16723064 reads; of these: 16723064 (100.00%) were paired; of these: 2819889 (16.86%) aligned concordantly 0 times 13329135 (79.71%) aligned concordantly exactly 1 time 574040 (3.43%) aligned concordantly >1 times ---- 2819889 pairs aligned concordantly 0 times; of these: 59345 (2.10%) aligned discordantly 1 time ---- 2760544 pairs aligned 0 times concordantly or discordantly; of these: 5521088 mates make up the pairs; of these: 4038802 (73.15%) aligned 0 times 1217543 (22.05%) aligned exactly 1 time 264743 (4.80%) aligned >1 times 87.92% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/100.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/100.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 15904404 reads; of these: 15904404 (100.00%) were paired; of these: 2863972 (18.01%) aligned concordantly 0 times 12512725 (78.67%) aligned concordantly exactly 1 time 527707 (3.32%) aligned concordantly >1 times ---- 2863972 pairs aligned concordantly 0 times; of these: 53104 (1.85%) aligned discordantly 1 time ---- 2810868 pairs aligned 0 times concordantly or discordantly; of these: 5621736 mates make up the pairs; of these: 4370309 (77.74%) aligned 0 times 1075342 (19.13%) aligned exactly 1 time 176085 (3.13%) aligned >1 times 86.26% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/107.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/107.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 21023862 reads; of these: 21023862 (100.00%) were paired; of these: 5161089 (24.55%) aligned concordantly 0 times 15247863 (72.53%) aligned concordantly exactly 1 time 614910 (2.92%) aligned concordantly >1 times ---- 5161089 pairs aligned concordantly 0 times; of these: 75292 (1.46%) aligned discordantly 1 time ---- 5085797 pairs aligned 0 times concordantly or discordantly; of these: 10171594 mates make up the pairs; of these: 7883696 (77.51%) aligned 0 times 1844958 (18.14%) aligned exactly 1 time 442940 (4.35%) aligned >1 times 81.25% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/108.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/108.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 20663384 reads; of these: 20663384 (100.00%) were paired; of these: 3918571 (18.96%) aligned concordantly 0 times 16020286 (77.53%) aligned concordantly exactly 1 time 724527 (3.51%) aligned concordantly >1 times ---- 3918571 pairs aligned concordantly 0 times; of these: 68892 (1.76%) aligned discordantly 1 time ---- 3849679 pairs aligned 0 times concordantly or discordantly; of these: 7699358 mates make up the pairs; of these: 5695319 (73.97%) aligned 0 times 1570045 (20.39%) aligned exactly 1 time 433994 (5.64%) aligned >1 times 86.22% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/109.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/109.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 18424782 reads; of these: 18424782 (100.00%) were paired; of these: 4033410 (21.89%) aligned concordantly 0 times 13820581 (75.01%) aligned concordantly exactly 1 time 570791 (3.10%) aligned concordantly >1 times ---- 4033410 pairs aligned concordantly 0 times; of these: 67437 (1.67%) aligned discordantly 1 time ---- 3965973 pairs aligned 0 times concordantly or discordantly; of these: 7931946 mates make up the pairs; of these: 5936072 (74.84%) aligned 0 times 1722264 (21.71%) aligned exactly 1 time 273610 (3.45%) aligned >1 times 83.89% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/10.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/10.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 19839132 reads; of these: 19839132 (100.00%) were paired; of these: 3268615 (16.48%) aligned concordantly 0 times 15841105 (79.85%) aligned concordantly exactly 1 time 729412 (3.68%) aligned concordantly >1 times ---- 3268615 pairs aligned concordantly 0 times; of these: 67337 (2.06%) aligned discordantly 1 time ---- 3201278 pairs aligned 0 times concordantly or discordantly; of these: 6402556 mates make up the pairs; of these: 4735637 (73.96%) aligned 0 times 1401277 (21.89%) aligned exactly 1 time 265642 (4.15%) aligned >1 times 88.06% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/110.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/110.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 20711389 reads; of these: 20711389 (100.00%) were paired; of these: 3929424 (18.97%) aligned concordantly 0 times 16076050 (77.62%) aligned concordantly exactly 1 time 705915 (3.41%) aligned concordantly >1 times ---- 3929424 pairs aligned concordantly 0 times; of these: 73415 (1.87%) aligned discordantly 1 time ---- 3856009 pairs aligned 0 times concordantly or discordantly; of these: 7712018 mates make up the pairs; of these: 5827223 (75.56%) aligned 0 times 1546254 (20.05%) aligned exactly 1 time 338541 (4.39%) aligned >1 times 85.93% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/117.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/117.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 19651360 reads; of these: 19651360 (100.00%) were paired; of these: 3289079 (16.74%) aligned concordantly 0 times 15500312 (78.88%) aligned concordantly exactly 1 time 861969 (4.39%) aligned concordantly >1 times ---- 3289079 pairs aligned concordantly 0 times; of these: 70265 (2.14%) aligned discordantly 1 time ---- 3218814 pairs aligned 0 times concordantly or discordantly; of these: 6437628 mates make up the pairs; of these: 4613297 (71.66%) aligned 0 times 1541688 (23.95%) aligned exactly 1 time 282643 (4.39%) aligned >1 times 88.26% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/118.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/118.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 20841898 reads; of these: 20841898 (100.00%) were paired; of these: 3253581 (15.61%) aligned concordantly 0 times 16834707 (80.77%) aligned concordantly exactly 1 time 753610 (3.62%) aligned concordantly >1 times ---- 3253581 pairs aligned concordantly 0 times; of these: 69609 (2.14%) aligned discordantly 1 time ---- 3183972 pairs aligned 0 times concordantly or discordantly; of these: 6367944 mates make up the pairs; of these: 4765024 (74.83%) aligned 0 times 1373325 (21.57%) aligned exactly 1 time 229595 (3.61%) aligned >1 times 88.57% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/119.