 fragments hits: 14926257, hits per frag: 1.06945 processed 14500000 fragments hits: 15458760, hits per frag: 1.07135 processed 15000000 fragments hits: 15992175, hits per frag: 1.07089 processed 15500000 fragments hits: 16524752, hits per frag: 1.06909 processed 16000000 fragments hits: 17056770, hits per frag: 1.07382 processed 16500000 fragments hits: 17589329, hits per frag: 1.07101 processed 17000000 fragments hits: 18120935, hits per frag: 1.06828 processed 17500000 fragments hits: 18652268, hits per frag: 1.06689 processed 18000000 fragments hits: 19187272, hits per frag: 1.07364 processed 18500000 fragments hits: 19719493, hits per frag: 1.06938 processed 19000001 fragments hits: 20252181, hits per frag: 1.07202 processed 19500001 fragments hits: 20782875, hits per frag: 1.06828 processed 20000000 fragments hits: 21316231, hits per frag: 1.06954 processed 20500000 fragments hits: 21849861, hits per frag: 1.06725 processed 21000000 fragments hits: 22384808, hits per frag: 1.07052 processed 21500001 fragments hits: 22917557, hits per frag: 1.06831 processed 22000000 fragments hits: 23453811, hits per frag: 1.07021 processed 22500001 fragments hits: 23988164, hits per frag: 1.06967 processed 23000000 fragments hits: 24523646, hits per frag: 1.06731 processed 23500000 fragments hits: 25056805, hits per frag: 1.07017 processed 24000000 fragments hits: 25588521, hits per frag: 1.06885 processed 24500000 fragments hits: 26122209, hits per frag: 1.06794 processed 25000000 fragments hits: 26657742, hits per frag: 1.06728 processed 25500000 fragments hits: 27190394, hits per frag: 1.06984 processed 26000000 fragments hits: 27722031, hits per frag: 1.06827 [2019-01-24 20:44:12.119] [jointLog] [info] Computed 66512 rich equivalence classes for further processing [2019-01-24 20:44:12.119] [jointLog] [info] Counted 13487415 total reads in the equivalence classes [2019-01-24 20:44:12.130] [jointLog] [warning] 0.047308% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:44:12.130] [jointLog] [info] Mapping rate = 51.6943% [2019-01-24 20:44:12.130] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:44:12.130] [jointLog] [info] Starting optimizer [2019-01-24 20:44:12.230] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:44:12.231] [jointLog] [info] iteration = 0 | max rel diff. = 208.972 [2019-01-24 20:44:12.362] [jointLog] [info] iteration = 100 | max rel diff. = 0.115565 [2019-01-24 20:44:12.493] [jointLog] [info] iteration = 200 | max rel diff. = 0.0546013 [2019-01-24 20:44:12.622] [jointLog] [info] iteration = 300 | max rel diff. = 0.0373472 [2019-01-24 20:44:12.751] [jointLog] [info] iteration = 400 | max rel diff. = 0.029866 [2019-01-24 20:44:12.880] [jointLog] [info] iteration = 500 | max rel diff. = 0.0223884 [2019-01-24 20:44:13.009] [jointLog] [info] iteration = 600 | max rel diff. = 0.0182067 [2019-01-24 20:44:13.138] [jointLog] [info] iteration = 700 | max rel diff. = 0.0174467 [2019-01-24 20:44:13.267] [jointLog] [info] iteration = 800 | max rel diff. = 0.0143655 [2019-01-24 20:44:13.396] [jointLog] [info] iteration = 900 | max rel diff. = 0.0142059 [2019-01-24 20:44:13.526] [jointLog] [info] iteration = 1000 | max rel diff. = 0.011011 [2019-01-24 20:44:13.655] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0101312 [2019-01-24 20:44:13.785] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0101312 [2019-01-24 20:44:13.795] [jointLog] [info] iteration = 1209 | max rel diff. = 0.00993983 [2019-01-24 20:44:13.801] [jointLog] [info] Finished optimizer [2019-01-24 20:44:13.801] [jointLog] [info] writing output [2019-01-24 