CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P01-AGTTCC-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P01-AGTTCC-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_K5_01 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_K5_01 } ### [ threads ] => { 23 } Logs will be written to bleached_K5_01/logs [2019-03-05 23:08:14.765] [jointLog] [info] parsing read library format [2019-03-05 23:08:14.765] [jointLog] [info] There is 1 library. [2019-03-05 23:08:14.854] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:08:14.853] [jointLog] [info] Loading Quasi index [2019-03-05 23:08:14.854] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:08:14.913] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:08:14.925] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:08:14.928] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:08:14.930] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:08:14.930] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:08:15.261] [jointLog] [info] done [2019-03-05 23:08:15.261] [jointLog] [info] Index contained 5838 targets [2019-03-05 23:08:15.261] [stderrLog] [info] Done loading index  processed 500001 fragments hits: 95954, hits per frag: 0.193812 processed 1000000 fragments hits: 192125, hits per frag: 0.196607 processed 1500000 fragments hits: 287742, hits per frag: 0.203358 processed 2000000 fragments hits: 383963, hits per frag: 0.20149 processed 2500000 fragments hits: 480127, hits per frag: 0.20291 processed 3000000 fragments hits: 575344, hits per frag: 0.192767 processed 3500000 fragments hits: 671064, hits per frag: 0.202254 processed 4000000 fragments hits: 767967, hits per frag: 0.192807 processed 4500000 fragments hits: 863728, hits per frag: 0.19681 processed 5000001 fragments hits: 958386, hits per frag: 0.193566 processed 5500000 fragments hits: 1053760, hits per frag: 0.192763 processed 6000000 fragments hits: 1149154, hits per frag: 0.193603 processed 6500000 fragments hits: 1244539, hits per frag: 0.193107 processed 7000001 fragments hits: 1340447, hits per frag: 0.193443 processed 7500000 fragments hits: 1435431, hits per frag: 0.194401 processed 8000000 fragments hits: 1532388, hits per frag: 0.194137 processed 8500000 fragments hits: 1628141, hits per frag: 0.19336 processed 9000000 fragments hits: 1723390, hits per frag: 0.194736 processed 9500000 fragments hits: 1817943, hits per frag: 0.192942 processed 10000000 fragments hits: 1913231, hits per frag: 0.193399 processed 10500000 fragments hits: 2008575, hits per frag: 0.192132 processed 11000000 fragments hits: 2104706, hits per frag: 0.192654 processed 11500000 fragments hits: 2200068, hits per frag: 0.192162 processed 12000001 fragments hits: 2295255, hits per frag: 0.191436 processed 12500000 fragments hits: 2389789, hits per frag: 0.191927 processed 13000000 fragments hits: 2485722, hits per frag: 0.191307 processed 13500000 fragments hits: 2581832, hits per frag: 0.192015 processed 14000000 fragments hits: 2676072, hits per frag: 0.192242 processed 14500000 fragments hits: 2772483, hits per frag: 0.191408 processed 15000000 fragments hits: 2867807, hits per frag: 0.192239 processed 15500000 fragments hits: 2963275, hits per frag: 0.192495 processed 16000001 fragments hits: 3059635, hits per frag: 0.192587 processed 16500000 fragments hits: 3156186, hits per frag: 0.192175 processed 17000000 fragments hits: 3252150, hits per frag: 0.191436 processed 17500000 fragments hits: 3347045, hits per frag: 0.192651 processed 18000000 fragments hits: 3442921, hits per frag: 0.191565 processed 18500000 fragments hits: 3537895, hits per frag: 0.192168 processed 19000000 fragments hits: 3632641, hits per frag: 0.191856 processed 19500000 fragments hits: 3727673, hits per frag: 0.192211 processed 20000001 fragments hits: 3823283, hits per frag: 0.191953 processed 20500000 fragments hits: 3919146, hits per frag: 0.19222 processed 21000000 fragments hits: 4013597, hits per frag: 0.191587 processed 21500000 fragments hits: 4108667, hits per frag: 0.19137 processed 22000000 fragments hits: 4204288, hits per frag: 0.191446 processed 22500000 fragments hits: 4299649, hits per frag: 0.191192 processed 23000000 fragments hits: 4395956, hits per frag: 0.191701 processed 23500000 fragments hits: 4492224, hits per frag: 0.192087 processed 24000000 fragments hits: 4587300, hits per frag: 0.191488 processed 24500000 fragments hits: 4684383, hits per frag: 0.19135 [2019-03-05 23:10:39.965] [jointLog] [info] Computed 7374 rich equivalence classes for further processing [2019-03-05 23:10:39.965] [jointLog] [info] Counted 2259062 total reads in the equivalence classes [2019-03-05 23:10:39.976] [jointLog] [warning] 0.00989258% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-03-05 23:10:39.977] [jointLog] [warning] Only 2259062 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:10:39.977] [jointLog] [info] Mapping rate = 9.09192% [2019-03-05 23:10:39.977] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:10:39.978] [jointLog] [info] Starting optimizer [2019-03-05 23:10:40.002] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:10:40.039] [jointLog] [info] iteration = 0 | max rel diff. = 556.43 [2019-03-05 23:10:40.073] [jointLog] [info] iteration = 100 | max rel diff. = 0.118713 [2019-03-05 23:10:40.104] [jointLog] [info] iteration = 200 | max rel diff. = 0.0618653 [2019-03-05 23:10:40.129] [jointLog] [info] iteration = 300 | max rel diff. = 0.0435057 [2019-03-05 23:10:40.152] [jointLog] [info] iteration = 400 | max rel diff. = 0.0267597 [2019-03-05 23:10:40.173] [jointLog] [info] iteration = 500 | max rel diff. = 0.0203623 [2019-03-05 23:10:40.195] [jointLog] [info] iteration = 600 | max rel diff. = 0.0172347 [2019-03-05 23:10:40.217] [jointLog] [info] iteration = 700 | max rel diff. = 0.0139797 [2019-03-05 23:10:40.241] [jointLog] [info] iteration = 800 | max rel diff. = 0.012095 [2019-03-05 23:10:40.265] [jointLog] [info] iteration = 900 | max rel diff. = 0.0120125 [2019-03-05 23:10:40.286] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0101026 [2019-03-05 23:10:40.289] [jointLog] [info] iteration = 1015 | max rel diff. = 0.00970079 [2019-03-05 23:10:40.289] [jointLog] [info] Finished optimizer [2019-03-05 23:10:40.289] [jointLog] [info] writing output [2019-03-05 23:10:40.301] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_K5_01/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_K5_01/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > bleached_K5_01/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P06-GCCAAT-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P06-GCCAAT-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_K5_02 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_K5_02 } ### [ threads ] => { 23 } Logs will be written to bleached_K5_02/logs [2019-03-05 23:10:40.809] [jointLog] [info] parsing read library format [2019-03-05 23:10:40.809] [jointLog] [info] There is 1 library. [2019-03-05 23:10:40.896] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:10:40.896] [jointLog] [info] Loading Quasi index [2019-03-05 23:10:40.896] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:10:40.955] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:10:40.969] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:10:40.974] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:10:40.977] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:10:40.977] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:10:41.369] [stderrLog] [info] Done loading index [2019-03-05 23:10:41.369] [jointLog] [info] done [2019-03-05 23:10:41.369] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 84878, hits per frag: 0.2028 processed 1000000 fragments hits: 169917, hits per frag: 0.182964 processed 1500000 fragments hits: 255932, hits per frag: 0.18306 processed 2000000 fragments hits: 340889, hits per frag: 0.174212 processed 2500000 fragments hits: 425696, hits per frag: 0.175093 processed 3000000 fragments hits: 510928, hits per frag: 0.171707 processed 3500000 fragments hits: 595755, hits per frag: 0.175052 processed 4000000 fragments hits: 680583, hits per frag: 0.171947 processed 4500000 fragments hits: 765577, hits per frag: 0.171904 processed 5000000 fragments hits: 851087, hits per frag: 0.184342 processed 5500000 fragments hits: 935841, hits per frag: 0.173236 processed 6000000 fragments hits: 1019734, hits per frag: 0.170749 processed 6500000 fragments hits: 1105024, hits per frag: 0.174415 processed 7000000 fragments hits: 1190124, hits per frag: 0.172128 processed 7500000 fragments hits: 1275564, hits per frag: 0.171003 processed 8000000 fragments hits: 1360098, hits per frag: 0.176046 processed 8500000 fragments hits: 1444877, hits per frag: 0.172553 processed 9000000 fragments hits: 1530043, hits per frag: 0.172013 processed 9500000 fragments hits: 1615344, hits per frag: 0.171218 processed 10000000 fragments hits: 1700429, hits per frag: 0.170946 processed 10500000 fragments hits: 1785851, hits per frag: 0.171634 processed 11000000 fragments hits: 1870678, hits per frag: 0.170159 processed 11500000 fragments hits: 1955934, hits per frag: 0.170456 processed 12000000 fragments hits: 2041539, hits per frag: 0.17097 processed 12500001 fragments hits: 2125206, hits per frag: 0.170838 processed 13000000 fragments hits: 2209622, hits per frag: 0.170218 processed 13500000 fragments hits: 2295266, hits per frag: 0.171616 processed 14000000 fragments hits: 2380869, hits per frag: 0.170633 processed 14500000 fragments hits: 2465702, hits per frag: 0.171447 processed 15000000 fragments hits: 2552231, hits per frag: 0.17099 processed 15500000 fragments hits: 2637097, hits per frag: 0.171084 processed 16000000 fragments hits: 2722935, hits per frag: 0.171293 processed 16500000 fragments hits: 2808718, hits per frag: 0.171085 processed 17000000 fragments hits: 2893274, hits per frag: 0.170667 processed 17500000 fragments hits: 2978141, hits per frag: 0.171082 processed 18000000 fragments hits: 3064040, hits per frag: 0.170848 [2019-03-05 23:12:30.168] [jointLog] [info] Computed 7296 rich equivalence classes for further processing [2019-03-05 23:12:30.168] [jointLog] [info] Counted 1550851 total reads in the equivalence classes [2019-03-05 23:12:30.179] [jointLog] [warning] 0.0114771% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-03-05 23:12:30.179] [jointLog] [warning] Only 1550851 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:12:30.179] [jointLog] [info] Mapping rate = 8.4437% [2019-03-05 23:12:30.179] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:12:30.180] [jointLog] [info] Starting optimizer [2019-03-05 23:12:30.183] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:12:30.184] [jointLog] [info] iteration = 0 | max rel diff. = 415.314 [2019-03-05 23:12:30.206] [jointLog] [info] iteration = 100 | max rel diff. = 0.123526 [2019-03-05 23:12:30.226] [jointLog] [info] iteration = 200 | max rel diff. = 0.0531352 [2019-03-05 23:12:30.245] [jointLog] [info] iteration = 300 | max rel diff. = 0.0391209 [2019-03-05 23:12:30.263] [jointLog] [info] iteration = 400 | max rel diff. = 0.0282153 [2019-03-05 23:12:30.285] [jointLog] [info] iteration = 500 | max rel diff. = 0.0208171 [2019-03-05 23:12:30.304] [jointLog] [info] iteration = 600 | max rel diff. = 0.0169563 [2019-03-05 23:12:30.327] [jointLog] [info] iteration = 700 | max rel diff. = 0.0151657 [2019-03-05 23:12:30.346] [jointLog] [info] iteration = 800 | max rel diff. = 0.0115068 [2019-03-05 23:12:30.365] [jointLog] [info] iteration = 900 | max rel diff. = 0.0113232 [2019-03-05 23:12:30.381] [jointLog] [info] iteration = 987 | max rel diff. = 0.00954763 [2019-03-05 23:12:30.381] [jointLog] [info] Finished optimizer [2019-03-05 23:12:30.381] [jointLog] [info] writing output [2019-03-05 23:12:30.392] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_K5_02/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_K5_02/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > bleached_K5_02/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P07-AGTCAA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P07-AGTCAA-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_K5_03 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_K5_03 } ### [ threads ] => { 23 } Logs will be written to bleached_K5_03/logs [2019-03-05 23:12:30.794] [jointLog] [info] parsing read library format [2019-03-05 23:12:30.794] [jointLog] [info] There is 1 library. [2019-03-05 23:12:30.883] [jointLog] [info] Loading Quasi index [2019-03-05 23:12:30.883] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:12:30.883] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:12:31.009] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:12:31.023] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:12:31.029] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:12:31.032] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:12:31.032] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:12:31.374] [stderrLog] [info] Done loading index [2019-03-05 23:12:31.374] [jointLog] [info] done [2019-03-05 23:12:31.374] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 97483, hits per frag: 0.214258 processed 1000000 fragments hits: 195355, hits per frag: 0.205054 processed 1500000 fragments hits: 294261, hits per frag: 0.207223 processed 2000000 fragments hits: 392611, hits per frag: 0.203732 processed 2500000 fragments hits: 492051, hits per frag: 0.201438 processed 3000000 fragments hits: 591037, hits per frag: 0.204159 processed 3500000 fragments hits: 688438, hits per frag: 0.203903 processed 4000000 fragments hits: 785954, hits per frag: 0.202255 processed 4500000 fragments hits: 883508, hits per frag: 0.19911 processed 5000000 fragments hits: 982238, hits per frag: 0.19876 processed 5500000 fragments hits: 1080298, hits per frag: 0.199483 processed 6000000 fragments hits: 1178514, hits per frag: 0.200847 processed 6500000 fragments hits: 1276458, hits per frag: 0.200479 processed 7000000 fragments hits: 1375107, hits per frag: 0.197117 processed 7500000 fragments hits: 1472048, hits per frag: 0.197305 processed 8000001 fragments hits: 1569360, hits per frag: 0.198539 processed 8500001 fragments hits: 1667210, hits per frag: 0.197463 processed 9000000 fragments hits: 1765709, hits per frag: 0.196968 processed 9500000 fragments hits: 1864205, hits per frag: 0.198611 processed 10000001 fragments hits: 1961997, hits per frag: 0.197123 processed 10500000 fragments hits: 2060646, hits per frag: 0.196501 processed 11000000 fragments hits: 2160484, hits per frag: 0.197633 processed 11500000 fragments hits: 2259585, hits per frag: 0.197053 processed 12000000 fragments hits: 2357444, hits per frag: 0.197271 processed 12500000 fragments hits: 2456255, hits per frag: 0.196634 processed 13000000 fragments hits: 2554192, hits per frag: 0.197122 processed 13500000 fragments hits: 2651900, hits per frag: 0.197016 processed 14000000 fragments hits: 2749724, hits per frag: 0.197672 processed 14500002 fragments hits: 2848252, hits per frag: 0.197674 processed 15000000 fragments hits: 2946013, hits per frag: 0.198447 processed 15500000 fragments hits: 3044603, hits per frag: 0.197347 processed 16000000 fragments hits: 3142074, hits per frag: 0.197012 processed 16500000 fragments hits: 3239901, hits per frag: 0.197095 processed 17000000 fragments hits: 3337525, hits per frag: 0.198254 processed 17500000 fragments hits: 3435841, hits per frag: 0.196657 processed 18000000 fragments hits: 3532822, hits per frag: 0.197289 processed 18500000 fragments hits: 3631397, hits per frag: 0.19807 processed 19000000 fragments hits: 3730536, hits per frag: 0.196684 processed 19500000 fragments hits: 3828500, hits per frag: 0.196447 processed 20000001 fragments hits: 3926542, hits per frag: 0.197043 processed 20500000 fragments hits: 4023792, hits per frag: 0.197476 processed 21000000 fragments hits: 4122139, hits per frag: 0.196819 processed 21500000 fragments hits: 4219873, hits per frag: 0.196584 processed 22000000 fragments hits: 4317897, hits per frag: 0.196753 processed 22500000 fragments hits: 4416386, hits per frag: 0.196625 processed 23000000 fragments hits: 4514890, hits per frag: 0.196481 processed 23500000 fragments hits: 4612624, hits per frag: 0.197079 processed 24000000 fragments hits: 4710694, hits per frag: 0.196414 processed 24500000 fragments hits: 4807960, hits per frag: 0.196582 processed 25000001 fragments hits: 4906411, hits per frag: 0.196815 processed 25500000 fragments hits: 5003750, hits per frag: 0.197587 [2019-03-05 23:14:46.652] [jointLog] [info] Computed 7398 rich equivalence classes for further processing [2019-03-05 23:14:46.652] [jointLog] [info] Counted 2479140 total reads in the equivalence classes [2019-03-05 23:14:46.662] [jointLog] [warning] 0.0136297% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-03-05 23:14:46.663] [jointLog] [warning] Only 2479140 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:14:46.663] [jointLog] [info] Mapping rate = 9.56952% [2019-03-05 23:14:46.663] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:14:46.663] [jointLog] [info] Starting optimizer [2019-03-05 23:14:46.667] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:14:46.668] [jointLog] [info] iteration = 0 | max rel diff. = 615.841 [2019-03-05 23:14:46.700] [jointLog] [info] iteration = 100 | max rel diff. = 0.117144 [2019-03-05 23:14:46.723] [jointLog] [info] iteration = 200 | max rel diff. = 0.0565829 [2019-03-05 23:14:46.741] [jointLog] [info] iteration = 300 | max rel diff. = 0.0377845 [2019-03-05 23:14:46.761] [jointLog] [info] iteration = 400 | max rel diff. = 0.0253392 [2019-03-05 23:14:46.783] [jointLog] [info] iteration = 500 | max rel diff. = 0.0214205 [2019-03-05 23:14:46.803] [jointLog] [info] iteration = 600 | max rel diff. = 0.0177716 [2019-03-05 23:14:46.826] [jointLog] [info] iteration = 700 | max rel diff. = 0.0164722 [2019-03-05 23:14:46.861] [jointLog] [info] iteration = 800 | max rel diff. = 0.0123911 [2019-03-05 23:14:46.885] [jointLog] [info] iteration = 900 | max rel diff. = 0.0119454 [2019-03-05 23:14:46.904] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0106927 [2019-03-05 23:14:46.909] [jointLog] [info] iteration = 1027 | max rel diff. = 0.00912696 [2019-03-05 23:14:46.910] [jointLog] [info] Finished optimizer [2019-03-05 23:14:46.910] [jointLog] [info] writing output [2019-03-05 23:14:46.930] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_K5_03/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_K5_03/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > bleached_K5_03/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_K5_04 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_K5_04 } ### [ threads ] => { 23 } Logs will be written to bleached_K5_04/logs [2019-03-05 23:14:47.335] [jointLog] [info] parsing read library format [2019-03-05 23:14:47.335] [jointLog] [info] There is 1 library. [2019-03-05 23:14:47.432] [jointLog] [info] Loading Quasi index [2019-03-05 23:14:47.432] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:14:47.432] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:14:47.564] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:14:47.575] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:14:47.578] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:14:47.580] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:14:47.580] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:14:47.900] [stderrLog] [info] Done loading index [2019-03-05 23:14:47.900] [jointLog] [info] done [2019-03-05 23:14:47.900] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 96377, hits per frag: 0.295934 processed 1000000 fragments hits: 192468, hits per frag: 0.269572 processed 1500000 fragments hits: 289329, hits per frag: 0.216131 processed 2000000 fragments hits: 385798, hits per frag: 0.198964 processed 2500000 fragments hits: 481920, hits per frag: 0.193925 processed 3000000 fragments hits: 577807, hits per frag: 0.198049 processed 3500000 fragments hits: 673508, hits per frag: 0.194611 processed 4000000 fragments hits: 770530, hits per frag: 0.195209 processed 4500000 fragments hits: 867690, hits per frag: 0.194955 processed 5000000 fragments hits: 963784, hits per frag: 0.196413 processed 5500000 fragments hits: 1060934, hits per frag: 0.193204 processed 6000000 fragments hits: 1157726, hits per frag: 0.194466 processed 6500000 fragments hits: 1253707, hits per frag: 0.19622 processed 7000000 fragments hits: 1351138, hits per frag: 0.194689 processed 7500000 fragments hits: 1447902, hits per frag: 0.195784 processed 8000000 fragments hits: 1543363, hits per frag: 0.195055 processed 8500000 fragments hits: 1638992, hits per frag: 0.194841 processed 9000000 fragments hits: 1735008, hits per frag: 0.195888 processed 9500000 fragments hits: 1831408, hits per frag: 0.193249 processed 10000000 fragments hits: 1926764, hits per frag: 0.194293 processed 10500000 fragments hits: 2021951, hits per frag: 0.193401 processed 11000000 fragments hits: 2118428, hits per frag: 0.193789 processed 11500000 fragments hits: 2215280, hits per frag: 0.193723 processed 12000000 fragments hits: 2312033, hits per frag: 0.193839 processed 12500000 fragments hits: 2406272, hits per frag: 0.19333 processed 13000000 fragments hits: 2501275, hits per frag: 0.193032 processed 13500000 fragments hits: 2597570, hits per frag: 0.192857 processed 14000000 fragments hits: 2694010, hits per frag: 0.193122 processed 14500000 fragments hits: 2790413, hits per frag: 0.193576 processed 15000000 fragments hits: 2887129, hits per frag: 0.19273 processed 15500001 fragments hits: 2983146, hits per frag: 0.193217 processed 16000000 fragments hits: 3078633, hits per frag: 0.193234 processed 16500000 fragments hits: 3174792, hits per frag: 0.193929 processed 17000000 fragments hits: 3271501, hits per frag: 0.193486 processed 17500000 fragments hits: 3366836, hits per frag: 0.193837 processed 18000000 fragments hits: 3463046, hits per frag: 0.192489 processed 18500001 fragments hits: 3558918, hits per frag: 0.192936 processed 19000001 fragments hits: 3655878, hits per frag: 0.193145 processed 19500000 fragments hits: 3751105, hits per frag: 0.192813 processed 20000000 fragments hits: 3847892, hits per frag: 0.192958 processed 20500000 fragments hits: 3944605, hits per frag: 0.192818 processed 21000000 fragments hits: 4040646, hits per frag: 0.193445 processed 21500000 fragments hits: 4137658, hits per frag: 0.192693 processed 22000001 fragments hits: 4233674, hits per frag: 0.19288 processed 22500000 fragments hits: 4329618, hits per frag: 0.193395 processed 23000000 fragments hits: 4426317, hits per frag: 0.192971 processed 23500000 fragments hits: 4522505, hits per frag: 0.192966 processed 24000000 fragments hits: 4618487, hits per frag: 0.193233 processed 24500000 fragments hits: 4715174, hits per frag: 0.193405 processed 25000000 fragments hits: 4812267, hits per frag: 0.193635 processed 25500000 fragments hits: 4908508, hits per frag: 0.192944 processed 26000000 fragments hits: 5004223, hits per frag: 0.192652 processed 26500000 fragments hits: 5101208, hits per frag: 0.193138 processed 27000000 fragments hits: 5196979, hits per frag: 0.192972 processed 27500000 fragments hits: 5292189, hits per frag: 0.192822 processed 28000000 fragments hits: 5389012, hits per frag: 0.194611 [2019-03-05 23:17:21.552] [jointLog] [info] Computed 7401 rich equivalence classes for further processing [2019-03-05 23:17:21.552] [jointLog] [info] Counted 2716216 total reads in the equivalence classes [2019-03-05 23:17:21.565] [jointLog] [warning] 0.0118102% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-03-05 23:17:21.566] [jointLog] [warning] Only 2716216 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:17:21.566] [jointLog] [info] Mapping rate = 9.59013% [2019-03-05 23:17:21.566] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:17:21.566] [jointLog] [info] Starting optimizer [2019-03-05 23:17:21.570] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:17:21.570] [jointLog] [info] iteration = 0 | max rel diff. = 623.174 [2019-03-05 23:17:21.595] [jointLog] [info] iteration = 100 | max rel diff. = 0.126894 [2019-03-05 23:17:21.620] [jointLog] [info] iteration = 200 | max rel diff. = 0.063238 [2019-03-05 23:17:21.643] [jointLog] [info] iteration = 300 | max rel diff. = 0.043377 [2019-03-05 23:17:21.668] [jointLog] [info] iteration = 400 | max rel diff. = 0.0310135 [2019-03-05 23:17:21.693] [jointLog] [info] iteration = 500 | max rel diff. = 0.0246277 [2019-03-05 23:17:21.722] [jointLog] [info] iteration = 600 | max rel diff. = 0.0182674 [2019-03-05 