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/119.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 20092050 reads; of these: 20092050 (100.00%) were paired; of these: 3614357 (17.99%) aligned concordantly 0 times 15764147 (78.46%) aligned concordantly exactly 1 time 713546 (3.55%) aligned concordantly >1 times ---- 3614357 pairs aligned concordantly 0 times; of these: 72083 (1.99%) aligned discordantly 1 time ---- 3542274 pairs aligned 0 times concordantly or discordantly; of these: 7084548 mates make up the pairs; of these: 5162679 (72.87%) aligned 0 times 1663495 (23.48%) aligned exactly 1 time 258374 (3.65%) aligned >1 times 87.15% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/11.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/11.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 19281766 reads; of these: 19281766 (100.00%) were paired; of these: 3437988 (17.83%) aligned concordantly 0 times 15152957 (78.59%) aligned concordantly exactly 1 time 690821 (3.58%) aligned concordantly >1 times ---- 3437988 pairs aligned concordantly 0 times; of these: 70579 (2.05%) aligned discordantly 1 time ---- 3367409 pairs aligned 0 times concordantly or discordantly; of these: 6734818 mates make up the pairs; of these: 4910222 (72.91%) aligned 0 times 1538880 (22.85%) aligned exactly 1 time 285716 (4.24%) aligned >1 times 87.27% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/120.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/120.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 19933243 reads; of these: 19933243 (100.00%) were paired; of these: 8342182 (41.85%) aligned concordantly 0 times 11052505 (55.45%) aligned concordantly exactly 1 time 538556 (2.70%) aligned concordantly >1 times ---- 8342182 pairs aligned concordantly 0 times; of these: 76866 (0.92%) aligned discordantly 1 time ---- 8265316 pairs aligned 0 times concordantly or discordantly; of these: 16530632 mates make up the pairs; of these: 12990705 (78.59%) aligned 0 times 3193682 (19.32%) aligned exactly 1 time 346245 (2.09%) aligned >1 times 67.41% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/121.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/121.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 21818830 reads; of these: 21818830 (100.00%) were paired; of these: 4145035 (19.00%) aligned concordantly 0 times 16983191 (77.84%) aligned concordantly exactly 1 time 690604 (3.17%) aligned concordantly >1 times ---- 4145035 pairs aligned concordantly 0 times; of these: 76830 (1.85%) aligned discordantly 1 time ---- 4068205 pairs aligned 0 times concordantly or discordantly; of these: 8136410 mates make up the pairs; of these: 6069200 (74.59%) aligned 0 times 1758784 (21.62%) aligned exactly 1 time 308426 (3.79%) aligned >1 times 86.09% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/127.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/127.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 9343373 reads; of these: 9343373 (100.00%) were paired; of these: 2072887 (22.19%) aligned concordantly 0 times 7023754 (75.17%) aligned concordantly exactly 1 time 246732 (2.64%) aligned concordantly >1 times ---- 2072887 pairs aligned concordantly 0 times; of these: 35474 (1.71%) aligned discordantly 1 time ---- 2037413 pairs aligned 0 times concordantly or discordantly; of these: 4074826 mates make up the pairs; of these: 3035659 (74.50%) aligned 0 times 902988 (22.16%) aligned exactly 1 time 136179 (3.34%) aligned >1 times 83.76% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/128.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/128.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 8824155 reads; of these: 8824155 (100.00%) were paired; of these: 5563591 (63.05%) aligned concordantly 0 times 3131493 (35.49%) aligned concordantly exactly 1 time 129071 (1.46%) aligned concordantly >1 times ---- 5563591 pairs aligned concordantly 0 times; of these: 16304 (0.29%) aligned discordantly 1 time ---- 5547287 pairs aligned 0 times concordantly or discordantly; of these: 11094574 mates make up the pairs; of these: 9138140 (82.37%) aligned 0 times 531541 (4.79%) aligned exactly 1 time 1424893 (12.84%) aligned >1 times 48.22% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/129.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/129.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 19227757 reads; of these: 19227757 (100.00%) were paired; of these: 3822527 (19.88%) aligned concordantly 0 times 14753436 (76.73%) aligned concordantly exactly 1 time 651794 (3.39%) aligned concordantly >1 times ---- 3822527 pairs aligned concordantly 0 times; of these: 69926 (1.83%) aligned discordantly 1 time ---- 3752601 pairs aligned 0 times concordantly or discordantly; of these: 7505202 mates make up the pairs; of these: 5672334 (75.58%) aligned 0 times 1603293 (21.36%) aligned exactly 1 time 229575 (3.06%) aligned >1 times 85.25% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/12.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/12.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 8424948 reads; of these: 8424948 (100.00%) were paired; of these: 1948309 (23.13%) aligned concordantly 0 times 6241989 (74.09%) aligned concordantly exactly 1 time 234650 (2.79%) aligned concordantly >1 times ---- 1948309 pairs aligned concordantly 0 times; of these: 29858 (1.53%) aligned discordantly 1 time ---- 1918451 pairs aligned 0 times concordantly or discordantly; of these: 3836902 mates make up the pairs; of these: 2834646 (73.88%) aligned 0 times 802709 (20.92%) aligned exactly 1 time 199547 (5.20%) aligned >1 times 83.18% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/131.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/131.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 7728199 reads; of these: 7728199 (100.00%) were paired; of these: 1711458 (22.15%) aligned concordantly 0 times 5780410 (74.80%) aligned concordantly exactly 1 time 236331 (3.06%) aligned concordantly >1 times ---- 1711458 pairs aligned concordantly 0 times; of these: 26845 (1.57%) aligned discordantly 1 time ---- 1684613 pairs aligned 0 times concordantly or discordantly; of these: 3369226 mates make up the pairs; of these: 2590809 (76.90%) aligned 0 times 645172 (19.15%) aligned exactly 1 time 133245 (3.95%) aligned >1 times 83.24% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/137.