20:44:13.890] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: non-bleached_44_02/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_44_02/quant.sf /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.gene_trans_map > non-bleached_44_02/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P12-TGACCA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P12-TGACCA-READ2-Sequences.txt.gz_val_2.fq.gz) -o non-bleached_44_03 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { non-bleached_44_03 } ### [ threads ] => { 23 } Logs will be written to non-bleached_44_03/logs [2019-01-24 20:44:15.323] [jointLog] [info] parsing read library format [2019-01-24 20:44:15.323] [jointLog] [info] There is 1 library. [2019-01-24 20:44:15.384] [stderrLog] [info] Loading Suffix Array [2019-01-24 20:44:15.384] [jointLog] [info] Loading Quasi index [2019-01-24 20:44:15.384] [jointLog] [info] Loading 32-bit quasi index [2019-01-24 20:44:15.629] [stderrLog] [info] Loading Transcript Info [2019-01-24 20:44:15.695] [stderrLog] [info] Loading Rank-Select Bit Array [2019-01-24 20:44:15.721] [stderrLog] [info] There were 49695 set bits in the bit array [2019-01-24 20:44:15.734] [stderrLog] [info] Computing transcript lengths [2019-01-24 20:44:15.734] [stderrLog] [info] Waiting to finish loading hash [2019-01-24 20:44:18.240] [stderrLog] [info] Done loading index [2019-01-24 20:44:18.241] [jointLog] [info] done [2019-01-24 20:44:18.241] [jointLog] [info] Index contained 49695 targets  processed 500000 fragments hits: 506547, hits per frag: 1.15448 processed 1000002 fragments hits: 1010714, hits per frag: 1.06942 processed 1500000 fragments hits: 1516764, hits per frag: 1.0258 processed 2000000 fragments hits: 2019654, hits per frag: 1.05173 processed 2500000 fragments hits: 2523725, hits per frag: 1.0387 processed 3000000 fragments hits: 3026976, hits per frag: 1.04978 processed 3500001 fragments hits: 3531930, hits per frag: 1.02375 processed 4000000 fragments hits: 4036561, hits per frag: 1.02716 processed 4500000 fragments hits: 4543021, hits per frag: 1.03052 processed 5000000 fragments hits: 5047306, hits per frag: 1.02003 processed 5500000 fragments hits: 5553438, hits per frag: 1.02078 processed 6000001 fragments hits: 6061063, hits per frag: 1.02424 processed 6500000 fragments hits: 6565045, hits per frag: 1.01164 processed 7000000 fragments hits: 7067816, hits per frag: 1.02479 processed 7500000 fragments hits: 7574397, hits per frag: 1.02816 processed 8000000 fragments hits: 8078413, hits per frag: 1.01857 processed 8500001 fragments hits: 8583634, hits per frag: 1.0148 processed 9000000 fragments hits: 9086586, hits per frag: 1.01762 processed 9500000 fragments hits: 9591433, hits per frag: 1.01694 processed 10000000 fragments hits: 10094868, hits per frag: 1.01672 processed 10500000 fragments hits: 10599667, hits per frag: 1.01625 processed 11000000 fragments hits: 11106916, hits per frag: 1.01984 processed 11500000 fragments hits: 11612272, hits per frag: 1.02088 processed 12000000 fragments hits: 12117215, hits per frag: 1.0117 processed 12500001 fragments hits: 12620129, hits per frag: 1.01082 processed 13000000 fragments hits: 13126337, hits per frag: 1.01341 processed 13500000 fragments hits: 13632321, hits per frag: 1.01158 processed 14000001 fragments hits: 14140095, hits per frag: 1.01564 processed 14500000 fragments hits: 14644857, hits per frag: 1.01381 processed 15000001 fragments hits: 15150891, hits per frag: 1.01679 processed 15500000 fragments hits: 15654730, hits per frag: 1.01452 processed 16000000 fragments hits: 16157718, hits per frag: 1.013 processed 16500000 fragments hits: 