23:17:21.748] [jointLog] [info] iteration = 700 | max rel diff. = 0.0152065 [2019-03-05 23:17:21.771] [jointLog] [info] iteration = 800 | max rel diff. = 0.0128849 [2019-03-05 23:17:21.791] [jointLog] [info] iteration = 900 | max rel diff. = 0.0118756 [2019-03-05 23:17:21.812] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0110781 [2019-03-05 23:17:21.819] [jointLog] [info] iteration = 1034 | max rel diff. = 0.0098418 [2019-03-05 23:17:21.820] [jointLog] [info] Finished optimizer [2019-03-05 23:17:21.820] [jointLog] [info] writing output [2019-03-05 23:17:21.835] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_K5_04/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_K5_04/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > bleached_K5_04/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_K5_05 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_K5_05 } ### [ threads ] => { 23 } Logs will be written to bleached_K5_05/logs [2019-03-05 23:17:22.414] [jointLog] [info] parsing read library format [2019-03-05 23:17:22.414] [jointLog] [info] There is 1 library. [2019-03-05 23:17:22.493] [jointLog] [info] Loading Quasi index [2019-03-05 23:17:22.493] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:17:22.493] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:17:22.550] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:17:22.564] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:17:22.569] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:17:22.572] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:17:22.572] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:17:22.945] [stderrLog] [info] Done loading index [2019-03-05 23:17:22.945] [jointLog] [info] done [2019-03-05 23:17:22.945] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 88662, hits per frag: 0.201089 processed 1000000 fragments hits: 177906, hits per frag: 0.185474 processed 1500000 fragments hits: 265526, hits per frag: 0.226554 processed 2000000 fragments hits: 353938, hits per frag: 0.183414 processed 2500000 fragments hits: 442373, hits per frag: 0.184228 processed 3000000 fragments hits: 531339, hits per frag: 0.178225 processed 3500000 fragments hits: 619439, hits per frag: 0.17884 processed 4000000 fragments hits: 706988, hits per frag: 0.178086 processed 4500000 fragments hits: 796316, hits per frag: 0.180822 processed 5000000 fragments hits: 884764, hits per frag: 0.177208 processed 5500000 fragments hits: 972843, hits per frag: 0.181174 processed 6000001 fragments hits: 1061266, hits per frag: 0.178161 processed 6500000 fragments hits: 1150033, hits per frag: 0.181337 processed 7000000 fragments hits: 1238312, hits per frag: 0.179506 processed 7500000 fragments hits: 1325972, hits per frag: 0.179313 processed 8000000 fragments hits: 1413974, hits per frag: 0.177595 processed 8500000 fragments hits: 1502625, hits per frag: 0.178795 processed 9000000 fragments hits: 1591835, hits per frag: 0.17815 processed 9500000 fragments hits: 1680456, hits per frag: 0.177259 processed 10000000 fragments hits: 1768713, hits per frag: 0.17815 processed 10500000 fragments hits: 1856549, hits per frag: 0.178154 processed 11000000 fragments hits: 1943693, hits per frag: 0.177876 processed 11500000 fragments hits: 2031761, hits per frag: 0.179491 processed 12000000 fragments hits: 2119299, hits per frag: 0.177394 processed 12500000 fragments hits: 2207335, hits per frag: 0.177606 processed 13000000 fragments hits: 2294945, hits per frag: 0.177159 processed 13500000 fragments hits: 2382825, hits per frag: 0.176545 processed 14000000 fragments hits: 2470784, hits per frag: 0.177926 processed 14500000 fragments hits: 2559402, hits per frag: 0.177695 processed 15000000 fragments hits: 2647970, hits per frag: 0.177511 processed 15500000 fragments hits: 2735965, hits per frag: 0.177907 processed 16000000 fragments hits: 2824313, hits per frag: 0.177074 processed 16500000 fragments hits: 2913048, hits per frag: 0.177638 processed 17000000 fragments hits: 3001457, hits per frag: 0.17757 processed 17500000 fragments hits: 3089714, hits per frag: 0.178371 processed 18000000 fragments hits: 3177851, hits per frag: 0.177264 processed 18500000 fragments hits: 3265014, hits per frag: 0.176692 processed 19000000 fragments hits: 3352376, hits per frag: 0.176847 processed 19500000 fragments hits: 3440145, hits per frag: 0.176901 processed 20000000 fragments hits: 3527481, hits per frag: 0.177236 processed 20500000 fragments hits: 3615114, hits per frag: 0.177032 processed 21000000 fragments hits: 3703045, hits per frag: 0.176475 processed 21500000 fragments hits: 3791499, hits per frag: 0.176912 [2019-03-05 23:19:21.988] [jointLog] [info] Computed 6922 rich equivalence classes for further processing [2019-03-05 23:19:21.988] [jointLog] [info] Counted 1916701 total reads in the equivalence classes [2019-03-05 23:19:21.999] [jointLog] [warning] 0.0194906% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-03-05 23:19:22.000] [jointLog] [warning] Only 1916701 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:19:22.000] [jointLog] [info] Mapping rate = 8.75913% [2019-03-05 23:19:22.000] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:19:22.000] [jointLog] [info] Starting optimizer [2019-03-05 23:19:22.005] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:19:22.006] [jointLog] [info] iteration = 0 | max rel diff. = 428.658 [2019-03-05 23:19:22.028] [jointLog] [info] iteration = 100 | max rel diff. = 0.112633 [2019-03-05 23:19:22.055] [jointLog] [info] iteration = 200 | max rel diff. = 0.0561107 [2019-03-05 23:19:22.072] [jointLog] [info] iteration = 300 | max rel diff. = 0.036646 [2019-03-05 23:19:22.092] [jointLog] [info] iteration = 400 | max rel diff. = 0.0243101 [2019-03-05 23:19:22.110] [jointLog] [info] iteration = 500 | max rel diff. = 0.0243114 [2019-03-05 23:19:22.128] [jointLog] [info] iteration = 600 | max rel diff. = 0.0174517 [2019-03-05 23:19:22.149] [jointLog] [info] iteration = 700 | max rel diff. = 0.0150944 [2019-03-05 23:19:22.169] [jointLog] [info] iteration = 800 | max rel diff. = 0.0129991 [2019-03-05 23:19:22.191] [jointLog] [info] iteration = 900 | max rel diff. = 0.0116912 [2019-03-05 23:19:22.216] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0116915 [2019-03-05 23:19:22.226] [jointLog] [info] iteration = 1054 | max rel diff. = 0.00985086 [2019-03-05 23:19:22.227] [jointLog] [info] Finished optimizer [2019-03-05 23:19:22.227] [jointLog] [info] writing output [2019-03-05 23:19:22.237] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_K5_05/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_K5_05/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > bleached_K5_05/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_K5_06 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_K5_06 } ### [ threads ] => { 23 } Logs will be written to bleached_K5_06/logs [2019-03-05 23:19:22.546] [jointLog] [info] parsing read library format [2019-03-05 23:19:22.546] [jointLog] [info] There is 1 library. [2019-03-05 23:19:22.631] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:19:22.631] [jointLog] [info] Loading Quasi index [2019-03-05 23:19:22.631] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:19:22.728] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:19:22.740] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:19:22.743] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:19:22.745] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:19:22.745] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:19:23.067] [stderrLog] [info] Done loading index [2019-03-05 23:19:23.067] [jointLog] [info] done [2019-03-05 23:19:23.067] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 74492, hits per frag: 0.227921 processed 1000001 fragments hits: 149567, hits per frag: 0.162222 processed 1500000 fragments hits: 224759, hits per frag: 0.175651 processed 2000000 fragments hits: 298981, hits per frag: 0.153929 processed 2500000 fragments hits: 373664, hits per frag: 0.152862 processed 3000000 fragments hits: 447946, hits per frag: 0.160155 processed 3500000 fragments hits: 522370, hits per frag: 0.154104 processed 4000001 fragments hits: 595349, hits per frag: 0.152083 processed 4500000 fragments hits: 669273, hits per frag: 0.150874 processed 5000000 fragments hits: 744461, hits per frag: 0.150638 processed 5500000 fragments hits: 819700, hits per frag: 0.150636 processed 6000000 fragments hits: 894824, hits per frag: 0.156975 processed 6500000 fragments hits: 968377, hits per frag: 0.152662 processed 7000000 fragments hits: 1042047, hits per frag: 0.15473 processed 7500000 fragments hits: 1116308, hits per frag: 0.15069 processed 8000000 fragments hits: 1189920, hits per frag: 0.149422 processed 8500001 fragments hits: 1262862, hits per frag: 0.148885 processed 9000000 fragments hits: 1338076, hits per frag: 0.150709 processed 9500000 fragments hits: 1413003, hits per frag: 0.149579 processed 10000000 fragments hits: 1487402, hits per frag: 0.149839 processed 10500000 fragments hits: 1561642, hits per frag: 0.149679 processed 11000000 fragments hits: 1635794, hits per frag: 0.149887 processed 11500000 fragments hits: 1710119, hits per frag: 0.150178 processed 12000000 fragments hits: 1783802, hits per frag: 0.149965 processed 12500000 fragments hits: 1857690, hits per frag: 0.149278 processed 13000000 fragments hits: 1930860, hits per frag: 0.149229 processed 13500000 fragments hits: 2006491, hits per frag: 0.149059 processed 14000000 fragments hits: 2081221, hits per frag: 0.150403 processed 14500000 fragments hits: 2156415, hits per frag: 0.149966 processed 15000000 fragments hits: 2230431, hits per frag: 0.149217 processed 15500001 fragments hits: 2304344, hits per frag: 0.149627 processed 16000000 fragments hits: 2377769, hits per frag: 0.149716 processed 16500001 fragments hits: 2451345, hits per frag: 0.149934 processed 17000000 fragments hits: 2524258, hits per frag: 0.14904 [2019-03-05 23:20:58.252] [jointLog] [info] Computed 6627 rich equivalence classes for further processing [2019-03-05 23:20:58.252] [jointLog] [info] Counted 1294477 total reads in the equivalence classes [2019-03-05 23:20:58.265] [jointLog] [warning] 0.0100547% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-03-05 23:20:58.266] [jointLog] [warning] Only 1294477 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:20:58.266] [jointLog] [info] Mapping rate = 7.48881% [2019-03-05 23:20:58.266] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:20:58.266] [jointLog] [info] Starting optimizer [2019-03-05 23:20:58.271] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:20:58.272] [jointLog] [info] iteration = 0 | max rel diff. = 305.917 [2019-03-05 23:20:58.337] [jointLog] [info] iteration = 100 | max rel diff. = 0.113948 [2019-03-05 23:20:58.376] [jointLog] [info] iteration = 200 | max rel diff. = 0.0606275 [2019-03-05 23:20:58.407] [jointLog] [info] iteration = 300 | max rel diff. = 0.0432704 [2019-03-05 23:20:58.434] [jointLog] [info] iteration = 400 | max rel diff. = 0.0293287 [2019-03-05 23:20:58.467] [jointLog] [info] iteration = 500 | max rel diff. = 0.0218399 [2019-03-05 23:20:58.498] [jointLog] [info] iteration = 600 | max rel diff. = 0.0174288 [2019-03-05 23:20:58.534] [jointLog] [info] iteration = 700 | max rel diff. = 0.0147269 [2019-03-05 23:20:58.560] [jointLog] [info] iteration = 800 | max rel diff. = 0.0118559 [2019-03-05 23:20:58.587] [jointLog] [info] iteration = 900 | max rel diff. = 0.011151 [2019-03-05 23:20:58.610] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0113566 [2019-03-05 23:20:58.633] [jointLog] [info] iteration = 1091 | max rel diff. = 0.00876322 [2019-03-05 23:20:58.633] [jointLog] [info] Finished optimizer [2019-03-05 23:20:58.633] [jointLog] [info] writing output [2019-03-05 23:20:58.650] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_K5_06/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_K5_06/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > bleached_K5_06/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P03-ACTGAT-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P03-ACTGAT-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_44_01 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_44_01 } ### [ threads ] => { 23 } Logs will be written to bleached_44_01/logs [2019-03-05 23:20:59.114] [jointLog] [info] parsing read library format [2019-03-05 23:20:59.114] [jointLog] [info] There is 1 library. [2019-03-05 23:20:59.217] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:20:59.217] [jointLog] [info] Loading Quasi index [2019-03-05 23:20:59.217] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:20:59.323] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:20:59.336] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:20:59.339] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:20:59.341] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:20:59.341] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:20:59.715] [stderrLog] [info] Done loading index [2019-03-05 23:20:59.715] [jointLog] [info] done [2019-03-05 23:20:59.715] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 88862, hits per frag: 0.196277 processed 1000000 fragments hits: 178161, hits per frag: 0.195932 processed 1500000 fragments hits: 266506, hits per frag: 0.178656 processed 2000000 fragments hits: 355378, hits per frag: 0.180283 processed 2500000 fragments hits: 444328, hits per frag: 0.181034 processed 3000000 fragments hits: 531529, hits per frag: 0.178374 processed 3500000 fragments hits: 620652, hits per frag: 0.182295 processed 4000000 fragments hits: 709158, hits per frag: 0.181517 processed 4500000 fragments hits: 798875, hits per frag: 0.178698 processed 5000000 fragments hits: 888097, hits per frag: 0.181263 processed 5500000 fragments hits: 976885, hits per frag: 0.17918 processed 6000000 fragments hits: 1065050, hits per frag: 0.17991 processed 6500000 fragments hits: 1153914, hits per frag: 0.178748 processed 7000000 fragments hits: 1242440, hits per frag: 0.180024 processed 7500000 fragments hits: 1331748, hits per frag: 0.177847 processed 8000000 fragments hits: 1420365, hits per frag: 0.17769 processed 8500000 fragments hits: 1506805, hits per frag: 0.179621 processed 9000000 fragments hits: 1595495, hits per frag: 0.17793 processed 9500000 fragments hits: 1687243, hits per frag: 0.179269 processed 10000000 fragments hits: 1773358, hits per frag: 0.178442 processed 10500000 fragments hits: 1861697, hits per frag: 0.178224 processed 11000000 fragments hits: 1950640, hits per frag: 0.178529 processed 11500000 fragments hits: 2038583, hits per frag: 0.178117 processed 12000000 fragments hits: 2127660, hits per frag: 0.177937 processed 12500001 fragments hits: 2215443, hits per frag: 0.178576 processed 13000000 fragments hits: 2303353, hits per frag: 0.177686 processed 13500000 fragments hits: 2393140, hits per frag: 0.177952 processed 14000001 fragments hits: 2481848, hits per frag: 0.177742 processed 14500000 fragments hits: 2571169, hits per frag: 0.177989 processed 15000000 fragments hits: 2659639, hits per frag: 0.178548 processed 15500000 fragments hits: 2749229, hits per frag: 0.178149 processed 16000000 fragments hits: 2839829, hits per frag: 0.177755 processed 16500000 fragments hits: 2927998, hits per frag: 0.178589 processed 17000000 fragments hits: 3015985, hits per frag: 0.178101 processed 17500000 fragments hits: 3104507, hits per frag: 0.178005 processed 18000000 fragments hits: 3193098, hits per frag: 0.178172 processed 18500000 fragments hits: 3281319, hits per frag: 0.177848 processed 19000000 fragments hits: 3370470, hits per frag: 0.177853 processed 19500000 fragments hits: 3457898, hits per frag: 0.177615 processed 20000000 fragments hits: 3545731, hits per frag: 0.177353 processed 20500000 fragments hits: 3633930, hits per frag: 0.177371 processed 21000000 fragments hits: 3722601, hits per frag: 0.177529 processed 21500000 fragments hits: 3810378, hits per frag: 0.177775 processed 22000000 fragments hits: 3898847, hits per frag: 0.177505 processed 22500000 fragments hits: 3987330, hits per frag: 0.177687 processed 23000000 fragments hits: 4076823, hits per frag: 0.177743 [2019-03-05 23:22:47.840] [jointLog] [info] Computed 7727 rich equivalence classes for further processing [2019-03-05 23:22:47.840] [jointLog] [info] Counted 2025613 total reads in the equivalence classes [2019-03-05 23:22:47.852] [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. [2019-03-05 23:22:47.852] [jointLog] [warning] Only 2025613 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:22:47.852] [jointLog] [info] Mapping rate = 8.79746% [2019-03-05 23:22:47.852] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:22:47.853] [jointLog] [info] Starting optimizer [2019-03-05 23:22:47.857] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:22:47.857] [jointLog] [info] iteration = 0 | max rel diff. = 539.31 [2019-03-05 23:22:47.888] [jointLog] [info] iteration = 100 | max rel diff. = 0.113526 [2019-03-05 23:22:47.920] [jointLog] [info] iteration = 200 | max rel diff. = 0.0515013 [2019-03-05 23:22:47.939] [jointLog] [info] iteration = 300 | max rel diff. = 0.0364971 [2019-03-05 23:22:47.961] [jointLog] [info] iteration = 400 | max rel diff. = 0.0275276 [2019-03-05 23:22:47.980] [jointLog] [info] iteration = 500 | max rel diff. = 0.0205174 [2019-03-05 23:22:48.003] [jointLog] [info] iteration = 600 | max rel diff. = 0.0185715 [2019-03-05 23:22:48.022] [jointLog] [info] iteration = 700 | max rel diff. = 0.0165131 [2019-03-05 23:22:48.042] [jointLog] [info] iteration = 800 | max rel diff. = 0.0142167 [2019-03-05 23:22:48.064] [jointLog] [info] iteration = 900 | max rel diff. = 0.0142167 [2019-03-05 23:22:48.085] [jointLog] [info] iteration = 1000 | max rel diff. = 0.00918984 [2019-03-05 23:22:48.085] [jointLog] [info] iteration = 1001 | max rel diff. = 0.00918984 [2019-03-05 23:22:48.085] [jointLog] [info] Finished optimizer [2019-03-05 23:22:48.085] [jointLog] [info] writing output [2019-03-05 23:22:48.097] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_44_01/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_44_01/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > bleached_44_01/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P11-ACTTGA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P11-ACTTGA-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_44_02 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_44_02 } ### [ threads ] => { 23 } Logs will be written to bleached_44_02/logs [2019-03-05 23:22:48.453] [jointLog] [info] parsing read library format [2019-03-05 23:22:48.453] [jointLog] [info] There is 1 library. [2019-03-05 23:22:48.528] [jointLog] [info] Loading Quasi index [2019-03-05 23:22:48.528] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:22:48.528] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:22:48.588] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:22:48.599] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:22:48.603] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:22:48.605] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:22:48.605] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:22:48.961] [stderrLog] [info] Done loading index [2019-03-05 23:22:48.961] [jointLog] [info] done [2019-03-05 23:22:48.961] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 94548, hits per frag: 0.233612 processed 1000000 fragments hits: 189729, hits per frag: 0.220662 processed 1500000 fragments hits: 285435, hits per frag: 0.203999 processed 2000001 fragments hits: 380474, hits per frag: 0.196649 processed 2500000 fragments hits: 475464, hits per frag: 0.192777 processed 3000000 fragments hits: 571785, hits per frag: 0.193217 processed 3500000 fragments hits: 666500, hits per frag: 0.195061 processed 4000000 fragments hits: 761717, hits per frag: 0.196859 processed 4500000 fragments hits: 856519, hits per frag: 0.196321 processed 5000000 fragments hits: 951323, hits per frag: 0.192908 processed 5500000 fragments hits: 1045236, hits per frag: 0.19299 processed 6000000 fragments hits: 1139584, hits per frag: 0.190097 processed 6500001 fragments hits: 1234095, hits per frag: 0.189991 processed 7000000 fragments hits: 1328904, hits per frag: 0.1922 processed 7500000 fragments hits: 1423227, hits per frag: 0.191906 processed 8000000 fragments hits: 1517550, hits per frag: 0.191987 processed 8500000 fragments hits: 1611667, hits per frag: 0.192034 processed 9000001 fragments hits: 1705199, hits per frag: 0.191385 processed 9500000 fragments hits: 1798416, hits per frag: 0.18988 processed 10000000 fragments hits: 1893080, hits per frag: 0.193268 processed 10500000 fragments hits: 1986639, hits per frag: 0.189709 processed 11000000 fragments hits: 2081889, hits per frag: 0.190446 processed 11500000 fragments hits: 2176804, hits per frag: 0.189783 processed 12000001 fragments hits: 2271137, hits per frag: 0.189596 processed 12500000 fragments hits: 2365466, hits per frag: 0.189608 processed 13000000 fragments hits: 2460536, hits per frag: 0.19067 processed 13500000 fragments hits: 2555102, hits per frag: 0.189292 processed 14000000 fragments hits: 2649552, hits per frag: 0.189833 processed 14500000 fragments hits: 2744322, hits per frag: 0.189746 processed 15000000 fragments hits: 2838777, hits per frag: 0.190011 processed 15500000 fragments hits: 2933556, hits per frag: 0.190291 processed 16000000 fragments hits: 3028782, hits per frag: 0.191009 processed 16500000 fragments hits: 3124385, hits per frag: 0.190338 processed 17000000 fragments hits: 3217856, hits per frag: 0.189846 processed 17500001 fragments hits: 3311903, hits per frag: 0.190259 processed 18000000 fragments hits: 3406165, hits per frag: 0.190851 processed 18500000 fragments hits: 3500815, hits per frag: 0.189405 processed 19000000 fragments hits: 3594355, hits per frag: 0.189981 processed 19500000 fragments hits: 3688760, hits per frag: 0.189876 processed 20000001 fragments hits: 3783104, hits per frag: 0.189586 processed 20500000 fragments hits: 3876784, hits per frag: 0.190361 processed 21000001 fragments hits: 3972184, hits per frag: 0.190411 processed 21500000 fragments hits: 4066761, hits per frag: 0.189738 [2019-03-05 23:24:54.915] [jointLog] [info] Computed 7631 rich equivalence classes for further processing [2019-03-05 23:24:54.915] [jointLog] [info] Counted 2077905 total reads in the equivalence classes [2019-03-05 23:24:54.928] [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. [2019-03-05 23:24:54.928] [jointLog] [warning] Only 2077905 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:24:54.928] [jointLog] [info] Mapping rate = 9.47121% [2019-03-05 23:24:54.928] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:24:54.929] [jointLog] [info] Starting optimizer [2019-03-05 23:24:54.934] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:24:54.935] [jointLog] [info] iteration = 0 | max rel diff. = 467.28 [2019-03-05 23:24:54.970] [jointLog] [info] iteration = 100 | max rel diff. = 0.123836 [2019-03-05 23:24:54.991] [jointLog] [info] iteration = 200 | max rel diff. = 0.060062 [2019-03-05 23:24:55.014] [jointLog] [info] iteration = 300 | max rel diff. = 0.0368941 [2019-03-05 23:24:55.035] [jointLog] [info] iteration = 400 | max rel diff. = 0.0285354 [2019-03-05 23:24:55.057] [jointLog] [info] iteration = 500 | max rel diff. = 0.019887 [2019-03-05 23:24:55.078] [jointLog] [info] iteration = 600 | max rel diff. = 0.020303 [2019-03-05 23:24:55.101] [jointLog] [info] iteration = 700 | max rel diff. = 0.0157147 [2019-03-05 23:24:55.123] [jointLog] [info] iteration = 800 | max rel diff. = 0.0121671 [2019-03-05 23:24:55.143] [jointLog] [info] iteration = 900 | max rel diff. = 0.0116239 [2019-03-05 23:24:55.170] [jointLog] [info] iteration = 1000 | max rel diff. = 0.011624 [2019-03-05 23:24:55.173] [jointLog] [info] iteration = 1015 | max rel diff. = 0.00982971 [2019-03-05 23:24:55.193] [jointLog] [info] Finished optimizer [2019-03-05 23:24:55.193] [jointLog] [info] writing output [2019-03-05 23:24:55.212] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: bleached_44_02/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl bleached_44_02/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > bleached_44_02/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P14-GTGGCC-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P14-GTGGCC-READ2-Sequences.txt.gz_val_2.fq.gz) -o bleached_44_03 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { bleached_44_03 } ### [ threads ] => { 23 } Logs will be written to bleached_44_03/logs [2019-03-05 