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/137.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 7914394 reads; of these: 7914394 (100.00%) were paired; of these: 1554178 (19.64%) aligned concordantly 0 times 6109130 (77.19%) aligned concordantly exactly 1 time 251086 (3.17%) aligned concordantly >1 times ---- 1554178 pairs aligned concordantly 0 times; of these: 27574 (1.77%) aligned discordantly 1 time ---- 1526604 pairs aligned 0 times concordantly or discordantly; of these: 3053208 mates make up the pairs; of these: 2322716 (76.07%) aligned 0 times 622218 (20.38%) aligned exactly 1 time 108274 (3.55%) aligned >1 times 85.33% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/138.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/138.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 9025836 reads; of these: 9025836 (100.00%) were paired; of these: 1701474 (18.85%) aligned concordantly 0 times 7017725 (77.75%) aligned concordantly exactly 1 time 306637 (3.40%) aligned concordantly >1 times ---- 1701474 pairs aligned concordantly 0 times; of these: 33957 (2.00%) aligned discordantly 1 time ---- 1667517 pairs aligned 0 times concordantly or discordantly; of these: 3335034 mates make up the pairs; of these: 2399338 (71.94%) aligned 0 times 802661 (24.07%) aligned exactly 1 time 133035 (3.99%) aligned >1 times 86.71% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/139.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/139.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 17283375 reads; of these: 17283375 (100.00%) were paired; of these: 4191162 (24.25%) aligned concordantly 0 times 12597348 (72.89%) aligned concordantly exactly 1 time 494865 (2.86%) aligned concordantly >1 times ---- 4191162 pairs aligned concordantly 0 times; of these: 60594 (1.45%) aligned discordantly 1 time ---- 4130568 pairs aligned 0 times concordantly or discordantly; of these: 8261136 mates make up the pairs; of these: 6298085 (76.24%) aligned 0 times 1645139 (19.91%) aligned exactly 1 time 317912 (3.85%) aligned >1 times 81.78% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/13.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/13.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 8847132 reads; of these: 8847132 (100.00%) were paired; of these: 1798918 (20.33%) aligned concordantly 0 times 6784576 (76.69%) aligned concordantly exactly 1 time 263638 (2.98%) aligned concordantly >1 times ---- 1798918 pairs aligned concordantly 0 times; of these: 31890 (1.77%) aligned discordantly 1 time ---- 1767028 pairs aligned 0 times concordantly or discordantly; of these: 3534056 mates make up the pairs; of these: 2556313 (72.33%) aligned 0 times 827496 (23.41%) aligned exactly 1 time 150247 (4.25%) aligned >1 times 85.55% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/140.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/140.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 8149461 reads; of these: 8149461 (100.00%) were paired; of these: 1735272 (21.29%) aligned concordantly 0 times 6187587 (75.93%) aligned concordantly exactly 1 time 226602 (2.78%) aligned concordantly >1 times ---- 1735272 pairs aligned concordantly 0 times; of these: 27619 (1.59%) aligned discordantly 1 time ---- 1707653 pairs aligned 0 times concordantly or discordantly; of these: 3415306 mates make up the pairs; of these: 2595174 (75.99%) aligned 0 times 699594 (20.48%) aligned exactly 1 time 120538 (3.53%) aligned >1 times 84.08% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/147.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/147.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 23084741 reads; of these: 23084741 (100.00%) were paired; of these: 5362929 (23.23%) aligned concordantly 0 times 17026556 (73.76%) aligned concordantly exactly 1 time 695256 (3.01%) aligned concordantly >1 times ---- 5362929 pairs aligned concordantly 0 times; of these: 90577 (1.69%) aligned discordantly 1 time ---- 5272352 pairs aligned 0 times concordantly or discordantly; of these: 10544704 mates make up the pairs; of these: 8616123 (81.71%) aligned 0 times 1660636 (15.75%) aligned exactly 1 time 267945 (2.54%) aligned >1 times 81.34% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/148.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/148.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 89957700 reads; of these: 89957700 (100.00%) were paired; of these: 35888383 (39.89%) aligned concordantly 0 times 51990478 (57.79%) aligned concordantly exactly 1 time 2078839 (2.31%) aligned concordantly >1 times ---- 35888383 pairs aligned concordantly 0 times; of these: 244957 (0.68%) aligned discordantly 1 time ---- 35643426 pairs aligned 0 times concordantly or discordantly; of these: 71286852 mates make up the pairs; of these: 60083092 (84.28%) aligned 0 times 4842237 (6.79%) aligned exactly 1 time 6361523 (8.92%) aligned >1 times 66.60% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/149.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/149.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 25502427 reads; of these: 25502427 (100.00%) were paired; of these: 6573994 (25.78%) aligned concordantly 0 times 18198014 (71.36%) aligned concordantly exactly 1 time 730419 (2.86%) aligned concordantly >1 times ---- 6573994 pairs aligned concordantly 0 times; of these: 92362 (1.40%) aligned discordantly 1 time ---- 6481632 pairs aligned 0 times concordantly or discordantly; of these: 12963264 mates make up the pairs; of these: 10797133 (83.29%) aligned 0 times 1708622 (13.18%) aligned exactly 1 time 457509 (3.53%) aligned >1 times 78.83% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/150.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/150.