16660450, hits per frag: 1.01172 processed 17000000 fragments hits: 17166845, hits per frag: 1.01158 processed 17500000 fragments hits: 17673463, hits per frag: 1.01847 processed 18000000 fragments hits: 18177856, hits per frag: 1.01447 processed 18500000 fragments hits: 18684066, hits per frag: 1.01051 processed 19000000 fragments hits: 19190478, hits per frag: 1.01553 processed 19500000 fragments hits: 19694823, hits per frag: 1.01408 processed 20000000 fragments hits: 20200503, hits per frag: 1.01556 processed 20500000 fragments hits: 20706724, hits per frag: 1.01698 processed 21000000 fragments hits: 21210737, hits per frag: 1.01412 processed 21500002 fragments hits: 21715773, hits per frag: 1.01446 processed 22000000 fragments hits: 22218984, hits per frag: 1.01352 processed 22500000 fragments hits: 22725210, hits per frag: 1.01507 processed 23000000 fragments hits: 23229046, hits per frag: 1.01078 processed 23500000 fragments hits: 23733674, hits per frag: 1.01044 processed 24000000 fragments hits: 24240809, hits per frag: 1.0157 processed 24500000 fragments hits: 24746211, hits per frag: 1.01238 processed 25000001 fragments hits: 25252056, hits per frag: 1.0138 processed 25500000 fragments hits: 25756044, hits per frag: 1.01333 processed 26000000 fragments hits: 26260408, hits per frag: 1.01231 [2019-01-24 20:45:23.043] [jointLog] [info] Computed 69502 rich equivalence classes for further processing [2019-01-24 20:45:23.043] [jointLog] [info] Counted 13292770 total reads in the equivalence classes [2019-01-24 20:45:23.051] [jointLog] [warning] 0.0152392% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-01-24 20:45:23.051] [jointLog] [info] Mapping rate = 50.2284% [2019-01-24 20:45:23.051] [jointLog] [info] finished quantifyLibrary() [2019-01-24 20:45:23.051] [jointLog] [info] Starting optimizer [2019-01-24 20:45:23.161] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-01-24 20:45:23.162] [jointLog] [info] iteration = 0 | max rel diff. = 218.487 [2019-01-24 20:45:23.292] [jointLog] [info] iteration = 100 | max rel diff. = 0.108188 [2019-01-24 20:45:23.422] [jointLog] [info] iteration = 200 | max rel diff. = 0.0545827 [2019-01-24 20:45:23.551] [jointLog] [info] iteration = 300 | max rel diff. = 0.0417025 [2019-01-24 20:45:23.680] [jointLog] [info] iteration = 400 | max rel diff. = 0.0274441 [2019-01-24 20:45:23.810] [jointLog] [info] iteration = 500 | max rel diff. = 0.0231876 [2019-01-24 20:45:23.940] [jointLog] [info] iteration = 600 | max rel diff. = 0.0182964 [2019-01-24 20:45:24.069] [jointLog] [info] iteration = 700 | max rel diff. = 0.0200548 [2019-01-24 20:45:24.203] [jointLog] [info] iteration = 800 | max rel diff. = 0.0145479 [2019-01-24 20:45:24.330] [jointLog] [info] iteration = 900 | max rel diff. = 0.0124898 [2019-01-24 20:45:24.460] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0111515 [2019-01-24 20:45:24.587] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0119575 [2019-01-24 20:45:24.715] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0102503 [2019-01-24 20:45:24.844] [jointLog] [info] iteration = 1300 | max rel diff. = 0.0102504 [2019-01-24 20:45:24.871] [jointLog] [info] iteration = 1322 | max rel diff. = 0.00815404 [2019-01-24 20:45:24.877] [jointLog] [info] Finished optimizer [2019-01-24 20:45:24.877] [jointLog] [info] writing output [2019-01-24 20:45:24.966] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: non-bleached_44_03/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_44_03/quant.sf /media/sam/4TB_toshiba/porites/coral_transcripts/Trinity.coral.fasta.gene_trans_map > non-bleached_44_03/quant.sf.genes