23:24:55.738] [jointLog] [info] parsing read library format [2019-03-05 23:24:55.738] [jointLog] [info] There is 1 library. [2019-03-05 23:24:55.821] [jointLog] [info] Loading Quasi index [2019-03-05 23:24:55.821] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:24:55.821] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:24:55.910] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:24:55.938] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:24:55.943] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:24:55.945] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:24:55.945] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:24:56.307] [stderrLog] [info] Done loading index [2019-03-05 23:24:56.307] [jointLog] [info] done [2019-03-05 23:24:56.307] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 92658, hits per frag: 0.199781 processed 1000000 fragments hits: 185350, hits per frag: 0.206262 processed 1500000 fragments hits: 277578, hits per frag: 0.197785 processed 2000000 fragments hits: 370031, hits per frag: 0.188518 processed 2500000 fragments hits: 464451, hits per frag: 0.189018 processed 3000000 fragments hits: 556771, hits per frag: 0.189484 processed 3500000 fragments hits: 649858, hits per frag: 0.19531 processed 4000000 fragments hits: 743378, hits per frag: 0.187172 processed 4500000 fragments hits: 835475, hits per frag: 0.186582 processed 5000000 fragments hits: 928649, hits per frag: 0.188136 processed 5500000 fragments hits: 1021661, hits per frag: 0.189301 processed 6000000 fragments hits: 1114257, hits per frag: 0.186179 processed 6500000 fragments hits: 1208575, hits per frag: 0.187416 processed 7000001 fragments hits: 1301515, hits per frag: 0.190693 processed 7500000 fragments hits: 1395434, hits per frag: 0.187867 processed 8000000 fragments hits: 1488072, hits per frag: 0.188166 processed 8500000 fragments hits: 1580351, hits per frag: 0.186957 processed 9000000 fragments hits: 1672935, hits per frag: 0.188184 processed 9500000 fragments hits: 1764995, hits per frag: 0.188553 processed 10000000 fragments hits: 1857934, hits per frag: 0.18957 processed 10500001 fragments hits: 1950482, hits per frag: 0.187357 processed 11000000 fragments hits: 2042555, hits per frag: 0.186868 processed 11500000 fragments hits: 2135518, hits per frag: 0.186436 processed 12000000 fragments hits: 2229180, hits per frag: 0.186995 processed 12500000 fragments hits: 2321383, hits per frag: 0.187573 processed 13000000 fragments hits: 2414832, hits per frag: 0.186303 processed 13500000 fragments hits: 2506159, hits per frag: 0.186247 processed 14000000 fragments hits: 2599472, hits per frag: 0.186297 processed 14500000 fragments hits: 2691351, hits per frag: 0.187388 processed 15000000 fragments hits: 2783511, hits per frag: 0.186281 processed 15500001 fragments hits: 2875955, hits per frag: 0.186962 processed 16000000 fragments hits: 2967859, hits per frag: 0.185975 processed 16500000 fragments hits: 3061637, hits per frag: 0.185654 processed 17000000 fragments hits: 3154464, hits per frag: 0.188256 processed 17500000 fragments hits: 3246988, hits per frag: 0.186214 processed 18000000 fragments hits: 3338944, hits per frag: 0.185622 processed 18500000 fragments hits: 3430773, hits per frag: 0.18576 processed 19000000 fragments hits: 3523567, hits per frag: 0.185985 processed 19500000 fragments hits: 3617009, hits per frag: 0.187023 processed 20000002 fragments hits: 3709816, hits per frag: 0.186209 processed 20500000 fragments hits: 3803228, hits per frag: 0.185586 processed 21000001 fragments hits: 3896995, hits per frag: 0.186511 processed 21500000 fragments hits: 3990441, hits per frag: 0.185988 processed 22000000 fragments hits: 4083833, hits per frag: 0.187109 processed 22500001 fragments hits: 4177320, hits per frag: 0.18645 processed 23000000 fragments hits: 4269925, hits per frag: 0.18651 processed 23500000 fragments hits: 4362909, hits per frag: 0.186051 processed 24000000 fragments hits: 4455581, hits per frag: 0.185971 processed 24500000 fragments hits: 4547870, hits per frag: 0.186273 processed 25000000 fragments hits: 4640078, hits per frag: 0.18639 processed 25500000 fragments hits: 4732933, hits per frag: 0.186293 processed 26000000 fragments hits: 4825449, hits per frag: 0.185697 processed 26500000 fragments hits: 4918456, hits per frag: 0.185923 processed 27000000 fragments hits: 5010349, hits per frag: 0.186238 processed 27500000 fragments hits: 5102965, hits per frag: 0.186695 processed 28000000 fragments hits: 5195144, hits per frag: 0.185613 processed 28500000 fragments hits: 5286878, hits per frag: 0.185966 processed 29000000 fragments hits: 5379335, hits per frag: 0.185883 processed 29500000 fragments hits: 5471123, hits per frag: 0.185736 processed 30000000 fragments hits: 5563742, hits per frag: 0.185479 processed 30500000 fragments hits: 5655915, hits per frag: 0.187087 processed 31000000 fragments hits: 5747684, hits per frag: 0.185884 processed 31500000 fragments hits: 5840869, hits per frag: 0.186676 [2019-03-05 23:28:24.010] [jointLog] [info] Computed 8044 rich equivalence classes for further processing [2019-03-05 23:28:24.010] [jointLog] [info] Counted 2909485 total reads in the equivalence classes [2019-03-05 23:28:24.023] [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. [2019-03-05 23:28:24.023] [jointLog] [warning] Only 2909485 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:28:24.023] [jointLog] [info] Mapping rate = 9.19069% [2019-03-05 23:28:24.023] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:28:24.024] [jointLog] [info] Starting optimizer [2019-03-05 23:28:24.028] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:28:24.028] [jointLog] [info] iteration = 0 | max rel diff. = 793.533 [2019-03-05 23:28:24.070] [jointLog] [info] iteration = 100 | max rel diff. = 0.119625 [2019-03-05 23:28:24.102] [jointLog] [info] iteration = 200 | max rel diff. = 0.054258 [2019-03-05 23:28:24.138] [jointLog] [info] iteration = 300 | max rel diff. = 0.03699 [2019-03-05 23:28:24.169] [jointLog] [info] iteration = 400 | max rel diff. = 0.0288367 [2019-03-05 23:28:24.196] [jointLog] [info] iteration = 500 | max rel diff. = 0.0234562 [2019-03-05 23:28:24.225] [jointLog] [info] iteration = 600 | max rel diff. = 0.0175279 [2019-03-05 23:28:24.252] [jointLog] [info] iteration = 700 | max rel diff. = 0.0169277 [2019-03-05 23:28:24.275] [jointLog] [info] iteration = 800 | max rel diff. = 0.0117825 [2019-03-05 23:28:24.306] [jointLog] [info] iteration = 900 | max rel diff. = 0.0117832 [2019-03-05 23:28:24.341] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0104581 [2019-03-05 23:28:24.393] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0102834 [2019-03-05 23:28:24.399] [jointLog] [info] iteration = 1114 | max rel diff. = 0.00872382 [2019-03-05 23:28:24.399] [jointLog] [info] Finished optimizer [2019-03-05 23:28:24.399] [jointLog] [info] writing output [2019-03-05 23:28:24.429] [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/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > bleached_44_03/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P02-ACAGTG-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P02-ACAGTG-READ2-Sequences.txt.gz_val_2.fq.gz) -o non-bleached_K5_01 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { non-bleached_K5_01 } ### [ threads ] => { 23 } Logs will be written to non-bleached_K5_01/logs [2019-03-05 23:28:24.846] [jointLog] [info] parsing read library format [2019-03-05 23:28:24.846] [jointLog] [info] There is 1 library. [2019-03-05 23:28:24.918] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:28:24.918] [jointLog] [info] Loading Quasi index [2019-03-05 23:28:24.918] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:28:24.966] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:28:24.979] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:28:24.984] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:28:24.988] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:28:24.988] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:28:25.340] [jointLog] [info] done [2019-03-05 23:28:25.340] [jointLog] [info] Index contained 5838 targets [2019-03-05 23:28:25.340] [stderrLog] [info] Done loading index  processed 500000 fragments hits: 98484, hits per frag: 0.301935 processed 1000000 fragments hits: 198039, hits per frag: 0.203658 processed 1500000 fragments hits: 295930, hits per frag: 0.210654 processed 2000000 fragments hits: 396535, hits per frag: 0.206904 processed 2500000 fragments hits: 496005, hits per frag: 0.209923 processed 3000000 fragments hits: 595418, hits per frag: 0.200305 processed 3500000 fragments hits: 694844, hits per frag: 0.200456 processed 4000000 fragments hits: 793701, hits per frag: 0.206079 processed 4500000 fragments hits: 892049, hits per frag: 0.204272 processed 5000000 fragments hits: 990873, hits per frag: 0.200202 processed 5500000 fragments hits: 1089888, hits per frag: 0.202532 processed 6000000 fragments hits: 1189153, hits per frag: 0.20043 processed 6500000 fragments hits: 1288160, hits per frag: 0.203199 processed 7000000 fragments hits: 1386920, hits per frag: 0.198662 processed 7500000 fragments hits: 1485439, hits per frag: 0.204036 processed 8000000 fragments hits: 1584686, hits per frag: 0.198947 processed 8500001 fragments hits: 1683770, hits per frag: 0.198502 processed 9000000 fragments hits: 1782856, hits per frag: 0.20054 processed 9500000 fragments hits: 1880987, hits per frag: 0.198973 processed 10000000 fragments hits: 1981195, hits per frag: 0.202296 processed 10500000 fragments hits: 2079071, hits per frag: 0.198922 processed 11000000 fragments hits: 2177775, hits per frag: 0.198314 processed 11500000 fragments hits: 2276626, hits per frag: 0.198092 processed 12000000 fragments hits: 2375449, hits per frag: 0.204075 processed 12500000 fragments hits: 2473836, hits per frag: 0.198795 processed 13000000 fragments hits: 2572717, hits per frag: 0.198107 processed 13500000 fragments hits: 2670008, hits per frag: 0.199438 processed 14000000 fragments hits: 2768459, hits per frag: 0.198978 processed 14500000 fragments hits: 2866541, hits per frag: 0.197823 processed 15000000 fragments hits: 2965797, hits per frag: 0.198462 processed 15500000 fragments hits: 3065096, hits per frag: 0.199015 processed 16000000 fragments hits: 3164251, hits per frag: 0.198497 processed 16500000 fragments hits: 3262563, hits per frag: 0.198471 processed 17000000 fragments hits: 3360774, hits per frag: 0.198103 processed 17500000 fragments hits: 3461229, hits per frag: 0.198276 processed 18000000 fragments hits: 3560718, hits per frag: 0.198843 processed 18500000 fragments hits: 3658730, hits per frag: 0.198162 processed 19000000 fragments hits: 3758147, hits per frag: 0.19943 processed 19500000 fragments hits: 3857899, hits per frag: 0.198445 processed 20000000 fragments hits: 3956106, hits per frag: 0.199783 processed 20500000 fragments hits: 4055491, hits per frag: 0.198029 processed 21000000 fragments hits: 4154130, hits per frag: 0.197897 processed 21500000 fragments hits: 4253149, hits per frag: 0.198437 processed 22000000 fragments hits: 4352905, hits per frag: 0.198477 processed 22500000 fragments hits: 4452192, hits per frag: 0.198788 processed 23000000 fragments hits: 4551409, hits per frag: 0.198455 processed 23500000 fragments hits: 4649894, hits per frag: 0.198211 [2019-03-05 23:30:49.656] [jointLog] [info] Computed 7091 rich equivalence classes for further processing [2019-03-05 23:30:49.656] [jointLog] [info] Counted 2346516 total reads in the equivalence classes [2019-03-05 23:30:49.669] [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. [2019-03-05 23:30:49.670] [jointLog] [warning] Only 2346516 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:30:49.670] [jointLog] [info] Mapping rate = 9.83271% [2019-03-05 23:30:49.670] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:30:49.671] [jointLog] [info] Starting optimizer [2019-03-05 23:30:49.674] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:30:49.675] [jointLog] [info] iteration = 0 | max rel diff. = 538.3 [2019-03-05 23:30:49.721] [jointLog] [info] iteration = 100 | max rel diff. = 0.11848 [2019-03-05 23:30:49.784] [jointLog] [info] iteration = 200 | max rel diff. = 0.0573701 [2019-03-05 23:30:49.821] [jointLog] [info] iteration = 300 | max rel diff. = 0.039137 [2019-03-05 23:30:49.852] [jointLog] [info] iteration = 400 | max rel diff. = 0.0273515 [2019-03-05 23:30:49.883] [jointLog] [info] iteration = 500 | max rel diff. = 0.0220555 [2019-03-05 23:30:49.925] [jointLog] [info] iteration = 600 | max rel diff. = 0.0192173 [2019-03-05 23:30:49.953] [jointLog] [info] iteration = 700 | max rel diff. = 0.0157131 [2019-03-05 23:30:49.977] [jointLog] [info] iteration = 800 | max rel diff. = 0.0128053 [2019-03-05 23:30:49.998] [jointLog] [info] iteration = 900 | max rel diff. = 0.0111954 [2019-03-05 23:30:50.023] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0107777 [2019-03-05 23:30:50.039] [jointLog] [info] iteration = 1065 | max rel diff. = 0.00971628 [2019-03-05 23:30:50.040] [jointLog] [info] Finished optimizer [2019-03-05 23:30:50.040] [jointLog] [info] writing output [2019-03-05 23:30:50.058] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: non-bleached_K5_01/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_K5_01/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > non-bleached_K5_01/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P10-TAGCTT-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P10-TAGCTT-READ2-Sequences.txt.gz_val_2.fq.gz) -o non-bleached_K5_02 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { non-bleached_K5_02 } ### [ threads ] => { 23 } Logs will be written to non-bleached_K5_02/logs [2019-03-05 23:30:50.574] [jointLog] [info] parsing read library format [2019-03-05 23:30:50.574] [jointLog] [info] There is 1 library. [2019-03-05 23:30:50.651] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:30:50.651] [jointLog] [info] Loading Quasi index [2019-03-05 23:30:50.651] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:30:50.753] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:30:50.766] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:30:50.770] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:30:50.773] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:30:50.773] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:30:51.194] [jointLog] [info] done [2019-03-05 23:30:51.194] [jointLog] [info] Index contained 5838 targets [2019-03-05 23:30:51.194] [stderrLog] [info] Done loading index  processed 500001 fragments hits: 85091, hits per frag: 0.204719 processed 1000000 fragments hits: 169851, hits per frag: 0.208725 processed 1500000 fragments hits: 255197, hits per frag: 0.172738 processed 2000001 fragments hits: 339660, hits per frag: 0.177903 processed 2500000 fragments hits: 425595, hits per frag: 0.196533 processed 3000000 fragments hits: 510544, hits per frag: 0.17265 processed 3500000 fragments hits: 596732, hits per frag: 0.17289 processed 4000000 fragments hits: 682002, hits per frag: 0.172239 processed 4500000 fragments hits: 766700, hits per frag: 0.171719 processed 5000000 fragments hits: 851648, hits per frag: 0.172268 processed 5500000 fragments hits: 937303, hits per frag: 0.172129 processed 6000000 fragments hits: 1022782, hits per frag: 0.171575 processed 6500000 fragments hits: 1108133, hits per frag: 0.171306 processed 7000000 fragments hits: 1193799, hits per frag: 0.17278 processed 7500000 fragments hits: 1278960, hits per frag: 0.173227 processed 8000000 fragments hits: 1365180, hits per frag: 0.172385 processed 8500001 fragments hits: 1449879, hits per frag: 0.172985 processed 9000000 fragments hits: 1535332, hits per frag: 0.171715 processed 9500000 fragments hits: 1621177, hits per frag: 0.170756 processed 10000000 fragments hits: 1707107, hits per frag: 0.172426 processed 10500000 fragments hits: 1792369, hits per frag: 0.172257 processed 11000000 fragments hits: 1877401, hits per frag: 0.171556 processed 11500000 fragments hits: 1962415, hits per frag: 0.171549 processed 12000000 fragments hits: 2047754, hits per frag: 0.1716 processed 12500001 fragments hits: 2132620, hits per frag: 0.171172 processed 13000000 fragments hits: 2217744, hits per frag: 0.17154 processed 13500000 fragments hits: 2303037, hits per frag: 0.17151 processed 14000000 fragments hits: 2387332, hits per frag: 0.171372 processed 14500001 fragments hits: 2473372, hits per frag: 0.170996 processed 15000000 fragments hits: 2557480, hits per frag: 0.171318 processed 15500000 fragments hits: 2642332, hits per frag: 0.1706 processed 16000000 fragments hits: 2726362, hits per frag: 0.171905 processed 16500000 fragments hits: 2811744, hits per frag: 0.170927 processed 17000000 fragments hits: 2897606, hits per frag: 0.17085 processed 17500001 fragments hits: 2984132, hits per frag: 0.1744 processed 18000000 fragments hits: 3068337, hits per frag: 0.171005 processed 18500000 fragments hits: 3153132, hits per frag: 0.17125 processed 19000000 fragments hits: 3238269, hits per frag: 0.170776 processed 19500000 fragments hits: 3323171, hits per frag: 0.171196 processed 20000000 fragments hits: 3409367, hits per frag: 0.171284 processed 20500000 fragments hits: 3494881, hits per frag: 0.171093 processed 21000000 fragments hits: 3579268, hits per frag: 0.170914 processed 21500001 fragments hits: 3664801, hits per frag: 0.170738 processed 22000000 fragments hits: 3750151, hits per frag: 0.170466 processed 22500000 fragments hits: 3834746, hits per frag: 0.171304 processed 23000000 fragments hits: 3920977, hits per frag: 0.170806 processed 23500000 fragments hits: 4006672, hits per frag: 0.170514 processed 24000000 fragments hits: 4092454, hits per frag: 0.171101 processed 24500000 fragments hits: 4177902, hits per frag: 0.1708 processed 25000000 fragments hits: 4264590, hits per frag: 0.170823 processed 25500000 fragments hits: 4350751, hits per frag: 0.170816 processed 26000000 fragments hits: 4436167, hits per frag: 0.172414 processed 26500001 fragments hits: 4519683, hits per frag: 0.17093 processed 27000000 fragments hits: 4604893, hits per frag: 0.17081 processed 27500000 fragments hits: 4689442, hits per frag: 0.170956 processed 28000000 fragments hits: 4775327, hits per frag: 0.171057 processed 28500000 fragments hits: 4860145, hits per frag: 0.170577 processed 29000000 fragments hits: 4945147, hits per frag: 0.171081 processed 29500000 fragments hits: 5031992, hits per frag: 0.171065 processed 30000000 fragments hits: 5116642, hits per frag: 0.170717 processed 30500000 fragments hits: 5202354, hits per frag: 0.170712 processed 31000000 fragments hits: 5287618, hits per frag: 0.170876 processed 31500000 fragments hits: 5372553, hits per frag: 0.170855 processed 32000000 fragments hits: 5457470, hits per frag: 0.170631 processed 32500000 fragments hits: 5541763, hits per frag: 0.171026 processed 33000000 fragments hits: 5627109, hits per frag: 0.171002 [2019-03-05 23:33:59.710] [jointLog] [info] Computed 8127 rich equivalence classes for further processing [2019-03-05 23:33:59.710] [jointLog] [info] Counted 2818911 total reads in the equivalence classes [2019-03-05 23:33:59.722] [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. [2019-03-05 23:33:59.723] [jointLog] [warning] Only 2818911 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:33:59.723] [jointLog] [info] Mapping rate = 8.52724% [2019-03-05 23:33:59.723] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:33:59.723] [jointLog] [info] Starting optimizer [2019-03-05 23:33:59.734] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:33:59.735] [jointLog] [info] iteration = 0 | max rel diff. = 673.367 [2019-03-05 23:33:59.784] [jointLog] [info] iteration = 100 | max rel diff. = 0.123864 [2019-03-05 23:33:59.820] [jointLog] [info] iteration = 200 | max rel diff. = 0.0596478 [2019-03-05 23:33:59.842] [jointLog] [info] iteration = 300 | max rel diff. = 0.0380172 [2019-03-05 23:33:59.863] [jointLog] [info] iteration = 400 | max rel diff. = 0.0270397 [2019-03-05 23:33:59.882] [jointLog] [info] iteration = 500 | max rel diff. = 0.0249081 [2019-03-05 23:33:59.902] [jointLog] [info] iteration = 600 | max rel diff. = 0.0153599 [2019-03-05 23:33:59.922] [jointLog] [info] iteration = 700 | max rel diff. = 0.0153333 [2019-03-05 23:33:59.942] [jointLog] [info] iteration = 800 | max rel diff. = 0.0134629 [2019-03-05 23:33:59.961] [jointLog] [info] iteration = 900 | max rel diff. = 0.0114257 [2019-03-05 23:33:59.978] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0102503 [2019-03-05 23:33:59.997] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0102505 [2019-03-05 23:34:00.017] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0102506 [2019-03-05 23:34:00.021] [jointLog] [info] iteration = 1224 | max rel diff. = 0.00902963 [2019-03-05 23:34:00.021] [jointLog] [info] Finished optimizer [2019-03-05 23:34:00.021] [jointLog] [info] writing output [2019-03-05 23:34:00.046] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: non-bleached_K5_02/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_K5_02/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > non-bleached_K5_02/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P15-GTTTCG-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P15-GTTTCG-READ2-Sequences.txt.gz_val_2.fq.gz) -o non-bleached_K5_03 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { non-bleached_K5_03 } ### [ threads ] => { 23 } Logs will be written to non-bleached_K5_03/logs [2019-03-05 23:34:00.404] [jointLog] [info] parsing read library format [2019-03-05 23:34:00.404] [jointLog] [info] There is 1 library. [2019-03-05 23:34:00.475] [jointLog] [info] Loading Quasi index [2019-03-05 23:34:00.475] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:34:00.476] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:34:00.521] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:34:00.531] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:34:00.535] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:34:00.536] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:34:00.536] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:34:00.940] [stderrLog] [info] Done loading index [2019-03-05 23:34:00.940] [jointLog] [info] done [2019-03-05 23:34:00.940] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 92998, hits per frag: 0.208165 processed 1000000 fragments hits: 184910, hits per frag: 0.195265 processed 1500000 fragments hits: 277281, hits per frag: 0.202554 processed 2000000 fragments hits: 370140, hits per frag: 0.194049 processed 2500000 fragments hits: 463115, hits per frag: 0.188377 processed 3000000 fragments hits: 555675, hits per frag: 0.187496 processed 3500000 fragments hits: 648449, hits per frag: 0.186512 processed 4000000 fragments hits: 741582, hits per frag: 0.188702 processed 4500001 fragments hits: 834103, hits per frag: 0.188694 processed 5000000 fragments hits: 926520, hits per frag: 0.187101 processed 5500001 fragments hits: 1019073, hits per frag: 0.187013 processed 6000000 fragments hits: 1111560, hits per frag: 0.185989 processed 6500000 fragments hits: 1204566, hits per frag: 0.187328 processed 7000000 fragments hits: 1295938, hits per frag: 0.186962 processed 7500000 fragments hits: 1388634, hits per frag: 0.187826 processed 8000000 fragments hits: 1480642, hits per frag: 0.186423 processed 8500000 fragments hits: 1572414, hits per frag: 0.186114 processed 9000000 fragments hits: 1665909, hits per frag: 0.190021 processed 9500000 fragments hits: 1758348, hits per frag: 0.188516 processed 10000000 fragments hits: 1851326, hits per frag: 0.186733 processed 10500000 fragments hits: 1944302, hits per frag: 0.186261 processed 11000000 fragments hits: 2036466, hits per frag: 0.18752 processed 11500000 fragments hits: 2130339, hits per frag: 0.185528 processed 12000000 fragments hits: 2223447, hits per frag: 0.185573 processed 12500000 fragments hits: 2316654, hits per frag: 0.186025 processed 13000000 fragments hits: 2409096, hits per frag: 0.186051 processed 13500000 fragments hits: 2502539, hits per frag: 0.186904 processed 14000000 fragments hits: 2595751, hits per frag: 0.188301 processed 14500000 fragments hits: 2688743, hits per frag: 0.185676 processed 15000000 fragments hits: 2781262, hits per frag: 0.185969 processed 15500000 fragments hits: 2873574, hits per frag: 0.187953 processed 16000000 fragments hits: 2965291, hits per frag: 0.185847 processed 16500000 fragments hits: 3058357, hits per frag: 0.185824 processed 17000000 fragments hits: 