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 16557161 reads; of these: 16557161 (100.00%) were paired; of these: 3677914 (22.21%) aligned concordantly 0 times 12361911 (74.66%) aligned concordantly exactly 1 time 517336 (3.12%) aligned concordantly >1 times ---- 3677914 pairs aligned concordantly 0 times; of these: 59536 (1.62%) aligned discordantly 1 time ---- 3618378 pairs aligned 0 times concordantly or discordantly; of these: 7236756 mates make up the pairs; of these: 5449449 (75.30%) aligned 0 times 1467204 (20.27%) aligned exactly 1 time 320103 (4.42%) aligned >1 times 83.54% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/18.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/18.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 16644478 reads; of these: 16644478 (100.00%) were paired; of these: 3023809 (18.17%) aligned concordantly 0 times 13104492 (78.73%) aligned concordantly exactly 1 time 516177 (3.10%) aligned concordantly >1 times ---- 3023809 pairs aligned concordantly 0 times; of these: 51279 (1.70%) aligned discordantly 1 time ---- 2972530 pairs aligned 0 times concordantly or discordantly; of these: 5945060 mates make up the pairs; of these: 4503856 (75.76%) aligned 0 times 1194417 (20.09%) aligned exactly 1 time 246787 (4.15%) aligned >1 times 86.47% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/19.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/19.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 21250812 reads; of these: 21250812 (100.00%) were paired; of these: 5291036 (24.90%) aligned concordantly 0 times 15471897 (72.81%) aligned concordantly exactly 1 time 487879 (2.30%) aligned concordantly >1 times ---- 5291036 pairs aligned concordantly 0 times; of these: 77008 (1.46%) aligned discordantly 1 time ---- 5214028 pairs aligned 0 times concordantly or discordantly; of these: 10428056 mates make up the pairs; of these: 8279200 (79.39%) aligned 0 times 1955133 (18.75%) aligned exactly 1 time 193723 (1.86%) aligned >1 times 80.52% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/19-G.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/19-G.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 22425158 reads; of these: 22425158 (100.00%) were paired; of these: 4351981 (19.41%) aligned concordantly 0 times 17317289 (77.22%) aligned concordantly exactly 1 time 755888 (3.37%) aligned concordantly >1 times ---- 4351981 pairs aligned concordantly 0 times; of these: 78691 (1.81%) aligned discordantly 1 time ---- 4273290 pairs aligned 0 times concordantly or discordantly; of these: 8546580 mates make up the pairs; of these: 6487116 (75.90%) aligned 0 times 1830520 (21.42%) aligned exactly 1 time 228944 (2.68%) aligned >1 times 85.54% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/19-S.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/19-S.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 19767194 reads; of these: 19767194 (100.00%) were paired; of these: 3874231 (19.60%) aligned concordantly 0 times 15271081 (77.25%) aligned concordantly exactly 1 time 621882 (3.15%) aligned concordantly >1 times ---- 3874231 pairs aligned concordantly 0 times; of these: 71032 (1.83%) aligned discordantly 1 time ---- 3803199 pairs aligned 0 times concordantly or discordantly; of these: 7606398 mates make up the pairs; of these: 5771392 (75.88%) aligned 0 times 1616955 (21.26%) aligned exactly 1 time 218051 (2.87%) aligned >1 times 85.40% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/1.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/1.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 16033456 reads; of these: 16033456 (100.00%) were paired; of these: 3853817 (24.04%) aligned concordantly 0 times 11673260 (72.81%) aligned concordantly exactly 1 time 506379 (3.16%) aligned concordantly >1 times ---- 3853817 pairs aligned concordantly 0 times; of these: 54284 (1.41%) aligned discordantly 1 time ---- 3799533 pairs aligned 0 times concordantly or discordantly; of these: 7599066 mates make up the pairs; of these: 5785176 (76.13%) aligned 0 times 1397886 (18.40%) aligned exactly 1 time 416004 (5.47%) aligned >1 times 81.96% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/20.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/20.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 22360696 reads; of these: 22360696 (100.00%) were paired; of these: 5318592 (23.79%) aligned concordantly 0 times 16506814 (73.82%) aligned concordantly exactly 1 time 535290 (2.39%) aligned concordantly >1 times ---- 5318592 pairs aligned concordantly 0 times; of these: 84639 (1.59%) aligned discordantly 1 time ---- 5233953 pairs aligned 0 times concordantly or discordantly; of these: 10467906 mates make up the pairs; of these: 8304581 (79.33%) aligned 0 times 1939576 (18.53%) aligned exactly 1 time 223749 (2.14%) aligned >1 times 81.43% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/20-G.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/20-G.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 15323188 reads; of these: 15323188 (100.00%) were paired; of these: 3164576 (20.65%) aligned concordantly 0 times 11630784 (75.90%) aligned concordantly exactly 1 time 527828 (3.44%) aligned concordantly >1 times ---- 3164576 pairs aligned concordantly 0 times; of these: 57129 (1.81%) aligned discordantly 1 time ---- 3107447 pairs aligned 0 times concordantly or discordantly; of these: 6214894 mates make up the pairs; of these: 4627896 (74.46%) aligned 0 times 1404061 (22.59%) aligned exactly 1 time 182937 (2.94%) aligned >1 times 84.90% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/20-S.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/20-S.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 16202198 reads; of these: 16202198 (100.00%) were paired; of these: 3608051 (22.27%) aligned concordantly 0 times 12085657 (74.59%) aligned concordantly exactly 1 time 508490 (3.14%) aligned concordantly >1 times ---- 3608051 pairs aligned concordantly 0 times; of these: 56174 (1.56%) aligned discordantly 1 time ---- 3551877 pairs aligned 0 times concordantly or discordantly; of these: 7103754 mates make up the pairs; of these: 5278536 (74.31%) aligned 0 times 1503859 (21.17%) aligned exactly 1 time 321359 (4.52%) aligned >1 times 83.71% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/21.