3150770, hits per frag: 0.186137 processed 17500000 fragments hits: 3243731, hits per frag: 0.186105 processed 18000000 fragments hits: 3336489, hits per frag: 0.187085 processed 18500000 fragments hits: 3428880, hits per frag: 0.186632 processed 19000000 fragments hits: 3520866, hits per frag: 0.186153 processed 19500000 fragments hits: 3612803, hits per frag: 0.185803 processed 20000000 fragments hits: 3704999, hits per frag: 0.185596 processed 20500000 fragments hits: 3796795, hits per frag: 0.186106 processed 21000000 fragments hits: 3889023, hits per frag: 0.185866 processed 21500001 fragments hits: 3981785, hits per frag: 0.185552 processed 22000000 fragments hits: 4074413, hits per frag: 0.185329 processed 22500000 fragments hits: 4165792, hits per frag: 0.185439 processed 23000000 fragments hits: 4259837, hits per frag: 0.185568 processed 23500000 fragments hits: 4351633, hits per frag: 0.185925 processed 24000000 fragments hits: 4445496, hits per frag: 0.185569 processed 24500000 fragments hits: 4537344, hits per frag: 0.186049 processed 25000000 fragments hits: 4630015, hits per frag: 0.185617 processed 25500000 fragments hits: 4721274, hits per frag: 0.185683 processed 26000000 fragments hits: 4814307, hits per frag: 0.185344 processed 26500000 fragments hits: 4907639, hits per frag: 0.185648 processed 27000000 fragments hits: 4999897, hits per frag: 0.18578 processed 27500000 fragments hits: 5092392, hits per frag: 0.185562 processed 28000000 fragments hits: 5185869, hits per frag: 0.185565 processed 28500000 fragments hits: 5278215, hits per frag: 0.188644 processed 29000001 fragments hits: 5369830, hits per frag: 0.186004 processed 29500000 fragments hits: 5461529, hits per frag: 0.186039 processed 30000000 fragments hits: 5554843, hits per frag: 0.185768 processed 30500000 fragments hits: 5647086, hits per frag: 0.185505 processed 31000000 fragments hits: 5740271, hits per frag: 0.185787 processed 31500000 fragments hits: 5832383, hits per frag: 0.185522 processed 32000000 fragments hits: 5923925, hits per frag: 0.185279 processed 32500000 fragments hits: 6017306, hits per frag: 0.185491 processed 33000000 fragments hits: 6110408, hits per frag: 0.185719 processed 33500000 fragments hits: 6203090, hits per frag: 0.185621 processed 34000000 fragments hits: 6295279, hits per frag: 0.185271 processed 34500000 fragments hits: 6387305, hits per frag: 0.185487 [2019-03-05 23:37:18.705] [jointLog] [info] Computed 7671 rich equivalence classes for further processing [2019-03-05 23:37:18.705] [jointLog] [info] Counted 3126572 total reads in the equivalence classes [2019-03-05 23:37:18.718] [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. [2019-03-05 23:37:18.718] [jointLog] [warning] Only 3126572 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:37:18.718] [jointLog] [info] Mapping rate = 9.05407% [2019-03-05 23:37:18.718] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:37:18.719] [jointLog] [info] Starting optimizer [2019-03-05 23:37:18.723] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:37:18.723] [jointLog] [info] iteration = 0 | max rel diff. = 713.33 [2019-03-05 23:37:18.760] [jointLog] [info] iteration = 100 | max rel diff. = 0.115427 [2019-03-05 23:37:18.785] [jointLog] [info] iteration = 200 | max rel diff. = 0.0575004 [2019-03-05 23:37:18.806] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433135 [2019-03-05 23:37:18.824] [jointLog] [info] iteration = 400 | max rel diff. = 0.0298499 [2019-03-05 23:37:18.842] [jointLog] [info] iteration = 500 | max rel diff. = 0.0247586 [2019-03-05 23:37:18.861] [jointLog] [info] iteration = 600 | max rel diff. = 0.0191565 [2019-03-05 23:37:18.882] [jointLog] [info] iteration = 700 | max rel diff. = 0.0155014 [2019-03-05 23:37:18.900] [jointLog] [info] iteration = 800 | max rel diff. = 0.0129273 [2019-03-05 23:37:18.921] [jointLog] [info] iteration = 900 | max rel diff. = 0.0101388 [2019-03-05 23:37:18.946] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0101358 [2019-03-05 23:37:18.969] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0101357 [2019-03-05 23:37:18.977] [jointLog] [info] iteration = 1143 | max rel diff. = 0.00895936 [2019-03-05 23:37:18.977] [jointLog] [info] Finished optimizer [2019-03-05 23:37:18.977] [jointLog] [info] writing output [2019-03-05 23:37:18.989] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: non-bleached_K5_03/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_K5_03/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > non-bleached_K5_03/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P04-GTCCGC-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P04-GTCCGC-READ2-Sequences.txt.gz_val_2.fq.gz) -o non-bleached_44_01 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { non-bleached_44_01 } ### [ threads ] => { 23 } Logs will be written to non-bleached_44_01/logs [2019-03-05 23:37:19.516] [jointLog] [info] parsing read library format [2019-03-05 23:37:19.516] [jointLog] [info] There is 1 library. [2019-03-05 23:37:19.611] [jointLog] [info] Loading Quasi index [2019-03-05 23:37:19.611] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:37:19.611] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:37:19.668] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:37:19.680] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:37:19.686] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:37:19.689] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:37:19.689] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:37:20.069] [stderrLog] [info] Done loading index [2019-03-05 23:37:20.069] [jointLog] [info] done [2019-03-05 23:37:20.069] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 93122, hits per frag: 0.257323 processed 1000000 fragments hits: 185825, hits per frag: 0.195589 processed 1500000 fragments hits: 278684, hits per frag: 0.188197 processed 2000000 fragments hits: 372023, hits per frag: 0.190036 processed 2500001 fragments hits: 465622, hits per frag: 0.190545 processed 3000000 fragments hits: 557363, hits per frag: 0.186501 processed 3500000 fragments hits: 649314, hits per frag: 0.189993 processed 4000000 fragments hits: 742452, hits per frag: 0.188355 processed 4500000 fragments hits: 835040, hits per frag: 0.187067 processed 5000000 fragments hits: 927990, hits per frag: 0.187346 processed 5500000 fragments hits: 1020647, hits per frag: 0.185775 processed 6000000 fragments hits: 1114050, hits per frag: 0.186248 processed 6500000 fragments hits: 1205658, hits per frag: 0.186955 processed 7000000 fragments hits: 1298083, hits per frag: 0.187202 processed 7500000 fragments hits: 1390912, hits per frag: 0.18723 processed 8000000 fragments hits: 1483405, hits per frag: 0.190733 processed 8500000 fragments hits: 1576470, hits per frag: 0.188332 processed 9000000 fragments hits: 1669079, hits per frag: 0.185951 processed 9500000 fragments hits: 1762668, hits per frag: 0.186728 processed 10000000 fragments hits: 1855222, hits per frag: 0.187243 processed 10500000 fragments hits: 1948312, hits per frag: 0.18645 processed 11000000 fragments hits: 2041478, hits per frag: 0.201007 processed 11500001 fragments hits: 2133983, hits per frag: 0.186851 processed 12000000 fragments hits: 2226692, hits per frag: 0.185924 processed 12500000 fragments hits: 2318410, hits per frag: 0.18702 processed 13000000 fragments hits: 2410866, hits per frag: 0.187436 processed 13500000 fragments hits: 2503245, hits per frag: 0.186077 processed 14000000 fragments hits: 2595545, hits per frag: 0.186709 processed 14500000 fragments hits: 2687823, hits per frag: 0.18599 processed 15000000 fragments hits: 2779933, hits per frag: 0.188444 processed 15500000 fragments hits: 2872943, hits per frag: 0.186333 processed 16000000 fragments hits: 2964130, hits per frag: 0.185606 processed 16500000 fragments hits: 3056208, hits per frag: 0.186298 processed 17000000 fragments hits: 3148530, hits per frag: 0.185676 processed 17500000 fragments hits: 3241913, hits per frag: 0.186858 processed 18000000 fragments hits: 3334264, hits per frag: 0.185688 processed 18500000 fragments hits: 3426116, hits per frag: 0.186852 processed 19000000 fragments hits: 3519588, hits per frag: 0.185269 processed 19500000 fragments hits: 3612278, hits per frag: 0.187049 processed 20000000 fragments hits: 3704840, hits per frag: 0.186406 processed 20500001 fragments hits: 3796295, hits per frag: 0.185537 processed 21000000 fragments hits: 3888745, hits per frag: 0.186567 processed 21500000 fragments hits: 3981970, hits per frag: 0.185722 processed 22000000 fragments hits: 4075535, hits per frag: 0.186519 [2019-03-05 23:39:47.418] [jointLog] [info] Computed 7356 rich equivalence classes for further processing [2019-03-05 23:39:47.418] [jointLog] [info] Counted 2065907 total reads in the equivalence classes [2019-03-05 23:39:47.431] [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. [2019-03-05 23:39:47.432] [jointLog] [warning] Only 2065907 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:39:47.432] [jointLog] [info] Mapping rate = 9.18309% [2019-03-05 23:39:47.432] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:39:47.432] [jointLog] [info] Starting optimizer [2019-03-05 23:39:47.436] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:39:47.437] [jointLog] [info] iteration = 0 | max rel diff. = 551.051 [2019-03-05 23:39:47.462] [jointLog] [info] iteration = 100 | max rel diff. = 0.124308 [2019-03-05 23:39:47.480] [jointLog] [info] iteration = 200 | max rel diff. = 0.062106 [2019-03-05 23:39:47.501] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433965 [2019-03-05 23:39:47.522] [jointLog] [info] iteration = 400 | max rel diff. = 0.0270723 [2019-03-05 23:39:47.541] [jointLog] [info] iteration = 500 | max rel diff. = 0.0244155 [2019-03-05 23:39:47.564] [jointLog] [info] iteration = 600 | max rel diff. = 0.016607 [2019-03-05 23:39:47.585] [jointLog] [info] iteration = 700 | max rel diff. = 0.0147569 [2019-03-05 23:39:47.609] [jointLog] [info] iteration = 800 | max rel diff. = 0.0137183 [2019-03-05 23:39:47.627] [jointLog] [info] iteration = 900 | max rel diff. = 0.0109868 [2019-03-05 23:39:47.644] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0109868 [2019-03-05 23:39:47.648] [jointLog] [info] iteration = 1020 | max rel diff. = 0.00873992 [2019-03-05 23:39:47.648] [jointLog] [info] Finished optimizer [2019-03-05 23:39:47.648] [jointLog] [info] writing output [2019-03-05 23:39:47.661] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: non-bleached_44_01/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_44_01/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > non-bleached_44_01/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P05-GAGTGG-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P05-GAGTGG-READ2-Sequences.txt.gz_val_2.fq.gz) -o non-bleached_44_02 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { non-bleached_44_02 } ### [ threads ] => { 23 } Logs will be written to non-bleached_44_02/logs [2019-03-05 23:39:47.922] [jointLog] [info] parsing read library format [2019-03-05 23:39:47.922] [jointLog] [info] There is 1 library. [2019-03-05 23:39:47.997] [jointLog] [info] Loading Quasi index [2019-03-05 23:39:47.997] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:39:47.997] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:39:48.065] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:39:48.077] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:39:48.080] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:39:48.083] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:39:48.083] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:39:48.428] [stderrLog] [info] Done loading index [2019-03-05 23:39:48.428] [jointLog] [info] done [2019-03-05 23:39:48.428] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 91844, hits per frag: 0.198927 processed 1000000 fragments hits: 183131, hits per frag: 0.186839 processed 1500000 fragments hits: 275508, hits per frag: 0.189949 processed 2000000 fragments hits: 368124, hits per frag: 0.188615 processed 2500000 fragments hits: 459538, hits per frag: 0.189748 processed 3000000 fragments hits: 551361, hits per frag: 0.189064 processed 3500001 fragments hits: 643082, hits per frag: 0.191531 processed 4000000 fragments hits: 734842, hits per frag: 0.184897 processed 4500000 fragments hits: 825520, hits per frag: 0.186107 processed 5000000 fragments hits: 917826, hits per frag: 0.184104 processed 5500000 fragments hits: 1009134, hits per frag: 0.188868 processed 6000000 fragments hits: 1100636, hits per frag: 0.183679 processed 6500000 fragments hits: 1192618, hits per frag: 0.183719 processed 7000000 fragments hits: 1283680, hits per frag: 0.186859 processed 7500000 fragments hits: 1375369, hits per frag: 0.183854 processed 8000000 fragments hits: 1467785, hits per frag: 0.183886 processed 8500000 fragments hits: 1559952, hits per frag: 0.183907 processed 9000001 fragments hits: 1653345, hits per frag: 0.185318 processed 9500000 fragments hits: 1744330, hits per frag: 0.185444 processed 10000000 fragments hits: 1836526, hits per frag: 0.184497 processed 10500001 fragments hits: 1928338, hits per frag: 0.184137 processed 11000000 fragments hits: 2020576, hits per frag: 0.183972 processed 11500000 fragments hits: 2113275, hits per frag: 0.185158 processed 12000000 fragments hits: 2204397, hits per frag: 0.186522 processed 12500000 fragments hits: 2296315, hits per frag: 0.184073 processed 13000000 fragments hits: 2388266, hits per frag: 0.184346 processed 13500000 fragments hits: 2479418, hits per frag: 0.184143 processed 14000000 fragments hits: 2571809, hits per frag: 0.184724 processed 14500000 fragments hits: 2663821, hits per frag: 0.184113 processed 15000000 fragments hits: 2755172, hits per frag: 0.184345 processed 15500000 fragments hits: 2846523, hits per frag: 0.184556 processed 16000000 fragments hits: 2936924, hits per frag: 0.183656 processed 16500000 fragments hits: 3028861, hits per frag: 0.184119 processed 17000000 fragments hits: 3120121, hits per frag: 0.184421 processed 17500000 fragments hits: 3212246, hits per frag: 0.184145 processed 18000000 fragments hits: 3303826, hits per frag: 0.183973 processed 18500000 fragments hits: 3395689, hits per frag: 0.183711 processed 19000000 fragments hits: 3487602, hits per frag: 0.184296 processed 19500000 fragments hits: 3579873, hits per frag: 0.183645 processed 20000001 fragments hits: 3671942, hits per frag: 0.184053 processed 20500000 fragments hits: 3763610, hits per frag: 0.184226 processed 21000000 fragments hits: 3856199, hits per frag: 0.18412 processed 21500000 fragments hits: 3948524, hits per frag: 0.184189 processed 22000000 fragments hits: 4041079, hits per frag: 0.185339 processed 22500000 fragments hits: 4133618, hits per frag: 0.184109 processed 23000000 fragments hits: 4225280, hits per frag: 0.184371 processed 23500000 fragments hits: 4317405, hits per frag: 0.184054 processed 24000000 fragments hits: 4408716, hits per frag: 0.185273 processed 24500000 fragments hits: 4500641, hits per frag: 0.184101 processed 25000000 fragments hits: 4593233, hits per frag: 0.184039 processed 25500000 fragments hits: 4683958, hits per frag: 0.183884 processed 26000000 fragments hits: 4774192, hits per frag: 0.184328 [2019-03-05 23:42:34.431] [jointLog] [info] Computed 7419 rich equivalence classes for further processing [2019-03-05 23:42:34.431] [jointLog] [info] Counted 2384873 total reads in the equivalence classes [2019-03-05 23:42:34.442] [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. [2019-03-05 23:42:34.442] [jointLog] [warning] Only 2384873 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:42:34.442] [jointLog] [info] Mapping rate = 9.14069% [2019-03-05 23:42:34.442] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:42:34.443] [jointLog] [info] Starting optimizer [2019-03-05 23:42:34.446] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:42:34.447] [jointLog] [info] iteration = 0 | max rel diff. = 587.754 [2019-03-05 23:42:34.488] [jointLog] [info] iteration = 100 | max rel diff. = 0.116773 [2019-03-05 23:42:34.514] [jointLog] [info] iteration = 200 | max rel diff. = 0.0558709 [2019-03-05 23:42:34.543] [jointLog] [info] iteration = 300 | max rel diff. = 0.0365182 [2019-03-05 23:42:34.575] [jointLog] [info] iteration = 400 | max rel diff. = 0.0289727 [2019-03-05 23:42:34.605] [jointLog] [info] iteration = 500 | max rel diff. = 0.0204904 [2019-03-05 23:42:34.629] [jointLog] [info] iteration = 600 | max rel diff. = 0.0189959 [2019-03-05 23:42:34.649] [jointLog] [info] iteration = 700 | max rel diff. = 0.016184 [2019-03-05 23:42:34.670] [jointLog] [info] iteration = 800 | max rel diff. = 0.0129729 [2019-03-05 23:42:34.689] [jointLog] [info] iteration = 900 | max rel diff. = 0.0120724 [2019-03-05 23:42:34.711] [jointLog] [info] iteration = 1000 | max rel diff. = 0.00959481 [2019-03-05 23:42:34.712] [jointLog] [info] Finished optimizer [2019-03-05 23:42:34.712] [jointLog] [info] writing output [2019-03-05 23:42:34.736] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: non-bleached_44_02/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_44_02/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > non-bleached_44_02/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P12-TGACCA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P12-TGACCA-READ2-Sequences.txt.gz_val_2.fq.gz) -o non-bleached_44_03 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { non-bleached_44_03 } ### [ threads ] => { 23 } Logs will be written to non-bleached_44_03/logs [2019-03-05 23:42:35.143] [jointLog] [info] parsing read library format [2019-03-05 23:42:35.143] [jointLog] [info] There is 1 library. [2019-03-05 23:42:35.286] [jointLog] [info] Loading Quasi index [2019-03-05 23:42:35.286] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:42:35.286] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:42:35.327] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:42:35.339] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:42:35.344] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:42:35.347] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:42:35.347] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:42:35.711] [stderrLog] [info] Done loading index [2019-03-05 23:42:35.711] [jointLog] [info] done [2019-03-05 23:42:35.711] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 88058, hits per frag: 0.186789 processed 1000000 fragments hits: 176206, hits per frag: 0.184994 processed 1500000 fragments hits: 264482, hits per frag: 0.181817 processed 2000000 fragments hits: 352093, hits per frag: 0.176559 processed 2500000 fragments hits: 439576, hits per frag: 0.181448 processed 3000000 fragments hits: 526085, hits per frag: 0.178867 processed 3500000 fragments hits: 614446, hits per frag: 0.178279 processed 4000000 fragments hits: 702109, hits per frag: 0.178267 processed 4500000 fragments hits: 790214, hits per frag: 0.177973 processed 5000000 fragments hits: 878749, hits per frag: 0.181615 processed 5500000 fragments hits: 967072, hits per frag: 0.17827 processed 6000000 fragments hits: 1054875, hits per frag: 0.177023 processed 6500000 fragments hits: 1142210, hits per frag: 0.177434 processed 7000000 fragments hits: 1229561, hits per frag: 0.176399 processed 7500000 fragments hits: 1316483, hits per frag: 0.176559 processed 8000000 fragments hits: 1402972, hits per frag: 0.177809 processed 8500000 fragments hits: 1490513, hits per frag: 0.176281 processed 9000000 fragments hits: 1577845, hits per frag: 0.176927 processed 9500000 fragments hits: 1664888, hits per frag: 0.175394 processed 10000000 fragments hits: 1752718, hits per frag: 0.176896 processed 10500000 fragments hits: 1840134, hits per frag: 0.182187 processed 11000001 fragments hits: 1929278, hits per frag: 0.176337 processed 11500000 fragments hits: 2017718, hits per frag: 0.176996 processed 12000000 fragments hits: 2103795, hits per frag: 0.175906 processed 12500001 fragments hits: 2190107, hits per frag: 0.175919 processed 13000000 fragments hits: 2277692, hits per frag: 0.175711 processed 13500000 fragments hits: 2365196, hits per frag: 0.175363 processed 14000000 fragments hits: 2453260, hits per frag: 0.176486 processed 14500000 fragments hits: 2540928, hits per frag: 0.175984 processed 15000000 fragments hits: 2628386, hits per frag: 0.176383 processed 15500000 fragments hits: 2715741, hits per frag: 0.175802 processed 16000000 fragments hits: 2803385, hits per frag: 0.175671 processed 16500000 fragments hits: 2890306, hits per frag: 0.176205 processed 17000000 fragments hits: 2979558, hits per frag: 0.17589 processed 17500000 fragments hits: 3067820, hits per frag: 0.176067 processed 18000000 fragments hits: 3155956, hits per frag: 0.17566 processed 18500000 fragments hits: 3243184, hits per frag: 0.176165 processed 19000001 fragments hits: 3331319, hits per frag: 0.176311 processed 19500000 fragments hits: 3419518, hits per frag: 0.177011 processed 20000000 fragments hits: 3507473, hits per frag: 0.175761 processed 20500001 fragments hits: 3596480, hits per frag: 0.176258 processed 21000000 fragments hits: 3683576, hits per frag: 0.175904 processed 21500000 fragments hits: 3771201, hits per frag: 0.175556 processed 22000000 fragments hits: 3858823, hits per frag: 0.17563 processed 22500000 fragments hits: 3946377, hits per frag: 0.17564 processed 23000000 fragments hits: 4033463, hits per frag: 0.17559 processed 23500000 fragments hits: 4120530, hits per frag: 0.177865 processed 24000000 fragments hits: 4208930, hits per frag: 0.175947 processed 24500000 fragments hits: 4296302, hits per frag: 0.175473 processed 25000000 fragments hits: 4384070, hits per frag: 0.175389 processed 25500000 fragments hits: 4471759, hits per frag: 0.175672 processed 26000001 fragments hits: 4558589, hits per frag: 0.175541 [2019-03-05 23:45:06.207] [jointLog] [info] Computed 7721 rich equivalence classes for further processing [2019-03-05 23:45:06.207] [jointLog] [info] Counted 2334407 total reads in the equivalence classes [2019-03-05 23:45:06.220] [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. [2019-03-05 23:45:06.221] [jointLog] [warning] Only 2334407 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:45:06.221] [jointLog] [info] Mapping rate = 8.82085% [2019-03-05 23:45:06.221] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:45:06.221] [jointLog] [info] Starting optimizer [2019-03-05 23:45:06.225] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:45:06.225] [jointLog] [info] iteration = 0 | max rel diff. = 595.473 [2019-03-05 23:45:06.269] [jointLog] [info] iteration = 100 | max rel diff. = 0.123282 [2019-03-05 23:45:06.303] [jointLog] [info] iteration = 200 | max rel diff. = 0.0553217 [2019-03-05 23:45:06.343] [jointLog] [info] iteration = 300 | max rel diff. = 0.0417819 [2019-03-05 23:45:06.423] [jointLog] [info] iteration = 400 | max rel diff. = 0.0270019 [2019-03-05 23:45:06.451] [jointLog] [info] iteration = 500 | max rel diff. = 0.0220029 [2019-03-05 23:45:06.481] [jointLog] [info] iteration = 600 | max rel diff. = 0.0191776 [2019-03-05 23:45:06.506] [jointLog] [info] iteration = 700 | max rel diff. = 0.0199324 [2019-03-05 23:45:06.538] [jointLog] [info] iteration = 800 | max rel diff. = 0.0124206 [2019-03-05 23:45:06.561] [jointLog] [info] iteration = 900 | max rel diff. = 0.0124207 [2019-03-05 23:45:06.578] [jointLog] [info] iteration = 967 | max rel diff. = 0.00874311 [2019-03-05 23:45:06.579] [jointLog] [info] Finished optimizer [2019-03-05 23:45:06.579] [jointLog] [info] writing output [2019-03-05 23:45:06.601] [jointLog] [warning] NOTE: Read Lib [( /dev/fd/63, /dev/fd/62 )] : Greater than 5% of the fragments disagreed with the provided library type; check the file: non-bleached_44_03/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl non-bleached_44_03/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > non-bleached_44_03/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P03-ACTGAT-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P03-ACTGAT-READ2-Sequences.txt.gz_val_2.fq.gz) -o b_44_01 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { b_44_01 } ### [ threads ] => { 23 } Logs will be written to b_44_01/logs [2019-03-05 23:45:07.053] [jointLog] [info] parsing read library format [2019-03-05 23:45:07.053] [jointLog] [info] There is 1 library. [2019-03-05 23:45:07.126] [jointLog] [info] Loading Quasi index [2019-03-05 23:45:07.126] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:45:07.126] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:45:07.246] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:45:07.259] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:45:07.263] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:45:07.266] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:45:07.266] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:45:07.635] [stderrLog] [info] Done loading index [2019-03-05 23:45:07.635] [jointLog] [info] done [2019-03-05 23:45:07.635] [jointLog] [info] Index contained 5838 targets  processed 500001 fragments hits: 88877, hits per frag: 0.211691 processed 1000001 fragments hits: 178182, hits per frag: 0.182893 processed 1500000 fragments hits: 266398, hits per frag: 0.191995 processed 2000000 fragments hits: 355339, hits per frag: 0.191042 processed 2500000 fragments hits: 444149, hits per frag: 0.181173 processed 3000000 fragments hits: 531583, hits per frag: 0.179682 processed 3500000 fragments hits: 620511, hits per frag: 0.178457 processed 4000000 fragments hits: 709206, hits per frag: 0.178659 processed 4500000 fragments hits: 798752, hits per frag: 0.178795 processed 5000000 fragments hits: 888141, hits per frag: 0.188473 processed 5500000 fragments hits: 976844, hits per frag: 0.178552 processed 6000000 fragments hits: 1064964, hits per frag: 0.178405 processed 6500000 fragments hits: 1153908, hits per frag: 0.179809 processed 7000000 fragments hits: 1242484, hits per frag: 0.178005 processed 7500000 fragments hits: 1331901, hits per frag: 0.179825 processed 8000001 fragments hits: 1420205, hits per frag: 0.178286 processed 8500000 fragments hits: 1506806, hits per frag: 0.179873 processed 9000000 fragments hits: 1595546, hits per frag: 0.178685 processed 9500000 fragments hits: 1685456, hits per frag: 0.177765 processed 10000000 fragments hits: 1773511, hits per frag: 0.177972 processed 10500000 fragments hits: 1861869, hits per frag: 0.17803 processed 11000000 fragments hits: 1950489, hits per frag: 0.179253 processed 11500000 fragments hits: 2038644, hits per frag: 0.178094 processed 12000000 fragments hits: 2127512, hits per frag: 0.17892 processed 12500001 fragments hits: 2215417, hits per frag: 0.178256 processed 13000000 fragments hits: 2303366, hits per frag: 0.178225 processed 13500000 fragments hits: 2393058, hits per frag: 0.1788 processed 14000000 fragments hits: 2481953, hits per frag: 0.178617 processed 14500000 fragments hits: 2571164, hits per frag: 0.179246 processed 15000000 fragments hits: 2659640, hits per frag: 0.177664 processed 15500000 fragments hits: 2749269, hits per frag: 0.17809 processed 16000001 fragments hits: 2839708, hits per frag: 0.179451 processed 16500000 fragments hits: 2927909, hits per frag: 0.177875 processed 17000000 fragments hits: 3015984, hits per frag: 0.178216 processed 17500000 fragments hits: 3104464, hits per frag: 0.177738 processed 18000001 fragments hits: 3192974, hits per frag: 0.177492 processed 18500000 fragments hits: 3281209, hits per frag: 0.177812 processed 19000000 fragments hits: 3370364, hits per frag: 0.177697 processed 19500000 fragments hits: 3457875, hits per frag: 0.179062 processed 20000000 fragments hits: 3545804, hits per frag: 0.177981 processed 20500001 fragments hits: 3633935, hits per frag: 0.177353 processed 21000000 fragments hits: 3722628, hits per frag: 0.178002 processed 21500001 fragments hits: 3810426, hits per frag: 0.177398 processed 22000000 fragments hits: 3898893, hits per frag: 0.17764 processed 22500000 fragments hits: 3987408, hits per frag: 0.179948 processed 23000000 fragments hits: 4076793, hits per frag: 0.177875 [2019-03-05 23:47:19.937] [jointLog] [info] Computed 7727 rich equivalence classes for further processing [2019-03-05 23:47:19.937] [jointLog] [info] Counted 2025613 total reads in the equivalence classes [2019-03-05 23:47:19.950] [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. [2019-03-05 23:47:19.950] [jointLog] [warning] Only 2025613 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:47:19.950] [jointLog] [info] Mapping rate = 8.79746% [2019-03-05 23:47:19.950] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:47:19.951] [jointLog] [info] Starting optimizer [2019-03-05 23:47:19.954] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:47:19.955] [jointLog] [info] iteration = 0 | max rel diff. = 539.329 [2019-03-05 23:47:19.976] [jointLog] [info] iteration = 100 | max rel diff. = 0.113427 [2019-03-05 23:47:19.995] [jointLog] [info] iteration = 200 | max rel diff. = 0.0515085 [2019-03-05 23:47:20.013] [jointLog] [info] iteration = 300 | max rel diff. = 0.0362781 [2019-03-05 23:47:20.033] [jointLog] [info] iteration = 400 | max rel diff. = 0.0277852 [2019-03-05 23:47:20.051] [jointLog] [info] iteration = 500 | max rel diff. = 0.0205165 [2019-03-05 23:47:20.075] [jointLog] [info] iteration = 600 | max rel diff. = 0.0185185 [2019-03-05 23:47:20.094] [jointLog] [info] iteration = 700 | max rel diff. = 0.0165003 [2019-03-05 23:47:20.114] [jointLog] [info] iteration = 800 | max rel diff. = 0.0142154 [2019-03-05 23:47:20.134] [jointLog] [info] iteration = 900 | max rel diff. = 0.0142154 [2019-03-05 23:47:20.156] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0107983 [2019-03-05 23:47:20.157] [jointLog] [info] iteration = 1006 | max rel diff. = 0.00918975 [2019-03-05 23:47:20.161] [jointLog] [info] Finished optimizer [2019-03-05 23:47:20.161] [jointLog] [info] writing output [2019-03-05 23:47:20.180] [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: b_44_01/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl b_44_01/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > b_44_01/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P11-ACTTGA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P11-ACTTGA-READ2-Sequences.txt.gz_val_2.fq.gz) -o b_44_02 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { b_44_02 } ### [ threads ] => { 23 } Logs will be written to b_44_02/logs [2019-03-05 23:47:20.552] [jointLog] [info] parsing read library format [2019-03-05 23:47:20.552] [jointLog] [info] There is 1 library. [2019-03-05 23:47:20.619] [jointLog] [info] Loading Quasi index [2019-03-05 23:47:20.619] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:47:20.619] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:47:20.663] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:47:20.675] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:47:20.680] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:47:20.683] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:47:20.683] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:47:21.048] [stderrLog] [info] Done loading index [2019-03-05 23:47:21.048] [jointLog] [info] done [2019-03-05 23:47:21.048] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 94721, hits per frag: 0.211471 processed 1000000 fragments hits: 189781, hits per frag: 0.19849 processed 1500000 fragments hits: 285392, hits per frag: 0.203465 processed 2000000 fragments hits: 380572, hits per frag: 0.198178 processed 2500001 fragments hits: 475629, hits per frag: 0.194007 processed 3000000 fragments hits: 571796, hits per frag: 0.199222 processed 3500000 fragments hits: 666603, hits per frag: 0.191857 processed 4000000 fragments hits: 761690, hits per frag: 0.199085 processed 4500000 fragments hits: 856281, hits per frag: 0.194534 processed 5000000 fragments hits: 951507, hits per frag: 0.192738 processed 5500000 fragments hits: 1045261, hits per frag: 0.193537 processed 6000000 fragments hits: 1139678, hits per frag: 0.19334 processed 6500000 fragments hits: 1234046, hits per frag: 0.190267 processed 7000000 fragments hits: 1328958, hits per frag: 0.191546 processed 7500000 fragments hits: 1423515, hits per frag: 0.190483 processed 8000000 fragments hits: 1517560, hits per frag: 0.191237 processed 8500001 fragments hits: 1611843, hits per frag: 0.1916 processed 9000000 fragments hits: 1705207, hits per frag: 0.194424 processed 9500000 fragments hits: 1798512, hits per frag: 0.195076 processed 10000000 fragments hits: 1893028, hits per frag: 0.190669 processed 10500000 fragments hits: 1986699, hits per frag: 0.190737 processed 11000000 fragments hits: 2081908, hits per frag: 0.189909 processed 11500000 fragments hits: 2176612, hits per frag: 0.190561 processed 12000000 fragments hits: 2270983, hits per frag: 0.190119 processed 12500000 fragments hits: 2365400, hits per frag: 0.190059 processed 13000000 fragments hits: 2460552, hits per frag: 0.189948 processed 13500000 fragments hits: 2555032, hits per frag: 0.19027 processed 14000000 fragments hits: 2649522, hits per frag: 0.190222 processed 14500000 fragments hits: 2744297, hits per frag: 0.190041 processed 15000000 fragments hits: 2838912, hits per frag: 0.190282 processed 15500000 fragments hits: 2933490, hits per frag: 0.190274 processed 16000000 fragments hits: 3028696, hits per frag: 0.190043 processed 16500000 fragments hits: 3124352, hits per frag: 0.189767 processed 17000000 fragments hits: 3217863, hits per frag: 0.19034 processed 17500000 fragments hits: 3312123, hits per frag: 0.190975 processed 18000000 fragments hits: 3406187, hits per frag: 0.189758 processed 18500001 fragments hits: 3500905, hits per frag: 0.189711 processed 19000000 fragments hits: 3594419, hits per frag: 0.189955 processed 19500000 fragments hits: 3688711, hits per frag: 0.190467 processed 20000000 fragments hits: 3783009, hits per frag: 0.190303 processed 20500000 fragments hits: 3876779, hits per frag: 0.189492 processed 21000000 fragments hits: 3972155, hits per frag: 0.189588 processed 21500000 fragments hits: 4066634, hits per frag: 0.189383 [2019-03-05 23:49:37.009] [jointLog] [info] Computed 7631 rich equivalence classes for further processing [2019-03-05 23:49:37.009] [jointLog] [info] Counted 2077905 total reads in the equivalence classes [2019-03-05 23:49:37.021] [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. [2019-03-05 23:49:37.022] [jointLog] [warning] Only 2077905 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:49:37.022] [jointLog] [info] Mapping rate = 9.47121% [2019-03-05 23:49:37.022] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:49:37.022] [jointLog] [info] Starting optimizer [2019-03-05 23:49:37.026] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:49:37.027] [jointLog] [info] iteration = 0 | max rel diff. = 467.268 [2019-03-05 23:49:37.063] [jointLog] [info] iteration = 100 | max rel diff. = 0.123795 [2019-03-05 23:49:37.101] [jointLog] [info] iteration = 200 | max rel diff. = 0.0600161 [2019-03-05 23:49:37.128] [jointLog] [info] iteration = 300 | max rel diff. = 0.0368955 [2019-03-05 23:49:37.163] [jointLog] [info] iteration = 400 | max rel diff. = 0.0284262 [2019-03-05 23:49:37.187] [jointLog] [info] iteration = 500 | max rel diff. = 0.01989 [2019-03-05 23:49:37.209] [jointLog] [info] iteration = 600 | max rel diff. = 0.0203055 [2019-03-05 23:49:37.227] [jointLog] [info] iteration = 700 | max rel diff. = 0.0154497 [2019-03-05 23:49:37.245] [jointLog] [info] iteration = 800 | max rel diff. = 0.0121703 [2019-03-05 23:49:37.263] [jointLog] [info] iteration = 900 | max rel diff. = 0.0116241 [2019-03-05 23:49:37.281] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0116241 [2019-03-05 23:49:37.285] [jointLog] [info] iteration = 1015 | max rel diff. = 0.00997444 [2019-03-05 23:49:37.293] [jointLog] [info] Finished optimizer [2019-03-05 23:49:37.293] [jointLog] [info] writing output [2019-03-05 23:49:37.311] [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: b_44_02/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl b_44_02/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > b_44_02/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P14-GTGGCC-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P14-GTGGCC-READ2-Sequences.txt.gz_val_2.fq.gz) -o b_44_03 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { b_44_03 } ### [ threads ] => { 23 } Logs will be written to b_44_03/logs [2019-03-05 23:49:37.720] [jointLog] [info] parsing read library format [2019-03-05 23:49:37.720] [jointLog] [info] There is 1 library. [2019-03-05 23:49:37.817] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:49:37.817] [jointLog] [info] Loading Quasi index [2019-03-05 23:49:37.817] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:49:37.956] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:49:37.966] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:49:37.969] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:49:37.971] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:49:37.971] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:49:38.320] [stderrLog] [info] Done loading index [2019-03-05 23:49:38.320] [jointLog] [info] done [2019-03-05 23:49:38.320] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 92810, hits per frag: 0.205794 processed 1000000 fragments hits: 185262, hits per frag: 0.20542 processed 1500000 fragments hits: 277526, hits per frag: 0.188077 processed 2000000 fragments hits: 369989, hits per frag: 0.194358 processed 2500000 fragments hits: 463360, hits per frag: 0.186543 processed 3000000 fragments hits: 556908, hits per frag: 0.189111 processed 3500000 fragments hits: 649940, hits per frag: 0.188629 processed 4000000 fragments hits: 743367, hits per frag: 0.190561 processed 4500000 fragments hits: 835475, hits per frag: 0.188129 processed 5000000 fragments hits: 928502, hits per frag: 0.188914 processed 5500000 fragments hits: 1021729, hits per frag: 0.188121 processed 6000000 fragments hits: 1114929, hits per frag: 0.187909 processed 6500000 fragments hits: 1208795, hits per frag: 0.189926 processed 7000000 fragments hits: 1301669, hits per frag: 0.187011 processed 7500001 fragments hits: 1395312, hits per frag: 0.189232 processed 8000000 fragments hits: 1488032, hits per frag: 0.188802 processed 8500000 fragments hits: 1580514, hits per frag: 0.187498 processed 9000000 fragments hits: 1672762, hits per frag: 0.188347 processed 9500000 fragments hits: 1765133, hits per frag: 0.18743 processed 10000000 fragments hits: 1857714, hits per frag: 0.186695 processed 10500000 fragments hits: 1950553, hits per frag: 0.187117 processed 11000000 fragments hits: 2042520, hits per frag: 0.187823 processed 11500000 fragments hits: 2135688, hits per frag: 0.185837 processed 12000000 fragments hits: 2229067, hits per frag: 0.188833 processed 12500000 fragments hits: 2321394, hits per frag: 0.188768 processed 13000000 fragments hits: 2414798, hits per frag: 0.187925 processed 13500000 fragments hits: 2506166, hits per frag: 0.185656 processed 14000000 fragments hits: 2599349, hits per frag: 0.186828 processed 14500000 fragments hits: 2691331, hits per frag: 0.186814 processed 15000000 fragments hits: 2783550, hits per frag: 0.186593 processed 15500000 fragments hits: 2875928, hits per frag: 0.186246 processed 16000000 fragments hits: 2967977, hits per frag: 0.186286 processed 16500000 fragments hits: 3061687, hits per frag: 0.186137 processed 17000000 fragments hits: 3154341, hits per frag: 0.186905 processed 17500000 fragments hits: 3246990, hits per frag: 0.187071 processed 18000000 fragments hits: 3338814, hits per frag: 0.1861 processed 18500000 fragments hits: 3430861, hits per frag: 0.185749 processed 19000000 fragments hits: 3523537, hits per frag: 0.185974 processed 19500000 fragments hits: 3616902, hits per frag: 0.185881 processed 20000000 fragments hits: 3709756, hits per frag: 0.185982 processed 20500000 fragments hits: 3803345, hits per frag: 0.186124 processed 21000000 fragments hits: 3896870, hits per frag: 0.185904 processed 21500000 fragments hits: 3990352, hits per frag: 0.186119 processed 22000000 fragments hits: 4083770, hits per frag: 0.186634 processed 22500000 fragments hits: 4177225, hits per frag: 0.185886 processed 23000000 fragments hits: 4269952, hits per frag: 0.185997 processed 23500000 fragments hits: 4362818, hits per frag: 0.186388 processed 24000000 fragments hits: 4455605, hits per frag: 0.186051 processed 24500000 fragments hits: 4547792, hits per frag: 0.185793 processed 25000000 fragments hits: 4640097, hits per frag: 0.186161 processed 25500000 fragments hits: 4732959, hits per frag: 0.185818 processed 26000000 fragments hits: 4825441, hits per frag: 0.18616 processed 26500000 fragments hits: 4918563, hits per frag: 0.186018 processed 27000000 fragments hits: 5010164, hits per frag: 0.1867 processed 27500000 fragments hits: 5102926, hits per frag: 0.186258 processed 28000000 fragments hits: 5195066, hits per frag: 0.186148 processed 28500000 fragments hits: 5286908, hits per frag: 0.186233 processed 29000000 fragments hits: 5379267, hits per frag: 0.185633 processed 29500000 fragments hits: 5471201, hits per frag: 0.185698 processed 30000000 fragments hits: 5563621, hits per frag: 0.18613 processed 30500000 fragments hits: 5655945, hits per frag: 0.187074 processed 31000000 fragments hits: 5747742, hits per frag: 0.18568 processed 31500000 fragments hits: 5840924, hits per frag: 0.18601 [2019-03-05 23:52:42.652] [jointLog] [info] Computed 8044 rich equivalence classes for further processing [2019-03-05 23:52:42.652] [jointLog] [info] Counted 2909485 total reads in the equivalence classes [2019-03-05 23:52:42.666] [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. [2019-03-05 23:52:42.667] [jointLog] [warning] Only 2909485 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:52:42.667] [jointLog] [info] Mapping rate = 9.19069% [2019-03-05 23:52:42.667] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:52:42.668] [jointLog] [info] Starting optimizer [2019-03-05 23:52:42.674] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:52:42.674] [jointLog] [info] iteration = 0 | max rel diff. = 793.494 [2019-03-05 23:52:42.703] [jointLog] [info] iteration = 100 | max rel diff. = 0.119625 [2019-03-05 23:52:42.721] [jointLog] [info] iteration = 200 | max rel diff. = 0.0543001 [2019-03-05 23:52:42.741] [jointLog] [info] iteration = 300 | max rel diff. = 0.0369942 [2019-03-05 23:52:42.759] [jointLog] [info] iteration = 400 | max rel diff. = 0.0286949 [2019-03-05 23:52:42.777] [jointLog] [info] iteration = 500 | max rel diff. = 0.0233992 [2019-03-05 23:52:42.797] [jointLog] [info] iteration = 600 | max rel diff. = 0.0174692 [2019-03-05 23:52:42.818] [jointLog] [info] iteration = 700 | max rel diff. = 0.0169623 [2019-03-05 23:52:42.845] [jointLog] [info] iteration = 800 | max rel diff. = 0.0155595 [2019-03-05 23:52:42.864] [jointLog] [info] iteration = 900 | max rel diff. = 0.0122175 [2019-03-05 23:52:42.882] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0104245 [2019-03-05 23:52:42.901] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0102822 [2019-03-05 23:52:42.903] [jointLog] [info] iteration = 1114 | max rel diff. = 0.00885541 [2019-03-05 23:52:42.904] [jointLog] [info] Finished optimizer [2019-03-05 23:52:42.904] [jointLog] [info] writing output [2019-03-05 23:52:42.915] [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: b_44_03/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl b_44_03/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > b_44_03/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-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 nb_44_04 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { nb_44_04 } ### [ threads ] => { 23 } Logs will be written to nb_44_04/logs [2019-03-05 23:52:43.413] [jointLog] [info] parsing read library format [2019-03-05 23:52:43.413] [jointLog] [info] There is 1 library. [2019-03-05 23:52:43.484] [jointLog] [info] Loading Quasi index [2019-03-05 23:52:43.484] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:52:43.484] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:52:43.538] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:52:43.549] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:52:43.552] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:52:43.554] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:52:43.554] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:52:43.893] [jointLog] [info] done [2019-03-05 23:52:43.893] [jointLog] [info] Index contained 5838 targets [2019-03-05 23:52:43.893] [stderrLog] [info] Done loading index  processed 500000 fragments hits: 92761, hits per frag: 0.241621 processed 1000000 fragments hits: 185810, hits per frag: 0.194313 processed 1500000 fragments hits: 278782, hits per frag: 0.189719 processed 2000000 fragments hits: 372255, hits per frag: 0.190724 processed 2500000 fragments hits: 465550, hits per frag: 0.188832 processed 3000000 fragments hits: 557320, hits per frag: 0.191049 processed 3500000 fragments hits: 649303, hits per frag: 0.18988 processed 4000000 fragments hits: 742456, hits per frag: 0.188642 processed 4500000 fragments hits: 834923, hits per frag: 0.186604 processed 5000000 fragments hits: 928062, hits per frag: 0.190447 processed 5500000 fragments hits: 1020771, hits per frag: 0.186412 processed 6000000 fragments hits: 1113535, hits per frag: 0.186235 processed 6500000 fragments hits: 1205613, hits per frag: 0.190954 processed 7000000 fragments hits: 1298146, hits per frag: 0.186192 processed 7500000 fragments hits: 1390937, hits per frag: 0.186326 processed 8000000 fragments hits: 1483398, hits per frag: 0.185923 processed 8500000 fragments hits: 1576554, hits per frag: 0.188466 processed 9000000 fragments hits: 1669146, hits per frag: 0.188506 processed 9500000 fragments hits: 1762677, hits per frag: 0.187551 processed 10000000 fragments hits: 1855199, hits per frag: 0.187218 processed 10500000 fragments hits: 1948301, hits per frag: 0.186213 processed 11000000 fragments hits: 2041334, hits per frag: 0.186604 processed 11500000 fragments hits: 2133865, hits per frag: 0.187574 processed 12000000 fragments hits: 2226504, hits per frag: 0.186295 processed 12500000 fragments hits: 2318577, hits per frag: 0.188269 processed 13000000 fragments hits: 2410881, hits per frag: 0.186239 processed 13500000 fragments hits: 2503192, hits per frag: 0.186742 processed 14000000 fragments hits: 2595326, hits per frag: 0.185941 processed 14500000 fragments hits: 2687956, hits per frag: 0.186459 processed 15000000 fragments hits: 2779818, hits per frag: 0.186096 processed 15500000 fragments hits: 2872934, hits per frag: 0.185614 processed 16000000 fragments hits: 2963947, hits per frag: 0.185482 processed 16500000 fragments hits: 3056117, hits per frag: 0.185664 processed 17000000 fragments hits: 3148560, hits per frag: 0.185678 processed 17500001 fragments hits: 3241813, hits per frag: 0.186037 processed 18000000 fragments hits: 3334134, hits per frag: 0.186352 processed 18500000 fragments hits: 3426235, hits per frag: 0.185569 processed 19000000 fragments hits: 3519607, hits per frag: 0.185368 processed 19500000 fragments hits: 3612511, hits per frag: 0.186256 processed 20000000 fragments hits: 3705004, hits per frag: 0.185868 processed 20500000 fragments hits: 3796375, hits per frag: 0.185826 processed 21000000 fragments hits: 3888708, hits per frag: 0.185281 processed 21500000 fragments hits: 3981903, hits per frag: 0.185937 processed 22000000 fragments hits: 4075544, hits per frag: 0.18543 [2019-03-05 23:54:46.897] [jointLog] [info] Computed 7356 rich equivalence classes for further processing [2019-03-05 23:54:46.897] [jointLog] [info] Counted 2065907 total reads in the equivalence classes [2019-03-05 23:54:46.909] [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. [2019-03-05 23:54:46.910] [jointLog] [warning] Only 2065907 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:54:46.910] [jointLog] [info] Mapping rate = 9.18309% [2019-03-05 23:54:46.910] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:54:46.911] [jointLog] [info] Starting optimizer [2019-03-05 23:54:46.914] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:54:46.915] [jointLog] [info] iteration = 0 | max rel diff. = 551.053 [2019-03-05 23:54:46.938] [jointLog] [info] iteration = 100 | max rel diff. = 0.124186 [2019-03-05 23:54:46.955] [jointLog] [info] iteration = 200 | max rel diff. = 0.0621378 [2019-03-05 23:54:46.973] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433963 [2019-03-05 23:54:46.995] [jointLog] [info] iteration = 400 | max rel diff. = 0.0270723 [2019-03-05 23:54:47.016] [jointLog] [info] iteration = 500 | max rel diff. = 0.0244153 [2019-03-05 23:54:47.037] [jointLog] [info] iteration = 600 | max rel diff. = 0.016607 [2019-03-05 23:54:47.057] [jointLog] [info] iteration = 700 | max rel diff. = 0.0151728 [2019-03-05 23:54:47.078] [jointLog] [info] iteration = 800 | max rel diff. = 0.0137183 [2019-03-05 23:54:47.100] [jointLog] [info] iteration = 900 | max rel diff. = 0.0105981 [2019-03-05 