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/21.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 17689320 reads; of these: 17689320 (100.00%) were paired; of these: 3320974 (18.77%) aligned concordantly 0 times 13838183 (78.23%) aligned concordantly exactly 1 time 530163 (3.00%) aligned concordantly >1 times ---- 3320974 pairs aligned concordantly 0 times; of these: 60480 (1.82%) aligned discordantly 1 time ---- 3260494 pairs aligned 0 times concordantly or discordantly; of these: 6520988 mates make up the pairs; of these: 4833789 (74.13%) aligned 0 times 1451021 (22.25%) aligned exactly 1 time 236178 (3.62%) aligned >1 times 86.34% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/28.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/28.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 17546117 reads; of these: 17546117 (100.00%) were paired; of these: 4303914 (24.53%) aligned concordantly 0 times 12689125 (72.32%) aligned concordantly exactly 1 time 553078 (3.15%) aligned concordantly >1 times ---- 4303914 pairs aligned concordantly 0 times; of these: 68580 (1.59%) aligned discordantly 1 time ---- 4235334 pairs aligned 0 times concordantly or discordantly; of these: 8470668 mates make up the pairs; of these: 6434093 (75.96%) aligned 0 times 1729716 (20.42%) aligned exactly 1 time 306859 (3.62%) aligned >1 times 81.67% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/29.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/29.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 18269876 reads; of these: 18269876 (100.00%) were paired; of these: 3051808 (16.70%) aligned concordantly 0 times 14584766 (79.83%) aligned concordantly exactly 1 time 633302 (3.47%) aligned concordantly >1 times ---- 3051808 pairs aligned concordantly 0 times; of these: 64881 (2.13%) aligned discordantly 1 time ---- 2986927 pairs aligned 0 times concordantly or discordantly; of these: 5973854 mates make up the pairs; of these: 4490850 (75.18%) aligned 0 times 1266149 (21.19%) aligned exactly 1 time 216855 (3.63%) aligned >1 times 87.71% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/2.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/2.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 18428262 reads; of these: 18428262 (100.00%) were paired; of these: 3659933 (19.86%) aligned concordantly 0 times 14217212 (77.15%) aligned concordantly exactly 1 time 551117 (2.99%) aligned concordantly >1 times ---- 3659933 pairs aligned concordantly 0 times; of these: 65655 (1.79%) aligned discordantly 1 time ---- 3594278 pairs aligned 0 times concordantly or discordantly; of these: 7188556 mates make up the pairs; of these: 5334543 (74.21%) aligned 0 times 1575461 (21.92%) aligned exactly 1 time 278552 (3.87%) aligned >1 times 85.53% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/30.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/30.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 17724988 reads; of these: 17724988 (100.00%) were paired; of these: 2900621 (16.36%) aligned concordantly 0 times 14222835 (80.24%) aligned concordantly exactly 1 time 601532 (3.39%) aligned concordantly >1 times ---- 2900621 pairs aligned concordantly 0 times; of these: 54273 (1.87%) aligned discordantly 1 time ---- 2846348 pairs aligned 0 times concordantly or discordantly; of these: 5692696 mates make up the pairs; of these: 4070119 (71.50%) aligned 0 times 1478822 (25.98%) aligned exactly 1 time 143755 (2.53%) aligned >1 times 88.52% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/31.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/31.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 15243144 reads; of these: 15243144 (100.00%) were paired; of these: 2708283 (17.77%) aligned concordantly 0 times 12143837 (79.67%) aligned concordantly exactly 1 time 391024 (2.57%) aligned concordantly >1 times ---- 2708283 pairs aligned concordantly 0 times; of these: 56730 (2.09%) aligned discordantly 1 time ---- 2651553 pairs aligned 0 times concordantly or discordantly; of these: 5303106 mates make up the pairs; of these: 4118264 (77.66%) aligned 0 times 1042442 (19.66%) aligned exactly 1 time 142400 (2.69%) aligned >1 times 86.49% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/37.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/37.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 17036199 reads; of these: 17036199 (100.00%) were paired; of these: 3740330 (21.96%) aligned concordantly 0 times 12841589 (75.38%) aligned concordantly exactly 1 time 454280 (2.67%) aligned concordantly >1 times ---- 3740330 pairs aligned concordantly 0 times; of these: 61108 (1.63%) aligned discordantly 1 time ---- 3679222 pairs aligned 0 times concordantly or discordantly; of these: 7358444 mates make up the pairs; of these: 5543740 (75.34%) aligned 0 times 1383298 (18.80%) aligned exactly 1 time 431406 (5.86%) aligned >1 times 83.73% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/38.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/38.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 16828103 reads; of these: 16828103 (100.00%) were paired; of these: 3272167 (19.44%) aligned concordantly 0 times 13091906 (77.80%) aligned concordantly exactly 1 time 464030 (2.76%) aligned concordantly >1 times ---- 3272167 pairs aligned concordantly 0 times; of these: 63413 (1.94%) aligned discordantly 1 time ---- 3208754 pairs aligned 0 times concordantly or discordantly; of these: 6417508 mates make up the pairs; of these: 5023376 (78.28%) aligned 0 times 1227476 (19.13%) aligned exactly 1 time 166656 (2.60%) aligned >1 times 85.07% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/39.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/39.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 19136269 reads; of these: 19136269 (100.00%) were paired; of these: 4232398 (22.12%) aligned concordantly 0 times 14223183 (74.33%) aligned concordantly exactly 1 time 680688 (3.56%) aligned concordantly >1 times ---- 4232398 pairs aligned concordantly 0 times; of these: 73734 (1.74%) aligned discordantly 1 time ---- 4158664 pairs aligned 0 times concordantly or discordantly; of these: 8317328 mates make up the pairs; of these: 6307382 (75.83%) aligned 0 times 1624219 (19.53%) aligned exactly 1 time 385727 (4.64%) aligned >1 times 83.52% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/3.