23:54:47.120] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0105981 [2019-03-05 23:54:47.131] [jointLog] [info] iteration = 1055 | max rel diff. = 0.00874008 [2019-03-05 23:54:47.132] [jointLog] [info] Finished optimizer [2019-03-05 23:54:47.132] [jointLog] [info] writing output [2019-03-05 23:54:47.150] [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: nb_44_04/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl nb_44_04/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > nb_44_04/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-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 nb_44_05 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { nb_44_05 } ### [ threads ] => { 23 } Logs will be written to nb_44_05/logs [2019-03-05 23:54:47.588] [jointLog] [info] parsing read library format [2019-03-05 23:54:47.588] [jointLog] [info] There is 1 library. [2019-03-05 23:54:47.664] [jointLog] [info] Loading Quasi index [2019-03-05 23:54:47.664] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:54:47.664] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:54:47.722] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:54:47.732] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:54:47.735] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:54:47.737] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:54:47.737] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:54:48.116] [stderrLog] [info] Done loading index [2019-03-05 23:54:48.116] [jointLog] [info] done [2019-03-05 23:54:48.116] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 91845, hits per frag: 0.23489 processed 1000000 fragments hits: 183161, hits per frag: 0.200558 processed 1500000 fragments hits: 275422, hits per frag: 0.194478 processed 2000000 fragments hits: 368099, hits per frag: 0.19171 processed 2500000 fragments hits: 459440, hits per frag: 0.191331 processed 3000000 fragments hits: 551266, hits per frag: 0.197091 processed 3500000 fragments hits: 643036, hits per frag: 0.185938 processed 4000000 fragments hits: 734808, hits per frag: 0.188272 processed 4500001 fragments hits: 825620, hits per frag: 0.188064 processed 5000000 fragments hits: 917790, hits per frag: 0.187836 processed 5500000 fragments hits: 1008921, hits per frag: 0.185906 processed 6000000 fragments hits: 1100524, hits per frag: 0.184145 processed 6500000 fragments hits: 1192575, hits per frag: 0.18671 processed 7000000 fragments hits: 1284036, hits per frag: 0.18492 processed 7500000 fragments hits: 1375287, hits per frag: 0.18419 processed 8000000 fragments hits: 1467772, hits per frag: 0.18527 processed 8500000 fragments hits: 1560016, hits per frag: 0.18446 processed 9000000 fragments hits: 1653141, hits per frag: 0.187326 processed 9500000 fragments hits: 1744233, hits per frag: 0.185449 processed 10000000 fragments hits: 1836378, hits per frag: 0.183942 processed 10500000 fragments hits: 1928224, hits per frag: 0.184967 processed 11000000 fragments hits: 2020660, hits per frag: 0.184101 processed 11500000 fragments hits: 2113266, hits per frag: 0.186974 processed 12000000 fragments hits: 2204236, hits per frag: 0.186056 processed 12500000 fragments hits: 2296388, hits per frag: 0.185704 processed 13000000 fragments hits: 2388139, hits per frag: 0.184696 processed 13500000 fragments hits: 2479413, hits per frag: 0.183754 processed 14000000 fragments hits: 2571945, hits per frag: 0.189119 processed 14500000 fragments hits: 2663867, hits per frag: 0.184263 processed 15000000 fragments hits: 2755135, hits per frag: 0.185111 processed 15500000 fragments hits: 2846588, hits per frag: 0.184255 processed 16000000 fragments hits: 2937077, hits per frag: 0.184138 processed 16500000 fragments hits: 3028849, hits per frag: 0.183944 processed 17000000 fragments hits: 3120113, hits per frag: 0.18438 processed 17500000 fragments hits: 3212136, hits per frag: 0.184258 processed 18000000 fragments hits: 3303980, hits per frag: 0.183655 processed 18500000 fragments hits: 3395620, hits per frag: 0.18471 processed 19000000 fragments hits: 3487541, hits per frag: 0.184296 processed 19500000 fragments hits: 3579872, hits per frag: 0.184516 processed 20000000 fragments hits: 3671906, hits per frag: 0.185381 processed 20500000 fragments hits: 3763653, hits per frag: 0.18497 processed 21000000 fragments hits: 3856076, hits per frag: 0.184044 processed 21500000 fragments hits: 3948543, hits per frag: 0.183968 processed 22000000 fragments hits: 4040970, hits per frag: 0.184036 processed 22500001 fragments hits: 4133777, hits per frag: 0.183752 processed 23000000 fragments hits: 4225074, hits per frag: 0.184312 processed 23500000 fragments hits: 4317432, hits per frag: 0.184233 processed 24000000 fragments hits: 4408547, hits per frag: 0.183817 processed 24500000 fragments hits: 4500396, hits per frag: 0.184005 processed 25000000 fragments hits: 4593057, hits per frag: 0.183971 processed 25500000 fragments hits: 4684136, hits per frag: 0.184146 processed 26000001 fragments hits: 4774335, hits per frag: 0.184207 [2019-03-05 23:57:24.197] [jointLog] [info] Computed 7419 rich equivalence classes for further processing [2019-03-05 23:57:24.197] [jointLog] [info] Counted 2384873 total reads in the equivalence classes [2019-03-05 23:57:24.210] [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. [2019-03-05 23:57:24.211] [jointLog] [warning] Only 2384873 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:57:24.211] [jointLog] [info] Mapping rate = 9.14069% [2019-03-05 23:57:24.211] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:57:24.211] [jointLog] [info] Starting optimizer [2019-03-05 23:57:24.215] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:57:24.215] [jointLog] [info] iteration = 0 | max rel diff. = 587.742 [2019-03-05 23:57:24.262] [jointLog] [info] iteration = 100 | max rel diff. = 0.116773 [2019-03-05 23:57:24.316] [jointLog] [info] iteration = 200 | max rel diff. = 0.0557936 [2019-03-05 23:57:24.358] [jointLog] [info] iteration = 300 | max rel diff. = 0.0365196 [2019-03-05 23:57:24.403] [jointLog] [info] iteration = 400 | max rel diff. = 0.0288517 [2019-03-05 23:57:24.443] [jointLog] [info] iteration = 500 | max rel diff. = 0.020466 [2019-03-05 23:57:24.476] [jointLog] [info] iteration = 600 | max rel diff. = 0.0172819 [2019-03-05 23:57:24.500] [jointLog] [info] iteration = 700 | max rel diff. = 0.0160847 [2019-03-05 23:57:24.528] [jointLog] [info] iteration = 800 | max rel diff. = 0.012992 [2019-03-05 23:57:24.556] [jointLog] [info] iteration = 900 | max rel diff. = 0.0120729 [2019-03-05 23:57:24.579] [jointLog] [info] iteration = 1000 | max rel diff. = 0.00959498 [2019-03-05 23:57:24.580] [jointLog] [info] Finished optimizer [2019-03-05 23:57:24.580] [jointLog] [info] writing output [2019-03-05 23:57:24.608] [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: nb_44_05/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl nb_44_05/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > nb_44_05/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-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 nb_44_06 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { nb_44_06 } ### [ threads ] => { 23 } Logs will be written to nb_44_06/logs [2019-03-05 23:57:25.022] [jointLog] [info] parsing read library format [2019-03-05 23:57:25.023] [jointLog] [info] There is 1 library. [2019-03-05 23:57:25.103] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:57:25.102] [jointLog] [info] Loading Quasi index [2019-03-05 23:57:25.102] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:57:25.260] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:57:25.274] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:57:25.279] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:57:25.282] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:57:25.282] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:57:25.650] [stderrLog] [info] Done loading index [2019-03-05 23:57:25.650] [jointLog] [info] done [2019-03-05 23:57:25.650] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 88013, hits per frag: 0.216845 processed 1000000 fragments hits: 176169, hits per frag: 0.193524 processed 1500000 fragments hits: 264301, hits per frag: 0.18593 processed 2000000 fragments hits: 352008, hits per frag: 0.179917 processed 2500000 fragments hits: 439536, hits per frag: 0.182581 processed 3000000 fragments hits: 525845, hits per frag: 0.17746 processed 3500000 fragments hits: 614488, hits per frag: 0.178892 processed 4000000 fragments hits: 701912, hits per frag: 0.179964 processed 4500000 fragments hits: 790239, hits per frag: 0.1835 processed 5000000 fragments hits: 878690, hits per frag: 0.17924 processed 5500000 fragments hits: 967053, hits per frag: 0.177206 processed 6000000 fragments hits: 1054983, hits per frag: 0.180729 processed 6500000 fragments hits: 1142159, hits per frag: 0.176758 processed 7000000 fragments hits: 1229510, hits per frag: 0.176783 processed 7500000 fragments hits: 1316407, hits per frag: 0.176581 processed 8000000 fragments hits: 1402820, hits per frag: 0.175806 processed 8500000 fragments hits: 1490481, hits per frag: 0.175586 processed 9000000 fragments hits: 1577812, hits per frag: 0.176975 processed 9500000 fragments hits: 1665057, hits per frag: 0.176245 processed 10000000 fragments hits: 1752825, hits per frag: 0.175532 processed 10500000 fragments hits: 1840205, hits per frag: 0.175749 processed 11000000 fragments hits: 1929524, hits per frag: 0.176549 processed 11500000 fragments hits: 2017692, hits per frag: 0.175855 processed 12000000 fragments hits: 2103909, hits per frag: 0.176503 processed 12500000 fragments hits: 2190173, hits per frag: 0.175327 processed 13000001 fragments hits: 2277647, hits per frag: 0.175522 processed 13500000 fragments hits: 2365425, hits per frag: 0.176579 processed 14000000 fragments hits: 2453233, hits per frag: 0.177371 processed 14500000 fragments hits: 2540871, hits per frag: 0.175958 processed 15000000 fragments hits: 2628362, hits per frag: 0.176752 processed 15500000 fragments hits: 2715668, hits per frag: 0.176203 processed 16000000 fragments hits: 2803375, hits per frag: 0.177702 processed 16500000 fragments hits: 2890268, hits per frag: 0.176093 processed 17000000 fragments hits: 2979638, hits per frag: 0.175704 processed 17500000 fragments hits: 3067550, hits per frag: 0.176115 processed 18000000 fragments hits: 3156118, hits per frag: 0.176536 processed 18500000 fragments hits: 3243086, hits per frag: 0.176399 processed 19000000 fragments hits: 3331328, hits per frag: 0.175991 processed 19500001 fragments hits: 3422105, hits per frag: 0.176397 processed 20000000 fragments hits: 3507268, hits per frag: 0.175884 processed 20500000 fragments hits: 3596321, hits per frag: 0.17581 processed 21000000 fragments hits: 3683513, hits per frag: 0.175697 processed 21500000 fragments hits: 3770977, hits per frag: 0.176073 processed 22000000 fragments hits: 3858921, hits per frag: 0.176056 processed 22500000 fragments hits: 3946358, hits per frag: 0.176145 processed 23000000 fragments hits: 4033641, hits per frag: 0.176535 processed 23500000 fragments hits: 4120668, hits per frag: 0.175921 processed 24000000 fragments hits: 4208929, hits per frag: 0.175966 processed 24500000 fragments hits: 4296364, hits per frag: 0.175483 processed 25000000 fragments hits: 4384182, hits per frag: 0.175556 processed 25500001 fragments hits: 4471737, hits per frag: 0.176001 processed 26000000 fragments hits: 4558418, hits per frag: 0.175639 [2019-03-05 23:59:53.998] [jointLog] [info] Computed 7721 rich equivalence classes for further processing [2019-03-05 23:59:53.998] [jointLog] [info] Counted 2334407 total reads in the equivalence classes [2019-03-05 23:59:54.012] [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. [2019-03-05 23:59:54.012] [jointLog] [warning] Only 2334407 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-05 23:59:54.012] [jointLog] [info] Mapping rate = 8.82085% [2019-03-05 23:59:54.012] [jointLog] [info] finished quantifyLibrary() [2019-03-05 23:59:54.013] [jointLog] [info] Starting optimizer [2019-03-05 23:59:54.017] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-05 23:59:54.017] [jointLog] [info] iteration = 0 | max rel diff. = 595.475 [2019-03-05 23:59:54.051] [jointLog] [info] iteration = 100 | max rel diff. = 0.123241 [2019-03-05 23:59:54.086] [jointLog] [info] iteration = 200 | max rel diff. = 0.0553485 [2019-03-05 23:59:54.129] [jointLog] [info] iteration = 300 | max rel diff. = 0.0417821 [2019-03-05 23:59:54.157] [jointLog] [info] iteration = 400 | max rel diff. = 0.0270577 [2019-03-05 23:59:54.182] [jointLog] [info] iteration = 500 | max rel diff. = 0.0220018 [2019-03-05 23:59:54.207] [jointLog] [info] iteration = 600 | max rel diff. = 0.0195093 [2019-03-05 23:59:54.228] [jointLog] [info] iteration = 700 | max rel diff. = 0.0202457 [2019-03-05 23:59:54.254] [jointLog] [info] iteration = 800 | max rel diff. = 0.0124205 [2019-03-05 23:59:54.281] [jointLog] [info] iteration = 900 | max rel diff. = 0.0124206 [2019-03-05 23:59:54.298] [jointLog] [info] iteration = 967 | max rel diff. = 0.00879967 [2019-03-05 23:59:54.298] [jointLog] [info] Finished optimizer [2019-03-05 23:59:54.298] [jointLog] [info] writing output [2019-03-05 23:59:54.310] [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: nb_44_06/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl nb_44_06/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > nb_44_06/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-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 b_K5_01 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { b_K5_01 } ### [ threads ] => { 23 } Logs will be written to b_K5_01/logs [2019-03-05 23:59:54.759] [jointLog] [info] parsing read library format [2019-03-05 23:59:54.759] [jointLog] [info] There is 1 library. [2019-03-05 23:59:54.828] [stderrLog] [info] Loading Suffix Array [2019-03-05 23:59:54.828] [jointLog] [info] Loading Quasi index [2019-03-05 23:59:54.828] [jointLog] [info] Loading 32-bit quasi index [2019-03-05 23:59:54.906] [stderrLog] [info] Loading Transcript Info [2019-03-05 23:59:54.942] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-05 23:59:54.947] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-05 23:59:54.950] [stderrLog] [info] Computing transcript lengths [2019-03-05 23:59:54.950] [stderrLog] [info] Waiting to finish loading hash [2019-03-05 23:59:55.311] [stderrLog] [info] Done loading index [2019-03-05 23:59:55.311] [jointLog] [info] done [2019-03-05 23:59:55.311] [jointLog] [info] Index contained 5838 targets  processed 500001 fragments hits: 95993, hits per frag: 0.222029 processed 1000000 fragments hits: 192101, hits per frag: 0.196757 processed 1500000 fragments hits: 287615, hits per frag: 0.197019 processed 2000000 fragments hits: 383953, hits per frag: 0.199511 processed 2500000 fragments hits: 479956, hits per frag: 0.198698 processed 3000000 fragments hits: 574748, hits per frag: 0.194238 processed 3500000 fragments hits: 671190, hits per frag: 0.206202 processed 4000000 fragments hits: 767782, hits per frag: 0.19869 processed 4500000 fragments hits: 863747, hits per frag: 0.194432 processed 5000000 fragments hits: 958256, hits per frag: 0.19287 processed 5500000 fragments hits: 1053800, hits per frag: 0.192968 processed 6000000 fragments hits: 1149046, hits per frag: 0.19265 processed 6500000 fragments hits: 1244490, hits per frag: 0.195917 processed 7000000 fragments hits: 1340378, hits per frag: 0.192185 processed 7500000 fragments hits: 1435476, hits per frag: 0.192174 processed 8000000 fragments hits: 1532439, hits per frag: 0.193297 processed 8500000 fragments hits: 1628103, hits per frag: 0.192536 processed 9000000 fragments hits: 1723646, hits per frag: 0.194122 processed 9500000 fragments hits: 1817872, hits per frag: 0.193205 processed 10000000 fragments hits: 1913229, hits per frag: 0.192601 processed 10500000 fragments hits: 2008598, hits per frag: 0.193976 processed 11000000 fragments hits: 2104626, hits per frag: 0.19614 processed 11500000 fragments hits: 2200137, hits per frag: 0.191507 processed 12000000 fragments hits: 2295177, hits per frag: 0.193248 processed 12500001 fragments hits: 2389918, hits per frag: 0.192232 processed 13000000 fragments hits: 2485728, hits per frag: 0.193004 processed 13500000 fragments hits: 2581557, hits per frag: 0.191513 processed 14000000 fragments hits: 2676065, hits per frag: 0.19183 processed 14500000 fragments hits: 2772530, hits per frag: 0.19197 processed 15000000 fragments hits: 2867659, hits per frag: 0.192358 processed 15500000 fragments hits: 2963345, hits per frag: 0.192374 processed 16000000 fragments hits: 3059490, hits per frag: 0.192083 processed 16500000 fragments hits: 3155979, hits per frag: 0.191741 processed 17000000 fragments hits: 3252085, hits per frag: 0.191868 processed 17500000 fragments hits: 3346949, hits per frag: 0.191742 processed 18000000 fragments hits: 3442842, hits per frag: 0.19211 processed 18500001 fragments hits: 3538042, hits per frag: 0.192048 processed 19000000 fragments hits: 3632689, hits per frag: 0.191752 processed 19500001 fragments hits: 3727669, hits per frag: 0.194814 processed 20000000 fragments hits: 3823240, hits per frag: 0.191688 processed 20500000 fragments hits: 3919016, hits per frag: 0.195761 processed 21000000 fragments hits: 4013610, hits per frag: 0.19176 processed 21500000 fragments hits: 4108562, hits per frag: 0.192742 processed 22000000 fragments hits: 4204219, hits per frag: 0.191837 processed 22500000 fragments hits: 4299738, hits per frag: 0.192038 processed 23000000 fragments hits: 4396048, hits per frag: 0.191748 processed 23500000 fragments hits: 4492210, hits per frag: 0.191493 processed 24000000 fragments hits: 4587369, hits per frag: 0.191905 processed 24500000 fragments hits: 4684542, hits per frag: 0.192443 [2019-03-06 00:02:16.213] [jointLog] [info] Computed 7374 rich equivalence classes for further processing [2019-03-06 00:02:16.213] [jointLog] [info] Counted 2259062 total reads in the equivalence classes [2019-03-06 00:02:16.230] [jointLog] [warning] 0.00989258% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-03-06 00:02:16.230] [jointLog] [warning] Only 2259062 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-06 00:02:16.230] [jointLog] [info] Mapping rate = 9.09192% [2019-03-06 00:02:16.230] [jointLog] [info] finished quantifyLibrary() [2019-03-06 00:02:16.231] [jointLog] [info] Starting optimizer [2019-03-06 00:02:16.236] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-06 00:02:16.237] [jointLog] [info] iteration = 0 | max rel diff. = 556.41 [2019-03-06 00:02:16.305] [jointLog] [info] iteration = 100 | max rel diff. = 0.118711 [2019-03-06 00:02:16.359] [jointLog] [info] iteration = 200 | max rel diff. = 0.0618696 [2019-03-06 00:02:16.389] [jointLog] [info] iteration = 300 | max rel diff. = 0.043508 [2019-03-06 00:02:16.410] [jointLog] [info] iteration = 400 | max rel diff. = 0.0267595 [2019-03-06 00:02:16.431] [jointLog] [info] iteration = 500 | max rel diff. = 0.0203625 [2019-03-06 00:02:16.468] [jointLog] [info] iteration = 600 | max rel diff. = 0.0172348 [2019-03-06 00:02:16.498] [jointLog] [info] iteration = 700 | max rel diff. = 0.0139801 [2019-03-06 00:02:16.523] [jointLog] [info] iteration = 800 | max rel diff. = 0.0121107 [2019-03-06 00:02:16.548] [jointLog] [info] iteration = 900 | max rel diff. = 0.0120127 [2019-03-06 00:02:16.576] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0101031 [2019-03-06 00:02:16.579] [jointLog] [info] iteration = 1015 | max rel diff. = 0.00970051 [2019-03-06 00:02:16.579] [jointLog] [info] Finished optimizer [2019-03-06 00:02:16.579] [jointLog] [info] writing output [2019-03-06 00:02:16.603] [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: b_K5_01/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl b_K5_01/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > b_K5_01/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P06-GCCAAT-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P06-GCCAAT-READ2-Sequences.txt.gz_val_2.fq.gz) -o b_K5_02 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { b_K5_02 } ### [ threads ] => { 23 } Logs will be written to b_K5_02/logs [2019-03-06 00:02:16.950] [jointLog] [info] parsing read library format [2019-03-06 00:02:16.950] [jointLog] [info] There is 1 library. [2019-03-06 00:02:17.025] [jointLog] [info] Loading Quasi index [2019-03-06 00:02:17.025] [jointLog] [info] Loading 32-bit quasi index [2019-03-06 00:02:17.025] [stderrLog] [info] Loading Suffix Array [2019-03-06 00:02:17.086] [stderrLog] [info] Loading Transcript Info [2019-03-06 00:02:17.099] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-06 00:02:17.104] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-06 00:02:17.106] [stderrLog] [info] Computing transcript lengths [2019-03-06 00:02:17.106] [stderrLog] [info] Waiting to finish loading hash [2019-03-06 00:02:17.499] [stderrLog] [info] Done loading index [2019-03-06 00:02:17.499] [jointLog] [info] done [2019-03-06 00:02:17.499] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 84815, hits per frag: 0.214429 processed 1000000 fragments hits: 169844, hits per frag: 0.179662 processed 1500000 fragments hits: 255937, hits per frag: 0.174714 processed 2000000 fragments hits: 340916, hits per frag: 0.172378 processed 2500000 fragments hits: 425665, hits per frag: 0.17925 processed 3000000 fragments hits: 510917, hits per frag: 0.172582 processed 3500000 fragments hits: 595765, hits per frag: 0.172966 processed 4000000 fragments hits: 680590, hits per frag: 0.17285 processed 4500000 fragments hits: 765477, hits per frag: 0.172465 processed 5000000 fragments hits: 850934, hits per frag: 0.172626 processed 5500000 fragments hits: 935629, hits per frag: 0.179451 processed 6000001 fragments hits: 1019655, hits per frag: 0.171449 processed 6500000 fragments hits: 1105112, hits per frag: 0.171496 processed 7000000 fragments hits: 1190160, hits per frag: 0.172145 processed 7500001 fragments hits: 1275449, hits per frag: 0.171147 processed 8000000 fragments hits: 1360157, hits per frag: 0.171208 processed 8500000 fragments hits: 1444880, hits per frag: 0.170993 processed 9000000 fragments hits: 1530012, hits per frag: 0.171508 processed 9500000 fragments hits: 1615364, hits per frag: 0.172149 processed 10000000 fragments hits: 1700346, hits per frag: 0.17024 processed 10500000 fragments hits: 1785733, hits per frag: 0.170474 processed 11000000 fragments hits: 1870710, hits per frag: 0.170822 processed 11500000 fragments hits: 1955889, hits per frag: 0.171692 processed 12000000 fragments hits: 2041452, hits per frag: 0.171017 processed 12500001 fragments hits: 2125296, hits per frag: 0.171309 processed 13000000 fragments hits: 2209747, hits per frag: 0.171638 processed 13500001 fragments hits: 2295365, hits per frag: 0.170695 processed 14000000 fragments hits: 2380863, hits per frag: 0.171186 processed 14500000 fragments hits: 2465739, hits per frag: 0.176036 processed 15000000 fragments hits: 2552241, hits per frag: 0.170945 processed 15500000 fragments hits: 2637285, hits per frag: 0.170806 processed 16000000 fragments hits: 2723073, hits per frag: 0.172035 processed 16500000 fragments hits: 2808670, hits per frag: 0.170775 processed 17000000 fragments hits: 2893243, hits per frag: 0.171393 processed 17500001 fragments hits: 2978244, hits per frag: 0.170739 processed 18000000 fragments hits: 3064163, hits per frag: 0.17107 [2019-03-06 00:04:09.161] [jointLog] [info] Computed 7296 rich equivalence classes for further processing [2019-03-06 00:04:09.161] [jointLog] [info] Counted 1550851 total reads in the equivalence classes [2019-03-06 00:04:09.175] [jointLog] [warning] 0.0114771% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-03-06 00:04:09.176] [jointLog] [warning] Only 1550851 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-06 00:04:09.176] [jointLog] [info] Mapping rate = 8.4437% [2019-03-06 00:04:09.176] [jointLog] [info] finished quantifyLibrary() [2019-03-06 00:04:09.176] [jointLog] [info] Starting optimizer [2019-03-06 00:04:09.180] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-06 00:04:09.180] [jointLog] [info] iteration = 0 | max rel diff. = 415.301 [2019-03-06 00:04:09.207] [jointLog] [info] iteration = 100 | max rel diff. = 0.123525 [2019-03-06 00:04:09.227] [jointLog] [info] iteration = 200 | max rel diff. = 0.0531686 [2019-03-06 00:04:09.250] [jointLog] [info] iteration = 300 | max rel diff. = 0.0391549 [2019-03-06 00:04:09.271] [jointLog] [info] iteration = 400 | max rel diff. = 0.0282155 [2019-03-06 00:04:09.292] [jointLog] [info] iteration = 500 | max rel diff. = 0.0208175 [2019-03-06 00:04:09.310] [jointLog] [info] iteration = 600 | max rel diff. = 0.0169572 [2019-03-06 00:04:09.329] [jointLog] [info] iteration = 700 | max rel diff. = 0.0151663 [2019-03-06 00:04:09.347] [jointLog] [info] iteration = 800 | max rel diff. = 0.0115066 [2019-03-06 00:04:09.367] [jointLog] [info] iteration = 900 | max rel diff. = 0.0113234 [2019-03-06 00:04:09.384] [jointLog] [info] iteration = 987 | max rel diff. = 0.00951259 [2019-03-06 00:04:09.384] [jointLog] [info] Finished optimizer [2019-03-06 00:04:09.384] [jointLog] [info] writing output [2019-03-06 00:04:09.398] [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: b_K5_02/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl b_K5_02/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > b_K5_02/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P07-AGTCAA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P07-AGTCAA-READ2-Sequences.txt.gz_val_2.fq.gz) -o b_K5_03 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { b_K5_03 } ### [ threads ] => { 23 } Logs will be written to b_K5_03/logs [2019-03-06 00:04:09.764] [jointLog] [info] parsing read library format [2019-03-06 00:04:09.764] [jointLog] [info] There is 1 library. [2019-03-06 00:04:09.843] [stderrLog] [info] Loading Suffix Array [2019-03-06 00:04:09.843] [jointLog] [info] Loading Quasi index [2019-03-06 00:04:09.843] [jointLog] [info] Loading 32-bit quasi index [2019-03-06 00:04:09.898] [stderrLog] [info] Loading Transcript Info [2019-03-06 00:04:09.937] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-06 00:04:09.942] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-06 00:04:09.945] [stderrLog] [info] Computing transcript lengths [2019-03-06 00:04:09.945] [stderrLog] [info] Waiting to finish loading hash [2019-03-06 00:04:10.325] [stderrLog] [info] Done loading index [2019-03-06 00:04:10.325] [jointLog] [info] done [2019-03-06 00:04:10.325] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 97497, hits per frag: 0.218815 processed 1000000 fragments hits: 195257, hits per frag: 0.217192 processed 1500000 fragments hits: 294295, hits per frag: 0.207229 processed 2000000 fragments hits: 392861, hits per frag: 0.202254 processed 2500001 fragments hits: 491978, hits per frag: 0.200594 processed 3000000 fragments hits: 591018, hits per frag: 0.201271 processed 3500000 fragments hits: 688462, hits per frag: 0.206262 processed 4000000 fragments hits: 785914, hits per frag: 0.196814 processed 4500000 fragments hits: 883534, hits per frag: 0.198202 processed 5000000 fragments hits: 982337, hits per frag: 0.198071 processed 5500000 fragments hits: 1080327, hits per frag: 0.197732 processed 6000000 fragments hits: 1178644, hits per frag: 0.199065 processed 6500000 fragments hits: 1276466, hits per frag: 0.198864 processed 7000000 fragments hits: 1375000, hits per frag: 0.200419 processed 7500000 fragments hits: 1472027, hits per frag: 0.199273 processed 8000000 fragments hits: 1569569, hits per frag: 0.198818 processed 8500000 fragments hits: 1667035, hits per frag: 0.197195 processed 9000000 fragments hits: 1765668, hits per frag: 0.196244 processed 9500000 fragments hits: 1864229, hits per frag: 0.196648 processed 10000000 fragments hits: 1961775, hits per frag: 0.197781 processed 10500000 fragments hits: 2060611, hits per frag: 0.198476 processed 11000000 fragments hits: 2160528, hits per frag: 0.197709 processed 11500000 fragments hits: 2259342, hits per frag: 0.197477 processed 12000000 fragments hits: 2357470, hits per frag: 0.197896 processed 12500000 fragments hits: 2456174, hits per frag: 0.197522 processed 13000000 fragments hits: 2554237, hits per frag: 0.197234 processed 13500000 fragments hits: 2652005, hits per frag: 0.19811 processed 14000000 fragments hits: 2749718, hits per frag: 0.196697 processed 14500000 fragments hits: 2848212, hits per frag: 0.197442 processed 15000001 fragments hits: 2945875, hits per frag: 0.196561 processed 15500000 fragments hits: 3044555, hits per frag: 0.198634 processed 16000000 fragments hits: 3141980, hits per frag: 0.198593 processed 16500000 fragments hits: 3239928, hits per frag: 0.197663 processed 17000000 fragments hits: 3337278, hits per frag: 0.196795 processed 17500000 fragments hits: 3435732, hits per frag: 0.198353 processed 18000000 fragments hits: 3532620, hits per frag: 0.196575 processed 18500000 fragments hits: 3631438, hits per frag: 0.198093 processed 19000000 fragments hits: 3730402, hits per frag: 0.197006 processed 19500000 fragments hits: 3828352, hits per frag: 0.197859 processed 20000000 fragments hits: 3926636, hits per frag: 0.196824 processed 20500000 fragments hits: 4023688, hits per frag: 0.197017 processed 21000000 fragments hits: 4122267, hits per frag: 0.197089 processed 21500000 fragments hits: 4219856, hits per frag: 0.196522 processed 22000000 fragments hits: 4317787, hits per frag: 0.196712 processed 22500000 fragments hits: 4416069, hits per frag: 0.196391 processed 23000000 fragments hits: 4514816, hits per frag: 0.196693 processed 23500000 fragments hits: 4612538, hits per frag: 0.196526 processed 24000000 fragments hits: 4710770, hits per frag: 0.196806 processed 24500001 fragments hits: 4808059, hits per frag: 0.196439 processed 25000000 fragments hits: 4906342, hits per frag: 0.196909 processed 25500000 fragments hits: 5003743, hits per frag: 0.196814 [2019-03-06 00:06:44.883] [jointLog] [info] Computed 7398 rich equivalence classes for further processing [2019-03-06 00:06:44.883] [jointLog] [info] Counted 2479140 total reads in the equivalence classes [2019-03-06 00:06:44.896] [jointLog] [warning] 0.0136297% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-03-06 00:06:44.897] [jointLog] [warning] Only 2479140 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-06 00:06:44.897] [jointLog] [info] Mapping rate = 9.56952% [2019-03-06 00:06:44.897] [jointLog] [info] finished quantifyLibrary() [2019-03-06 00:06:44.897] [jointLog] [info] Starting optimizer [2019-03-06 00:06:44.901] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-06 00:06:44.902] [jointLog] [info] iteration = 0 | max rel diff. = 615.806 [2019-03-06 00:06:44.923] [jointLog] [info] iteration = 100 | max rel diff. = 0.117137 [2019-03-06 00:06:44.949] [jointLog] [info] iteration = 200 | max rel diff. = 0.0572564 [2019-03-06 00:06:44.968] [jointLog] [info] iteration = 300 | max rel diff. = 0.0377842 [2019-03-06 00:06:44.987] [jointLog] [info] iteration = 400 | max rel diff. = 0.0253426 [2019-03-06 00:06:45.007] [jointLog] [info] iteration = 500 | max rel diff. = 0.0214216 [2019-03-06 00:06:45.026] [jointLog] [info] iteration = 600 | max rel diff. = 0.017772 [2019-03-06 00:06:45.045] [jointLog] [info] iteration = 700 | max rel diff. = 0.015277 [2019-03-06 00:06:45.062] [jointLog] [info] iteration = 800 | max rel diff. = 0.0123902 [2019-03-06 00:06:45.080] [jointLog] [info] iteration = 900 | max rel diff. = 0.0119454 [2019-03-06 00:06:45.096] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0106938 [2019-03-06 00:06:45.100] [jointLog] [info] iteration = 1027 | max rel diff. = 0.00911089 [2019-03-06 00:06:45.101] [jointLog] [info] Finished optimizer [2019-03-06 00:06:45.101] [jointLog] [info] writing output [2019-03-06 00:06:45.112] [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: b_K5_03/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl b_K5_03/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > b_K5_03/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P08-CTTGTA-READ2-Sequences.txt.gz_val_2.fq.gz) -o b_K5_04 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { b_K5_04 } ### [ threads ] => { 23 } Logs will be written to b_K5_04/logs [2019-03-06 00:06:45.504] [jointLog] [info] parsing read library format [2019-03-06 00:06:45.504] [jointLog] [info] There is 1 library. [2019-03-06 00:06:45.580] [jointLog] [info] Loading Quasi index [2019-03-06 00:06:45.580] [jointLog] [info] Loading 32-bit quasi index [2019-03-06 00:06:45.580] [stderrLog] [info] Loading Suffix Array [2019-03-06 00:06:45.631] [stderrLog] [info] Loading Transcript Info [2019-03-06 00:06:45.663] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-06 00:06:45.668] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-06 00:06:45.671] [stderrLog] [info] Computing transcript lengths [2019-03-06 00:06:45.671] [stderrLog] [info] Waiting to finish loading hash [2019-03-06 00:06:46.052] [stderrLog] [info] Done loading index [2019-03-06 00:06:46.052] [jointLog] [info] done [2019-03-06 00:06:46.052] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 96333, hits per frag: 0.26038 processed 1000000 fragments hits: 192516, hits per frag: 0.195597 processed 1500000 fragments hits: 289515, hits per frag: 0.197565 processed 2000000 fragments hits: 385799, hits per frag: 0.198887 processed 2500000 fragments hits: 481835, hits per frag: 0.197743 processed 3000000 fragments hits: 577870, hits per frag: 0.198365 processed 3500000 fragments hits: 673412, hits per frag: 0.19592 processed 4000001 fragments hits: 770637, hits per frag: 0.195067 processed 4500000 fragments hits: 867613, hits per frag: 0.202988 processed 5000000 fragments hits: 963830, hits per frag: 0.195681 processed 5500001 fragments hits: 1060845, hits per frag: 0.194267 processed 6000000 fragments hits: 1157705, hits per frag: 0.194977 processed 6500000 fragments hits: 1253644, hits per frag: 0.193748 processed 7000000 fragments hits: 1351180, hits per frag: 0.195992 processed 7500000 fragments hits: 1447803, hits per frag: 0.194174 processed 8000000 fragments hits: 1543272, hits per frag: 0.195083 processed 8500000 fragments hits: 1639066, hits per frag: 0.193118 processed 9000002 fragments hits: 1735254, hits per frag: 0.193258 processed 9500000 fragments hits: 1831385, hits per frag: 0.193522 processed 10000000 fragments hits: 1926833, hits per frag: 0.193013 processed 10500001 fragments hits: 2022006, hits per frag: 0.194196 processed 11000000 fragments hits: 2118397, hits per frag: 0.195721 processed 11500000 fragments hits: 2214978, hits per frag: 0.193503 processed 12000000 fragments hits: 2312109, hits per frag: 0.193029 processed 12500000 fragments hits: 2406457, hits per frag: 0.194324 processed 13000000 fragments hits: 2501233, hits per frag: 0.193137 processed 13500000 fragments hits: 2597525, hits per frag: 0.194324 processed 14000000 fragments hits: 2694005, hits per frag: 0.193541 processed 14500000 fragments hits: 2790506, hits per frag: 0.192747 processed 15000000 fragments hits: 2887053, hits per frag: 0.192673 processed 15500000 fragments hits: 2983182, hits per frag: 0.193749 processed 16000000 fragments hits: 3078503, hits per frag: 0.193118 processed 16500001 fragments hits: 3174800, hits per frag: 0.193908 processed 17000000 fragments hits: 3270760, hits per frag: 0.193773 processed 17500000 fragments hits: 3366827, hits per frag: 0.193057 processed 18000000 fragments hits: 3463132, hits per frag: 0.192806 processed 18500000 fragments hits: 3558843, hits per frag: 0.192901 processed 19000000 fragments hits: 3655428, hits per frag: 0.193629 processed 19500000 fragments hits: 3751182, hits per frag: 0.1931 processed 20000000 fragments hits: 3847909, hits per frag: 0.192476 processed 20500000 fragments hits: 3944472, hits per frag: 0.19392 processed 21000000 fragments hits: 4040821, hits per frag: 0.193626 processed 21500000 fragments hits: 4137688, hits per frag: 0.19319 processed 22000000 fragments hits: 4233716, hits per frag: 0.192872 processed 22500000 fragments hits: 4329543, hits per frag: 0.193417 processed 23000000 fragments hits: 4426277, hits per frag: 0.19337 processed 23500001 fragments hits: 4522438, hits per frag: 0.192784 processed 24000000 fragments hits: 4618695, hits per frag: 0.193182 processed 24500000 fragments hits: 4715036, hits per frag: 0.192854 processed 25000000 fragments hits: 4812073, hits per frag: 0.192926 processed 25500000 fragments hits: 4908686, hits per frag: 0.192939 processed 26000000 fragments hits: 5004262, hits per frag: 0.19272 processed 26500000 fragments hits: 5101305, hits per frag: 0.192649 processed 27000000 fragments hits: 5197149, hits per frag: 0.192671 processed 27500000 fragments hits: 5292242, hits per frag: 0.192816 processed 28000000 fragments hits: 5389193, hits per frag: 0.192609 [2019-03-06 00:09:48.305] [jointLog] [info] Computed 7401 rich equivalence classes for further processing [2019-03-06 00:09:48.305] [jointLog] [info] Counted 2716216 total reads in the equivalence classes [2019-03-06 00:09:48.317] [jointLog] [warning] 0.0118102% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-03-06 00:09:48.318] [jointLog] [warning] Only 2716216 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-06 00:09:48.318] [jointLog] [info] Mapping rate = 9.59013% [2019-03-06 00:09:48.318] [jointLog] [info] finished quantifyLibrary() [2019-03-06 00:09:48.319] [jointLog] [info] Starting optimizer [2019-03-06 00:09:48.344] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-06 00:09:48.344] [jointLog] [info] iteration = 0 | max rel diff. = 623.198 [2019-03-06 00:09:48.382] [jointLog] [info] iteration = 100 | max rel diff. = 0.127016 [2019-03-06 00:09:48.406] [jointLog] [info] iteration = 200 | max rel diff. = 0.0631659 [2019-03-06 00:09:48.432] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433745 [2019-03-06 00:09:48.457] [jointLog] [info] iteration = 400 | max rel diff. = 0.0310142 [2019-03-06 00:09:48.488] [jointLog] [info] iteration = 500 | max rel diff. = 0.0246255 [2019-03-06 00:09:48.516] [jointLog] [info] iteration = 600 | max rel diff. = 0.0179889 [2019-03-06 00:09:48.541] [jointLog] [info] iteration = 700 | max rel diff. = 0.0157483 [2019-03-06 00:09:48.570] [jointLog] [info] iteration = 800 | max rel diff. = 0.0118747 [2019-03-06 00:09:48.597] [jointLog] [info] iteration = 900 | max rel diff. = 0.0118754 [2019-03-06 00:09:48.621] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0111016 [2019-03-06 00:09:48.629] [jointLog] [info] iteration = 1034 | max rel diff. = 0.00985192 [2019-03-06 00:09:48.630] [jointLog] [info] Finished optimizer [2019-03-06 00:09:48.630] [jointLog] [info] writing output [2019-03-06 00:09:48.651] [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: b_K5_04/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl b_K5_04/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > b_K5_04/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P09-GTGAAA-READ2-Sequences.txt.gz_val_2.fq.gz) -o b_K5_05 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { b_K5_05 } ### [ threads ] => { 23 } Logs will be written to b_K5_05/logs [2019-03-06 00:09:49.186] [jointLog] [info] parsing read library format [2019-03-06 00:09:49.186] [jointLog] [info] There is 1 library. [2019-03-06 00:09:49.266] [jointLog] [info] Loading Quasi index [2019-03-06 00:09:49.266] [jointLog] [info] Loading 32-bit quasi index [2019-03-06 00:09:49.266] [stderrLog] [info] Loading Suffix Array [2019-03-06 00:09:49.327] [stderrLog] [info] Loading Transcript Info [2019-03-06 00:09:49.342] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-06 00:09:49.347] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-06 00:09:49.350] [stderrLog] [info] Computing transcript lengths [2019-03-06 00:09:49.350] [stderrLog] [info] Waiting to finish loading hash [2019-03-06 00:09:49.708] [stderrLog] [info] Done loading index [2019-03-06 00:09:49.708] [jointLog] [info] done [2019-03-06 00:09:49.709] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 88769, hits per frag: 0.1807 processed 1000000 fragments hits: 177970, hits per frag: 0.209069 processed 1500000 fragments hits: 265491, hits per frag: 0.200584 processed 2000000 fragments hits: 353989, hits per frag: 0.183703 processed 2500000 fragments hits: 442348, hits per frag: 0.182869 processed 3000000 fragments hits: 531402, hits per frag: 0.189594 processed 3500000 fragments hits: 619451, hits per frag: 0.181179 processed 4000000 fragments hits: 706927, hits per frag: 0.178786 processed 4500000 fragments hits: 796400, hits per frag: 0.181915 processed 5000000 fragments hits: 884736, hits per frag: 0.179503 processed 5500000 fragments hits: 972991, hits per frag: 0.177144 processed 6000000 fragments hits: 1061350, hits per frag: 0.177746 processed 6500000 fragments hits: 1150045, hits per frag: 0.177258 processed 7000000 fragments hits: 1238324, hits per frag: 0.177852 processed 7500000 fragments hits: 1325922, hits per frag: 0.177036 processed 8000000 fragments hits: 1414026, hits per frag: 0.182217 processed 8500000 fragments hits: 1502667, hits per frag: 0.180031 processed 9000000 fragments hits: 1591794, hits per frag: 0.178576 processed 9500000 fragments hits: 1680404, hits per frag: 0.180943 processed 10000000 fragments hits: 1768850, hits per frag: 0.178254 processed 10500000 fragments hits: 1856678, hits per frag: 0.178505 processed 11000000 fragments hits: 1943661, hits per frag: 0.178344 processed 11500000 fragments hits: 2031699, hits per frag: 0.177111 processed 12000000 fragments hits: 2119232, hits per frag: 0.177643 processed 12500000 fragments hits: 2207486, hits per frag: 0.177644 processed 13000000 fragments hits: 2294934, hits per frag: 0.177223 processed 13500000 fragments hits: 2382878, hits per frag: 0.177603 processed 14000000 fragments hits: 2470753, hits per frag: 0.176579 processed 14500000 fragments hits: 2559373, hits per frag: 0.177227 processed 15000000 fragments hits: 2647962, hits per frag: 0.177001 processed 15500000 fragments hits: 2736042, hits per frag: 0.177427 processed 16000000 fragments hits: 2824408, hits per frag: 0.176908 processed 16500000 fragments hits: 2913027, hits per frag: 0.177179 processed 17000000 fragments hits: 3001479, hits per frag: 0.177008 processed 17500000 fragments hits: 3089636, hits per frag: 0.177006 processed 18000000 fragments hits: 3177737, hits per frag: 0.176971 processed 18500000 fragments hits: 3265075, hits per frag: 0.177436 processed 19000000 fragments hits: 3352423, hits per frag: 0.177817 processed 19500000 fragments hits: 3440128, hits per frag: 0.176927 processed 20000001 fragments hits: 3527591, hits per frag: 0.177088 processed 20500000 fragments hits: 3615261, hits per frag: 0.176611 processed 21000000 fragments hits: 3702896, hits per frag: 0.176921 processed 21500000 fragments hits: 3791577, hits per frag: 0.17693 [2019-03-06 00:11:52.977] [jointLog] [info] Computed 6922 rich equivalence classes for further processing [2019-03-06 00:11:52.977] [jointLog] [info] Counted 1916701 total reads in the equivalence classes [2019-03-06 00:11:52.989] [jointLog] [warning] 0.0194906% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-03-06 00:11:52.990] [jointLog] [warning] Only 1916701 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-06 00:11:52.990] [jointLog] [info] Mapping rate = 8.75913% [2019-03-06 00:11:52.990] [jointLog] [info] finished quantifyLibrary() [2019-03-06 00:11:52.991] [jointLog] [info] Starting optimizer [2019-03-06 00:11:52.994] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-06 00:11:52.995] [jointLog] [info] iteration = 0 | max rel diff. = 428.681 [2019-03-06 00:11:53.014] [jointLog] [info] iteration = 100 | max rel diff. = 0.112608 [2019-03-06 00:11:53.031] [jointLog] [info] iteration = 200 | max rel diff. = 0.0561083 [2019-03-06 00:11:53.048] [jointLog] [info] iteration = 300 | max rel diff. = 0.0366448 [2019-03-06 00:11:53.066] [jointLog] [info] iteration = 400 | max rel diff. = 0.0243075 [2019-03-06 00:11:53.086] [jointLog] [info] iteration = 500 | max rel diff. = 0.0243088 [2019-03-06 00:11:53.110] [jointLog] [info] iteration = 600 | max rel diff. = 0.0175249 [2019-03-06 00:11:53.130] [jointLog] [info] iteration = 700 | max rel diff. = 0.0150934 [2019-03-06 00:11:53.149] [jointLog] [info] iteration = 800 | max rel diff. = 0.0129977 [2019-03-06 00:11:53.180] [jointLog] [info] iteration = 900 | max rel diff. = 0.0115073 [2019-03-06 00:11:53.211] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0115076 [2019-03-06 00:11:53.227] [jointLog] [info] iteration = 1071 | max rel diff. = 0.00919479 [2019-03-06 00:11:53.228] [jointLog] [info] Finished optimizer [2019-03-06 00:11:53.228] [jointLog] [info] writing output [2019-03-06 00:11:53.244] [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: b_K5_05/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl b_K5_05/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > b_K5_05/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P13-ATCACG-READ2-Sequences.txt.gz_val_2.fq.gz) -o b_K5_06 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { b_K5_06 } ### [ threads ] => { 23 } Logs will be written to b_K5_06/logs [2019-03-06 00:11:53.590] [jointLog] [info] parsing read library format [2019-03-06 00:11:53.590] [jointLog] [info] There is 1 library. [2019-03-06 00:11:53.663] [jointLog] [info] Loading Quasi index [2019-03-06 00:11:53.663] [jointLog] [info] Loading 32-bit quasi index [2019-03-06 00:11:53.663] [stderrLog] [info] Loading Suffix Array [2019-03-06 00:11:53.745] [stderrLog] [info] Loading Transcript Info [2019-03-06 00:11:53.757] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-06 00:11:53.760] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-06 00:11:53.762] [stderrLog] [info] Computing transcript lengths [2019-03-06 00:11:53.762] [stderrLog] [info] Waiting to finish loading hash [2019-03-06 00:11:54.134] [stderrLog] [info] Done loading index [2019-03-06 00:11:54.134] [jointLog] [info] done [2019-03-06 00:11:54.134] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 74446, hits per frag: 0.180722 processed 1000001 fragments hits: 149489, hits per frag: 0.156476 processed 1500000 fragments hits: 224804, hits per frag: 0.160079 processed 2000000 fragments hits: 298853, hits per frag: 0.157198 processed 2500000 fragments hits: 373650, hits per frag: 0.155939 processed 3000000 fragments hits: 447825, hits per frag: 0.15157 processed 3500000 fragments hits: 522542, hits per frag: 0.155813 processed 4000000 fragments hits: 595177, hits per frag: 0.154218 processed 4500000 fragments hits: 669337, hits per frag: 0.152022 processed 5000000 fragments hits: 744394, hits per frag: 0.14971 processed 5500000 fragments hits: 819700, hits per frag: 0.151442 processed 6000000 fragments hits: 894682, hits per frag: 0.149339 processed 6500000 fragments hits: 968353, hits per frag: 0.149312 processed 7000000 fragments hits: 1042046, hits per frag: 0.150571 processed 7500001 fragments hits: 1116260, hits per frag: 0.150411 processed 8000000 fragments hits: 1189954, hits per frag: 0.151155 processed 8500000 fragments hits: 1262821, hits per frag: 0.148866 processed 9000001 fragments hits: 1338124, hits per frag: 0.149846 processed 9500000 fragments hits: 1412864, hits per frag: 0.14969 processed 10000000 fragments hits: 1487466, hits per frag: 0.149024 processed 10500000 fragments hits: 1561702, hits per frag: 0.148845 processed 11000000 fragments hits: 1635842, hits per frag: 0.149052 processed 11500000 fragments hits: 1710210, hits per frag: 0.149497 processed 12000000 fragments hits: 1783671, hits per frag: 0.149481 processed 12500000 fragments hits: 1857582, hits per frag: 0.149726 processed 13000000 fragments hits: 1930792, hits per frag: 0.149193 processed 13500000 fragments hits: 2006540, hits per frag: 0.149508 processed 14000000 fragments hits: 2081163, hits per frag: 0.149365 processed 14500000 fragments hits: 2156330, hits per frag: 0.149673 processed 15000001 fragments hits: 2230548, hits per frag: 0.149916 processed 15500000 fragments hits: 2304229, hits per frag: 0.149184 processed 16000000 fragments hits: 2377718, hits per frag: 0.149949 processed 16500000 fragments hits: 2451452, hits per frag: 0.148789 processed 17000000 fragments hits: 2524289, hits per frag: 0.149185 [2019-03-06 00:13:44.097] [jointLog] [info] Computed 6627 rich equivalence classes for further processing [2019-03-06 00:13:44.097] [jointLog] [info] Counted 1294477 total reads in the equivalence classes [2019-03-06 00:13:44.110] [jointLog] [warning] 0.0100547% of fragments were shorter than the k used to build the index (31). If this fraction is too large, consider re-building the index with a smaller k. The minimum read size found was 20. [2019-03-06 00:13:44.111] [jointLog] [warning] Only 1294477 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-06 00:13:44.111] [jointLog] [info] Mapping rate = 7.48881% [2019-03-06 00:13:44.111] [jointLog] [info] finished quantifyLibrary() [2019-03-06 00:13:44.111] [jointLog] [info] Starting optimizer [2019-03-06 00:13:44.115] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-06 