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/3.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 15520211 reads; of these: 15520211 (100.00%) were paired; of these: 4117065 (26.53%) aligned concordantly 0 times 11021192 (71.01%) aligned concordantly exactly 1 time 381954 (2.46%) aligned concordantly >1 times ---- 4117065 pairs aligned concordantly 0 times; of these: 58352 (1.42%) aligned discordantly 1 time ---- 4058713 pairs aligned 0 times concordantly or discordantly; of these: 8117426 mates make up the pairs; of these: 6204378 (76.43%) aligned 0 times 1254472 (15.45%) aligned exactly 1 time 658576 (8.11%) aligned >1 times 80.01% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/40.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/40.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 15181149 reads; of these: 15181149 (100.00%) were paired; of these: 4338388 (28.58%) aligned concordantly 0 times 10427178 (68.69%) aligned concordantly exactly 1 time 415583 (2.74%) aligned concordantly >1 times ---- 4338388 pairs aligned concordantly 0 times; of these: 56382 (1.30%) aligned discordantly 1 time ---- 4282006 pairs aligned 0 times concordantly or discordantly; of these: 8564012 mates make up the pairs; of these: 6342568 (74.06%) aligned 0 times 1118492 (13.06%) aligned exactly 1 time 1102952 (12.88%) aligned >1 times 79.11% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/41.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/41.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 17272203 reads; of these: 17272203 (100.00%) were paired; of these: 3193180 (18.49%) aligned concordantly 0 times 13529617 (78.33%) aligned concordantly exactly 1 time 549406 (3.18%) aligned concordantly >1 times ---- 3193180 pairs aligned concordantly 0 times; of these: 63662 (1.99%) aligned discordantly 1 time ---- 3129518 pairs aligned 0 times concordantly or discordantly; of these: 6259036 mates make up the pairs; of these: 4748982 (75.87%) aligned 0 times 1303067 (20.82%) aligned exactly 1 time 206987 (3.31%) aligned >1 times 86.25% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/47.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/47.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 18761830 reads; of these: 18761830 (100.00%) were paired; of these: 4123813 (21.98%) aligned concordantly 0 times 14162902 (75.49%) aligned concordantly exactly 1 time 475115 (2.53%) aligned concordantly >1 times ---- 4123813 pairs aligned concordantly 0 times; of these: 59384 (1.44%) aligned discordantly 1 time ---- 4064429 pairs aligned 0 times concordantly or discordantly; of these: 8128858 mates make up the pairs; of these: 6565560 (80.77%) aligned 0 times 1213788 (14.93%) aligned exactly 1 time 349510 (4.30%) aligned >1 times 82.50% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/48.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/48.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 18706798 reads; of these: 18706798 (100.00%) were paired; of these: 3680904 (19.68%) aligned concordantly 0 times 14526731 (77.65%) aligned concordantly exactly 1 time 499163 (2.67%) aligned concordantly >1 times ---- 3680904 pairs aligned concordantly 0 times; of these: 70115 (1.90%) aligned discordantly 1 time ---- 3610789 pairs aligned 0 times concordantly or discordantly; of these: 7221578 mates make up the pairs; of these: 5370992 (74.37%) aligned 0 times 1602110 (22.19%) aligned exactly 1 time 248476 (3.44%) aligned >1 times 85.64% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/49.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/49.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 19447157 reads; of these: 19447157 (100.00%) were paired; of these: 4302691 (22.13%) aligned concordantly 0 times 14542685 (74.78%) aligned concordantly exactly 1 time 601781 (3.09%) aligned concordantly >1 times ---- 4302691 pairs aligned concordantly 0 times; of these: 59370 (1.38%) aligned discordantly 1 time ---- 4243321 pairs aligned 0 times concordantly or discordantly; of these: 8486642 mates make up the pairs; of these: 6283859 (74.04%) aligned 0 times 1932125 (22.77%) aligned exactly 1 time 270658 (3.19%) aligned >1 times 83.84% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/4.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/4.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 17664425 reads; of these: 17664425 (100.00%) were paired; of these: 3449870 (19.53%) aligned concordantly 0 times 13670955 (77.39%) aligned concordantly exactly 1 time 543600 (3.08%) aligned concordantly >1 times ---- 3449870 pairs aligned concordantly 0 times; of these: 64449 (1.87%) aligned discordantly 1 time ---- 3385421 pairs aligned 0 times concordantly or discordantly; of these: 6770842 mates make up the pairs; of these: 5072640 (74.92%) aligned 0 times 1513611 (22.35%) aligned exactly 1 time 184591 (2.73%) aligned >1 times 85.64% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/50.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/50.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 18383280 reads; of these: 18383280 (100.00%) were paired; of these: 3220574 (17.52%) aligned concordantly 0 times 14584993 (79.34%) aligned concordantly exactly 1 time 577713 (3.14%) aligned concordantly >1 times ---- 3220574 pairs aligned concordantly 0 times; of these: 68601 (2.13%) aligned discordantly 1 time ---- 3151973 pairs aligned 0 times concordantly or discordantly; of these: 6303946 mates make up the pairs; of these: 4695196 (74.48%) aligned 0 times 1412178 (22.40%) aligned exactly 1 time 196572 (3.12%) aligned >1 times 87.23% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/57.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/57.