00:13:44.115] [jointLog] [info] iteration = 0 | max rel diff. = 305.935 [2019-03-06 00:13:44.201] [jointLog] [info] iteration = 100 | max rel diff. = 0.113983 [2019-03-06 00:13:44.245] [jointLog] [info] iteration = 200 | max rel diff. = 0.0606151 [2019-03-06 00:13:44.286] [jointLog] [info] iteration = 300 | max rel diff. = 0.0432671 [2019-03-06 00:13:44.329] [jointLog] [info] iteration = 400 | max rel diff. = 0.0293285 [2019-03-06 00:13:44.364] [jointLog] [info] iteration = 500 | max rel diff. = 0.021804 [2019-03-06 00:13:44.390] [jointLog] [info] iteration = 600 | max rel diff. = 0.0174295 [2019-03-06 00:13:44.414] [jointLog] [info] iteration = 700 | max rel diff. = 0.0147556 [2019-03-06 00:13:44.436] [jointLog] [info] iteration = 800 | max rel diff. = 0.0118543 [2019-03-06 00:13:44.457] [jointLog] [info] iteration = 900 | max rel diff. = 0.0111508 [2019-03-06 00:13:44.478] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0113564 [2019-03-06 00:13:44.500] [jointLog] [info] iteration = 1091 | max rel diff. = 0.0087625 [2019-03-06 00:13:44.501] [jointLog] [info] Finished optimizer [2019-03-06 00:13:44.501] [jointLog] [info] writing output [2019-03-06 00:13:44.531] [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: b_K5_06/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl b_K5_06/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > b_K5_06/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-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 nb_K5_07 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { nb_K5_07 } ### [ threads ] => { 23 } Logs will be written to nb_K5_07/logs [2019-03-06 00:13:44.962] [jointLog] [info] parsing read library format [2019-03-06 00:13:44.962] [jointLog] [info] There is 1 library. [2019-03-06 00:13:45.055] [jointLog] [info] Loading Quasi index [2019-03-06 00:13:45.055] [jointLog] [info] Loading 32-bit quasi index [2019-03-06 00:13:45.055] [stderrLog] [info] Loading Suffix Array [2019-03-06 00:13:45.131] [stderrLog] [info] Loading Transcript Info [2019-03-06 00:13:45.145] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-06 00:13:45.150] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-06 00:13:45.154] [stderrLog] [info] Computing transcript lengths [2019-03-06 00:13:45.154] [stderrLog] [info] Waiting to finish loading hash [2019-03-06 00:13:45.523] [stderrLog] [info] Done loading index [2019-03-06 00:13:45.523] [jointLog] [info] done [2019-03-06 00:13:45.523] [jointLog] [info] Index contained 5838 targets  processed 500000 fragments hits: 98634, hits per frag: 98634 processed 1000000 fragments hits: 197943, hits per frag: 0.217274 processed 1500000 fragments hits: 296012, hits per frag: 0.205984 processed 2000000 fragments hits: 396609, hits per frag: 0.200141 processed 2500000 fragments hits: 495817, hits per frag: 0.21006 processed 3000000 fragments hits: 595377, hits per frag: 0.199508 processed 3500000 fragments hits: 694654, hits per frag: 0.20272 processed 4000000 fragments hits: 793630, hits per frag: 0.19914 processed 4500000 fragments hits: 891923, hits per frag: 0.201768 processed 5000000 fragments hits: 990765, hits per frag: 0.202747 processed 5500000 fragments hits: 1089771, hits per frag: 0.199891 processed 6000000 fragments hits: 1189047, hits per frag: 0.20105 processed 6500000 fragments hits: 1288191, hits per frag: 0.200834 processed 7000000 fragments hits: 1386872, hits per frag: 0.200379 processed 7500000 fragments hits: 1485321, hits per frag: 0.198863 processed 8000001 fragments hits: 1584506, hits per frag: 0.199639 processed 8500001 fragments hits: 1683964, hits per frag: 0.19954 processed 9000000 fragments hits: 1782869, hits per frag: 0.201271 processed 9500000 fragments hits: 1880933, hits per frag: 0.198395 processed 10000001 fragments hits: 1981130, hits per frag: 0.198837 processed 10500000 fragments hits: 2079160, hits per frag: 0.199538 processed 11000000 fragments hits: 2177909, hits per frag: 0.19936 processed 11500000 fragments hits: 2276699, hits per frag: 0.199638 processed 12000000 fragments hits: 2375350, hits per frag: 0.198766 processed 12500000 fragments hits: 2473842, hits per frag: 0.198241 processed 13000000 fragments hits: 2572689, hits per frag: 0.199345 processed 13500001 fragments hits: 2669979, hits per frag: 0.199052 processed 14000000 fragments hits: 2768525, hits per frag: 0.19835 processed 14500000 fragments hits: 2866380, hits per frag: 0.198453 processed 15000000 fragments hits: 2965754, hits per frag: 0.198163 processed 15500000 fragments hits: 3065076, hits per frag: 0.198233 processed 16000000 fragments hits: 3164216, hits per frag: 0.198436 processed 16500000 fragments hits: 3262402, hits per frag: 0.19824 processed 17000000 fragments hits: 3360955, hits per frag: 0.198067 processed 17500001 fragments hits: 3461348, hits per frag: 0.198188 processed 18000000 fragments hits: 3560671, hits per frag: 0.198418 processed 18500000 fragments hits: 3658811, hits per frag: 0.198212 processed 19000000 fragments hits: 3758180, hits per frag: 0.198704 processed 19500000 fragments hits: 3857825, hits per frag: 0.198208 processed 20000000 fragments hits: 3956202, hits per frag: 0.198286 processed 20500000 fragments hits: 4055462, hits per frag: 0.198722 processed 21000000 fragments hits: 4154093, hits per frag: 0.198549 processed 21500000 fragments hits: 4253155, hits per frag: 0.198354 processed 22000000 fragments hits: 4352831, hits per frag: 0.197953 processed 22500000 fragments hits: 4452322, hits per frag: 0.198144 processed 23000000 fragments hits: 4551430, hits per frag: 0.198116 processed 23500001 fragments hits: 4649975, hits per frag: 0.198739 [2019-03-06 00:15:03.398] [jointLog] [info] Computed 7091 rich equivalence classes for further processing [2019-03-06 00:15:03.398] [jointLog] [info] Counted 2346516 total reads in the equivalence classes [2019-03-06 00:15:03.412] [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. [2019-03-06 00:15:03.412] [jointLog] [warning] Only 2346516 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-06 00:15:03.412] [jointLog] [info] Mapping rate = 9.83271% [2019-03-06 00:15:03.412] [jointLog] [info] finished quantifyLibrary() [2019-03-06 00:15:03.413] [jointLog] [info] Starting optimizer [2019-03-06 00:15:03.419] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-06 00:15:03.419] [jointLog] [info] iteration = 0 | max rel diff. = 538.295 [2019-03-06 00:15:03.437] [jointLog] [info] iteration = 100 | max rel diff. = 0.118472 [2019-03-06 00:15:03.453] [jointLog] [info] iteration = 200 | max rel diff. = 0.0574254 [2019-03-06 00:15:03.468] [jointLog] [info] iteration = 300 | max rel diff. = 0.0391373 [2019-03-06 00:15:03.483] [jointLog] [info] iteration = 400 | max rel diff. = 0.0274021 [2019-03-06 00:15:03.498] [jointLog] [info] iteration = 500 | max rel diff. = 0.0220555 [2019-03-06 00:15:03.513] [jointLog] [info] iteration = 600 | max rel diff. = 0.0192173 [2019-03-06 00:15:03.528] [jointLog] [info] iteration = 700 | max rel diff. = 0.0157132 [2019-03-06 00:15:03.543] [jointLog] [info] iteration = 800 | max rel diff. = 0.0134474 [2019-03-06 00:15:03.558] [jointLog] [info] iteration = 900 | max rel diff. = 0.0111955 [2019-03-06 00:15:03.573] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0108226 [2019-03-06 00:15:03.582] [jointLog] [info] iteration = 1061 | max rel diff. = 0.00971632 [2019-03-06 00:15:03.583] [jointLog] [info] Finished optimizer [2019-03-06 00:15:03.583] [jointLog] [info] writing output [2019-03-06 00:15:03.594] [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: nb_K5_07/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl nb_K5_07/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > nb_K5_07/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P10-TAGCTT-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P10-TAGCTT-READ2-Sequences.txt.gz_val_2.fq.gz) -o nb_K5_08 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { nb_K5_08 } ### [ threads ] => { 23 } Logs will be written to nb_K5_08/logs [2019-03-06 00:15:03.874] [jointLog] [info] parsing read library format [2019-03-06 00:15:03.874] [jointLog] [info] There is 1 library. [2019-03-06 00:15:03.935] [stderrLog] [info] Loading Suffix Array [2019-03-06 00:15:03.935] [jointLog] [info] Loading Quasi index [2019-03-06 00:15:03.935] [jointLog] [info] Loading 32-bit quasi index [2019-03-06 00:15:03.972] [stderrLog] [info] Loading Transcript Info [2019-03-06 00:15:03.981] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-06 00:15:03.985] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-06 00:15:03.986] [stderrLog] [info] Computing transcript lengths [2019-03-06 00:15:03.986] [stderrLog] [info] Waiting to finish loading hash [2019-03-06 00:15:04.326] [jointLog] [info] done [2019-03-06 00:15:04.326] [jointLog] [info] Index contained 5838 targets [2019-03-06 00:15:04.325] [stderrLog] [info] Done loading index  processed 500000 fragments hits: 85027, hits per frag: 0.194255 processed 1000000 fragments hits: 169839, hits per frag: 0.180893 processed 1500000 fragments hits: 255164, hits per frag: 0.180092 processed 2000000 fragments hits: 339782, hits per frag: 0.179304 processed 2500000 fragments hits: 425491, hits per frag: 0.171012 processed 3000000 fragments hits: 510739, hits per frag: 0.175826 processed 3500001 fragments hits: 596690, hits per frag: 0.173509 processed 4000000 fragments hits: 681973, hits per frag: 0.172018 processed 4500001 fragments hits: 766800, hits per frag: 0.175185 processed 5000000 fragments hits: 851563, hits per frag: 0.171953 processed 5500000 fragments hits: 937344, hits per frag: 0.172156 processed 6000000 fragments hits: 1022894, hits per frag: 0.17083 processed 6500001 fragments hits: 1108063, hits per frag: 0.171714 processed 7000000 fragments hits: 1193738, hits per frag: 0.170918 processed 7500000 fragments hits: 1278968, hits per frag: 0.172588 processed 8000001 fragments hits: 1365208, hits per frag: 0.173489 processed 8500000 fragments hits: 1449843, hits per frag: 0.172576 processed 9000000 fragments hits: 1535491, hits per frag: 0.171408 processed 9500000 fragments hits: 1621283, hits per frag: 0.173341 processed 10000001 fragments hits: 1706606, hits per frag: 0.172007 processed 10500000 fragments hits: 1792473, hits per frag: 0.17299 processed 11000000 fragments hits: 1877550, hits per frag: 0.171125 processed 11500000 fragments hits: 1962481, hits per frag: 0.171562 processed 12000000 fragments hits: 2047833, hits per frag: 0.171362 processed 12500001 fragments hits: 2132493, hits per frag: 0.172219 processed 13000000 fragments hits: 2217807, hits per frag: 0.17226 processed 13500000 fragments hits: 2303011, hits per frag: 0.171472 processed 14000000 fragments hits: 2387392, hits per frag: 0.172262 processed 14500000 fragments hits: 2473384, hits per frag: 0.171663 processed 15000000 fragments hits: 2557453, hits per frag: 0.171232 processed 15500000 fragments hits: 2642260, hits per frag: 0.17068 processed 16000000 fragments hits: 2726465, hits per frag: 0.17096 processed 16500000 fragments hits: 2811723, hits per frag: 0.170813 processed 17000000 fragments hits: 2897684, hits per frag: 0.171674 processed 17500000 fragments hits: 2984315, hits per frag: 0.171491 processed 18000001 fragments hits: 3068326, hits per frag: 0.17119 processed 18500000 fragments hits: 3153108, hits per frag: 0.17133 processed 19000000 fragments hits: 3238265, hits per frag: 0.170965 processed 19500001 fragments hits: 3323144, hits per frag: 0.171356 processed 20000000 fragments hits: 3409453, hits per frag: 0.171228 processed 20500001 fragments hits: 3494815, hits per frag: 0.170902 processed 21000000 fragments hits: 3579139, hits per frag: 0.171067 processed 21500000 fragments hits: 3664834, hits per frag: 0.17107 processed 22000000 fragments hits: 3749801, hits per frag: 0.170653 processed 22500001 fragments hits: 3834842, hits per frag: 0.170617 processed 23000001 fragments hits: 3921052, hits per frag: 0.170998 processed 23500000 fragments hits: 4006646, hits per frag: 0.171757 processed 24000001 fragments hits: 4092562, hits per frag: 0.171245 processed 24500000 fragments hits: 4177966, hits per frag: 0.170821 processed 25000000 fragments hits: 4264359, hits per frag: 0.170752 processed 25500001 fragments hits: 4350695, hits per frag: 0.170993 processed 26000000 fragments hits: 4436324, hits per frag: 0.171146 processed 26500000 fragments hits: 4519713, hits per frag: 0.170856 processed 27000000 fragments hits: 4605095, hits per frag: 0.170943 processed 27500000 fragments hits: 4689426, hits per frag: 0.170732 processed 28000000 fragments hits: 4775407, hits per frag: 0.171007 processed 28500001 fragments hits: 4859907, hits per frag: 0.171035 processed 29000000 fragments hits: 4945201, hits per frag: 0.171028 processed 29500000 fragments hits: 5031824, hits per frag: 0.171193 processed 30000000 fragments hits: 5116647, hits per frag: 0.171316 processed 30500000 fragments hits: 5202305, hits per frag: 0.170601 processed 31000000 fragments hits: 5287698, hits per frag: 0.17068 processed 31500000 fragments hits: 5372648, hits per frag: 0.171106 processed 32000001 fragments hits: 5457618, hits per frag: 0.17111 processed 32500000 fragments hits: 5541646, hits per frag: 0.170932 processed 33000000 fragments hits: 5627091, hits per frag: 0.170968 [2019-03-06 00:16:25.623] [jointLog] [info] Computed 8127 rich equivalence classes for further processing [2019-03-06 00:16:25.623] [jointLog] [info] Counted 2818911 total reads in the equivalence classes [2019-03-06 00:16:25.636] [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. [2019-03-06 00:16:25.637] [jointLog] [warning] Only 2818911 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-06 00:16:25.637] [jointLog] [info] Mapping rate = 8.52724% [2019-03-06 00:16:25.637] [jointLog] [info] finished quantifyLibrary() [2019-03-06 00:16:25.637] [jointLog] [info] Starting optimizer [2019-03-06 00:16:25.643] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-06 00:16:25.643] [jointLog] [info] iteration = 0 | max rel diff. = 673.368 [2019-03-06 00:16:25.662] [jointLog] [info] iteration = 100 | max rel diff. = 0.123822 [2019-03-06 00:16:25.678] [jointLog] [info] iteration = 200 | max rel diff. = 0.0598177 [2019-03-06 00:16:25.694] [jointLog] [info] iteration = 300 | max rel diff. = 0.03807 [2019-03-06 00:16:25.709] [jointLog] [info] iteration = 400 | max rel diff. = 0.0269147 [2019-03-06 00:16:25.725] [jointLog] [info] iteration = 500 | max rel diff. = 0.0249085 [2019-03-06 00:16:25.741] [jointLog] [info] iteration = 600 | max rel diff. = 0.0153394 [2019-03-06 00:16:25.756] [jointLog] [info] iteration = 700 | max rel diff. = 0.0153504 [2019-03-06 00:16:25.771] [jointLog] [info] iteration = 800 | max rel diff. = 0.013662 [2019-03-06 00:16:25.786] [jointLog] [info] iteration = 900 | max rel diff. = 0.0108634 [2019-03-06 00:16:25.802] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0101338 [2019-03-06 00:16:25.817] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0101341 [2019-03-06 00:16:25.833] [jointLog] [info] iteration = 1200 | max rel diff. = 0.0101341 [2019-03-06 00:16:25.840] [jointLog] [info] iteration = 1238 | max rel diff. = 0.00902883 [2019-03-06 00:16:25.840] [jointLog] [info] Finished optimizer [2019-03-06 00:16:25.840] [jointLog] [info] writing output [2019-03-06 00:16:25.852] [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: nb_K5_08/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl nb_K5_08/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > nb_K5_08/quant.sf.genes CMD: salmon quant -i /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx -l ISR -1 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P15-GTTTCG-READ1-Sequences.txt.gz_val_1.fq.gz) -2 <(gunzip -c /mnt/data/coral_RNAseq_2017/porites/20180311_fastqc_trimming/trimmed/4R041-L7-P15-GTTTCG-READ2-Sequences.txt.gz_val_2.fq.gz) -o nbK5_09 -p 23 Version Info: ### PLEASE UPGRADE SALMON ### ### A newer version of Salmon with important bug fixes and improvements is available. #### ### The newest version, available at https://github.com/COMBINE-lab/salmon/releases contains new features, improvements, and bug fixes; please upgrade at your earliest convenience. ### ### salmon (mapping-based) v0.9.1 ### [ program ] => salmon ### [ command ] => quant ### [ index ] => { /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.salmon_quasi.idx } ### [ libType ] => { ISR } ### [ mates1 ] => { /dev/fd/63 } ### [ mates2 ] => { /dev/fd/62 } ### [ output ] => { nbK5_09 } ### [ threads ] => { 23 } Logs will be written to nbK5_09/logs [2019-03-06 00:16:26.183] [jointLog] [info] parsing read library format [2019-03-06 00:16:26.183] [jointLog] [info] There is 1 library. [2019-03-06 00:16:26.244] [stderrLog] [info] Loading Suffix Array [2019-03-06 00:16:26.244] [jointLog] [info] Loading Quasi index [2019-03-06 00:16:26.244] [jointLog] [info] Loading 32-bit quasi index [2019-03-06 00:16:26.283] [stderrLog] [info] Loading Transcript Info [2019-03-06 00:16:26.291] [stderrLog] [info] Loading Rank-Select Bit Array [2019-03-06 00:16:26.295] [stderrLog] [info] There were 5838 set bits in the bit array [2019-03-06 00:16:26.296] [stderrLog] [info] Computing transcript lengths [2019-03-06 00:16:26.296] [stderrLog] [info] Waiting to finish loading hash [2019-03-06 00:16:26.635] [jointLog] [info] done [2019-03-06 00:16:26.635] [jointLog] [info] Index contained 5838 targets [2019-03-06 00:16:26.635] [stderrLog] [info] Done loading index  processed 500000 fragments hits: 93029, hits per frag: 0.202792 processed 1000000 fragments hits: 184808, hits per frag: 0.188909 processed 1500000 fragments hits: 277314, hits per frag: 0.193691 processed 2000001 fragments hits: 370150, hits per frag: 0.194007 processed 2500000 fragments hits: 463072, hits per frag: 0.194016 processed 3000000 fragments hits: 555633, hits per frag: 0.189732 processed 3500001 fragments hits: 648596, hits per frag: 0.187211 processed 4000001 fragments hits: 741547, hits per frag: 0.186481 processed 4500000 fragments hits: 834142, hits per frag: 0.189103 processed 5000001 fragments hits: 926505, hits per frag: 0.187905 processed 5500000 fragments hits: 1019122, hits per frag: 0.186562 processed 6000000 fragments hits: 1111495, hits per frag: 0.18589 processed 6500000 fragments hits: 1204540, hits per frag: 0.188361 processed 7000000 fragments hits: 1295976, hits per frag: 0.189925 processed 7500000 fragments hits: 1388535, hits per frag: 0.186708 processed 8000000 fragments hits: 1480544, hits per frag: 0.185562 processed 8500001 fragments hits: 1572531, hits per frag: 0.186345 processed 9000000 fragments hits: 1665918, hits per frag: 0.186277 processed 9500000 fragments hits: 1758424, hits per frag: 0.186908 processed 10000000 fragments hits: 1851277, hits per frag: 0.186009 processed 10500000 fragments hits: 1944294, hits per frag: 0.185467 processed 11000000 fragments hits: 2036313, hits per frag: 0.186472 processed 11500000 fragments hits: 2130203, hits per frag: 0.186082 processed 12000000 fragments hits: 2223475, hits per frag: 0.188505 processed 12500000 fragments hits: 2316749, hits per frag: 0.186523 processed 13000000 fragments hits: 2409255, hits per frag: 0.18612 processed 13500000 fragments hits: 2502596, hits per frag: 0.187365 processed 14000000 fragments hits: 2595899, hits per frag: 0.18647 processed 14500000 fragments hits: 2688578, hits per frag: 0.185621 processed 15000000 fragments hits: 2781320, hits per frag: 0.185492 processed 15500000 fragments hits: 2873569, hits per frag: 0.186358 processed 16000000 fragments hits: 2965228, hits per frag: 0.185598 processed 16500000 fragments hits: 3058443, hits per frag: 0.186761 processed 17000000 fragments hits: 3150665, hits per frag: 0.18573 processed 17500000 fragments hits: 3243736, hits per frag: 0.186356 processed 18000001 fragments hits: 3336555, hits per frag: 0.18589 processed 18500001 fragments hits: 3428913, hits per frag: 0.185509 processed 19000002 fragments hits: 3520945, hits per frag: 0.185625 processed 19500000 fragments hits: 3612575, hits per frag: 0.185569 processed 20000000 fragments hits: 3704805, hits per frag: 0.185548 processed 20500000 fragments hits: 3796901, hits per frag: 0.1858 processed 21000000 fragments hits: 3889202, hits per frag: 0.185648 processed 21500000 fragments hits: 3981875, hits per frag: 0.185554 processed 22000000 fragments hits: 4074394, hits per frag: 0.186207 processed 22500001 fragments hits: 4165759, hits per frag: 0.18595 processed 23000000 fragments hits: 4259739, hits per frag: 0.18539 processed 23500000 fragments hits: 4351776, hits per frag: 0.185788 processed 24000001 fragments hits: 4445462, hits per frag: 0.186014 processed 24500000 fragments hits: 4537431, hits per frag: 0.185427 processed 25000000 fragments hits: 4630134, hits per frag: 0.185794 processed 25500000 fragments hits: 4721332, hits per frag: 0.18535 processed 26000000 fragments hits: 4814334, hits per frag: 0.185864 processed 26500000 fragments hits: 4907701, hits per frag: 0.185879 processed 27000000 fragments hits: 4999857, hits per frag: 0.185539 processed 27500000 fragments hits: 5092286, hits per frag: 0.185856 processed 28000000 fragments hits: 5185833, hits per frag: 0.185491 processed 28500000 fragments hits: 5278236, hits per frag: 0.185565 processed 29000000 fragments hits: 5369815, hits per frag: 0.185851 processed 29500002 fragments hits: 5461606, hits per frag: 0.18553 processed 30000000 fragments hits: 5554955, hits per frag: 0.185837 processed 30000023 fragments hits: 5554955, hits per frag: 0.185931 processed 30500000 fragments hits: 5647101, hits per frag: 0.185202 processed 31000000 fragments hits: 5740351, hits per frag: 0.185716 processed 31500000 fragments hits: 5832523, hits per frag: 0.185969 processed 32000000 fragments hits: 5923983, hits per frag: 0.185423 processed 32500000 fragments hits: 6017323, hits per frag: 0.185577 processed 33000002 fragments hits: 6110348, hits per frag: 0.185726 processed 33500000 fragments hits: 6202910, hits per frag: 0.185209 processed 34000000 fragments hits: 6295274, hits per frag: 0.185555 processed 34500000 fragments hits: 6387315, hits per frag: 0.185423 [2019-03-06 00:17:48.357] [jointLog] [info] Computed 7671 rich equivalence classes for further processing [2019-03-06 00:17:48.357] [jointLog] [info] Counted 3126572 total reads in the equivalence classes [2019-03-06 00:17:48.368] [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. [2019-03-06 00:17:48.369] [jointLog] [warning] Only 3126572 fragments were mapped, but the number of burn-in fragments was set to 5000000. The effective lengths have been computed using the observed mappings. [2019-03-06 00:17:48.369] [jointLog] [info] Mapping rate = 9.05407% [2019-03-06 00:17:48.369] [jointLog] [info] finished quantifyLibrary() [2019-03-06 00:17:48.370] [jointLog] [info] Starting optimizer [2019-03-06 00:17:48.374] [jointLog] [info] Marked 0 weighted equivalence classes as degenerate [2019-03-06 00:17:48.374] [jointLog] [info] iteration = 0 | max rel diff. = 713.297 [2019-03-06 00:17:48.396] [jointLog] [info] iteration = 100 | max rel diff. = 0.115436 [2019-03-06 00:17:48.411] [jointLog] [info] iteration = 200 | max rel diff. = 0.0575028 [2019-03-06 00:17:48.426] [jointLog] [info] iteration = 300 | max rel diff. = 0.0433133 [2019-03-06 00:17:48.441] [jointLog] [info] iteration = 400 | max rel diff. = 0.029745 [2019-03-06 00:17:48.458] [jointLog] [info] iteration = 500 | max rel diff. = 0.024761 [2019-03-06 00:17:48.476] [jointLog] [info] iteration = 600 | max rel diff. = 0.019143 [2019-03-06 00:17:48.493] [jointLog] [info] iteration = 700 | max rel diff. = 0.0155036 [2019-03-06 00:17:48.511] [jointLog] [info] iteration = 800 | max rel diff. = 0.0129289 [2019-03-06 00:17:48.529] [jointLog] [info] iteration = 900 | max rel diff. = 0.0101354 [2019-03-06 00:17:48.547] [jointLog] [info] iteration = 1000 | max rel diff. = 0.0101352 [2019-03-06 00:17:48.562] [jointLog] [info] iteration = 1100 | max rel diff. = 0.0101351 [2019-03-06 00:17:48.569] [jointLog] [info] iteration = 1143 | max rel diff. = 0.00896299 [2019-03-06 00:17:48.569] [jointLog] [info] Finished optimizer [2019-03-06 00:17:48.569] [jointLog] [info] writing output [2019-03-06 00:17:48.580] [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: nbK5_09/lib_format_counts.json for details CMD: /home/shared/Trinityrnaseq-v2.6.6/util/support_scripts/salmon_trans_to_gene_results.pl nbK5_09/quant.sf /media/sam/4TB_toshiba/porites/20190129_sp_coral_transcripts/Trinity.sp.coral.fasta.gene_trans_map > nbK5_09/quant.sf.genes