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 26705405 reads; of these: 26705405 (100.00%) were paired; of these: 5705552 (21.36%) aligned concordantly 0 times 20334503 (76.14%) aligned concordantly exactly 1 time 665350 (2.49%) aligned concordantly >1 times ---- 5705552 pairs aligned concordantly 0 times; of these: 98813 (1.73%) aligned discordantly 1 time ---- 5606739 pairs aligned 0 times concordantly or discordantly; of these: 11213478 mates make up the pairs; of these: 8616257 (76.84%) aligned 0 times 2359925 (21.05%) aligned exactly 1 time 237296 (2.12%) aligned >1 times 83.87% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/57-G.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/57-G.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 12171985 reads; of these: 12171985 (100.00%) were paired; of these: 6442672 (52.93%) aligned concordantly 0 times 5470545 (44.94%) aligned concordantly exactly 1 time 258768 (2.13%) aligned concordantly >1 times ---- 6442672 pairs aligned concordantly 0 times; of these: 36392 (0.56%) aligned discordantly 1 time ---- 6406280 pairs aligned 0 times concordantly or discordantly; of these: 12812560 mates make up the pairs; of these: 10794628 (84.25%) aligned 0 times 1151041 (8.98%) aligned exactly 1 time 866891 (6.77%) aligned >1 times 55.66% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/57-S.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/57-S.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 18304505 reads; of these: 18304505 (100.00%) were paired; of these: 4240687 (23.17%) aligned concordantly 0 times 13553850 (74.05%) aligned concordantly exactly 1 time 509968 (2.79%) aligned concordantly >1 times ---- 4240687 pairs aligned concordantly 0 times; of these: 68735 (1.62%) aligned discordantly 1 time ---- 4171952 pairs aligned 0 times concordantly or discordantly; of these: 8343904 mates make up the pairs; of these: 6440021 (77.18%) aligned 0 times 1605113 (19.24%) aligned exactly 1 time 298770 (3.58%) aligned >1 times 82.41% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/58.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/58.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 27294475 reads; of these: 27294475 (100.00%) were paired; of these: 5988260 (21.94%) aligned concordantly 0 times 20691923 (75.81%) aligned concordantly exactly 1 time 614292 (2.25%) aligned concordantly >1 times ---- 5988260 pairs aligned concordantly 0 times; of these: 99901 (1.67%) aligned discordantly 1 time ---- 5888359 pairs aligned 0 times concordantly or discordantly; of these: 11776718 mates make up the pairs; of these: 8903145 (75.60%) aligned 0 times 2623334 (22.28%) aligned exactly 1 time 250239 (2.12%) aligned >1 times 83.69% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/58-G.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/58-G.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 14552346 reads; of these: 14552346 (100.00%) were paired; of these: 3901967 (26.81%) aligned concordantly 0 times 10365630 (71.23%) aligned concordantly exactly 1 time 284749 (1.96%) aligned concordantly >1 times ---- 3901967 pairs aligned concordantly 0 times; of these: 53178 (1.36%) aligned discordantly 1 time ---- 3848789 pairs aligned 0 times concordantly or discordantly; of these: 7697578 mates make up the pairs; of these: 6339262 (82.35%) aligned 0 times 1103991 (14.34%) aligned exactly 1 time 254325 (3.30%) aligned >1 times 78.22% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/58-S.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/58-S.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 17460890 reads; of these: 17460890 (100.00%) were paired; of these: 3283864 (18.81%) aligned concordantly 0 times 13640805 (78.12%) aligned concordantly exactly 1 time 536221 (3.07%) aligned concordantly >1 times ---- 3283864 pairs aligned concordantly 0 times; of these: 48870 (1.49%) aligned discordantly 1 time ---- 3234994 pairs aligned 0 times concordantly or discordantly; of these: 6469988 mates make up the pairs; of these: 4818898 (74.48%) aligned 0 times 1449823 (22.41%) aligned exactly 1 time 201267 (3.11%) aligned >1 times 86.20% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/59.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/59.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 18540171 reads; of these: 18540171 (100.00%) were paired; of these: 3736435 (20.15%) aligned concordantly 0 times 14198047 (76.58%) aligned concordantly exactly 1 time 605689 (3.27%) aligned concordantly >1 times ---- 3736435 pairs aligned concordantly 0 times; of these: 68637 (1.84%) aligned discordantly 1 time ---- 3667798 pairs aligned 0 times concordantly or discordantly; of these: 7335596 mates make up the pairs; of these: 5432658 (74.06%) aligned 0 times 1552604 (21.17%) aligned exactly 1 time 350334 (4.78%) aligned >1 times 85.35% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/5.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/5.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 19032564 reads; of these: 19032564 (100.00%) were paired; of these: 3922766 (20.61%) aligned concordantly 0 times 14529005 (76.34%) aligned concordantly exactly 1 time 580793 (3.05%) aligned concordantly >1 times ---- 3922766 pairs aligned concordantly 0 times; of these: 72360 (1.84%) aligned discordantly 1 time ---- 3850406 pairs aligned 0 times concordantly or discordantly; of these: 7700812 mates make up the pairs; of these: 5682090 (73.79%) aligned 0 times 1708830 (22.19%) aligned exactly 1 time 309892 (4.02%) aligned >1 times 85.07% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/60.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/60.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 19181842 reads; of these: 19181842 (100.00%) were paired; of these: 4012824 (20.92%) aligned concordantly 0 times 14558503 (75.90%) aligned concordantly exactly 1 time 610515 (3.18%) aligned concordantly >1 times ---- 4012824 pairs aligned concordantly 0 times; of these: 64937 (1.62%) aligned discordantly 1 time ---- 3947887 pairs aligned 0 times concordantly or discordantly; of these: 7895774 mates make up the pairs; of these: 5803398 (73.50%) aligned 0 times 1682457 (21.31%) aligned exactly 1 time 409919 (5.19%) aligned >1 times 84.87% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/67.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/67.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 19063538 reads; of these: 19063538 (100.00%) were paired; of these: 3777906 (19.82%) aligned concordantly 0 times 14689807 (77.06%) aligned concordantly exactly 1 time 595825 (3.13%) aligned concordantly >1 times ---- 3777906 pairs aligned concordantly 0 times; of these: 70262 (1.86%) aligned discordantly 1 time ---- 3707644 pairs aligned 0 times concordantly or discordantly; of these: 7415288 mates make up the pairs; of these: 5486492 (73.99%) aligned 0 times 1645548 (22.19%) aligned exactly 1 time 283248 (3.82%) aligned >1 times 85.61% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/68.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/68.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 16372600 reads; of these: 16372600 (100.00%) were paired; of these: 3244071 (19.81%) aligned concordantly 0 times 12663008 (77.34%) aligned concordantly exactly 1 time 465521 (2.84%) aligned concordantly >1 times ---- 3244071 pairs aligned concordantly 0 times; of these: 61579 (1.90%) aligned discordantly 1 time ---- 3182492 pairs aligned 0 times concordantly or discordantly; of these: 6364984 mates make up the pairs; of these: 4868589 (76.49%) aligned 0 times 1290045 (20.27%) aligned exactly 1 time 206350 (3.24%) aligned >1 times 85.13% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/69.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/69.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 14308031 reads; of these: 14308031 (100.00%) were paired; of these: 2850723 (19.92%) aligned concordantly 0 times 11034175 (77.12%) aligned concordantly exactly 1 time 423133 (2.96%) aligned concordantly >1 times ---- 2850723 pairs aligned concordantly 0 times; of these: 50398 (1.77%) aligned discordantly 1 time ---- 2800325 pairs aligned 0 times concordantly or discordantly; of these: 5600650 mates make up the pairs; of these: 4235129 (75.62%) aligned 0 times 1145365 (20.45%) aligned exactly 1 time 220156 (3.93%) aligned >1 times 85.20% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/70.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/70.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 16961387 reads; of these: 16961387 (100.00%) were paired; of these: 3169623 (18.69%) aligned concordantly 0 times 13169652 (77.64%) aligned concordantly exactly 1 time 622112 (3.67%) aligned concordantly >1 times ---- 3169623 pairs aligned concordantly 0 times; of these: 63967 (2.02%) aligned discordantly 1 time ---- 3105656 pairs aligned 0 times concordantly or discordantly; of these: 6211312 mates make up the pairs; of these: 4751512 (76.50%) aligned 0 times 1114680 (17.95%) aligned exactly 1 time 345120 (5.56%) aligned >1 times 85.99% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/78.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/78.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 17656675 reads; of these: 17656675 (100.00%) were paired; of these: 3155367 (17.87%) aligned concordantly 0 times 13868940 (78.55%) aligned concordantly exactly 1 time 632368 (3.58%) aligned concordantly >1 times ---- 3155367 pairs aligned concordantly 0 times; of these: 63581 (2.02%) aligned discordantly 1 time ---- 3091786 pairs aligned 0 times concordantly or discordantly; of these: 6183572 mates make up the pairs; of these: 4589824 (74.23%) aligned 0 times 1352305 (21.87%) aligned exactly 1 time 241443 (3.90%) aligned >1 times 87.00% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/79.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/79.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 13704765 reads; of these: 13704765 (100.00%) were paired; of these: 2769845 (20.21%) aligned concordantly 0 times 10498417 (76.60%) aligned concordantly exactly 1 time 436503 (3.19%) aligned concordantly >1 times ---- 2769845 pairs aligned concordantly 0 times; of these: 53119 (1.92%) aligned discordantly 1 time ---- 2716726 pairs aligned 0 times concordantly or discordantly; of these: 5433452 mates make up the pairs; of these: 4108884 (75.62%) aligned 0 times 1102718 (20.29%) aligned exactly 1 time 221850 (4.08%) aligned >1 times 85.01% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/80.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/80.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 15437259 reads; of these: 15437259 (100.00%) were paired; of these: 2517874 (16.31%) aligned concordantly 0 times 12447118 (80.63%) aligned concordantly exactly 1 time 472267 (3.06%) aligned concordantly >1 times ---- 2517874 pairs aligned concordantly 0 times; of these: 56337 (2.24%) aligned discordantly 1 time ---- 2461537 pairs aligned 0 times concordantly or discordantly; of these: 4923074 mates make up the pairs; of these: 3718269 (75.53%) aligned 0 times 1015153 (20.62%) aligned exactly 1 time 189652 (3.85%) aligned >1 times 87.96% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/83.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/83.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 18736055 reads; of these: 18736055 (100.00%) were paired; of these: 5815786 (31.04%) aligned concordantly 0 times 12349774 (65.91%) aligned concordantly exactly 1 time 570495 (3.04%) aligned concordantly >1 times ---- 5815786 pairs aligned concordantly 0 times; of these: 68105 (1.17%) aligned discordantly 1 time ---- 5747681 pairs aligned 0 times concordantly or discordantly; of these: 11495362 mates make up the pairs; of these: 9420767 (81.95%) aligned 0 times 1620534 (14.10%) aligned exactly 1 time 454061 (3.95%) aligned >1 times 74.86% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/88.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/88.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 17003449 reads; of these: 17003449 (100.00%) were paired; of these: 4072613 (23.95%) aligned concordantly 0 times 12407450 (72.97%) aligned concordantly exactly 1 time 523386 (3.08%) aligned concordantly >1 times ---- 4072613 pairs aligned concordantly 0 times; of these: 63754 (1.57%) aligned discordantly 1 time ---- 4008859 pairs aligned 0 times concordantly or discordantly; of these: 8017718 mates make up the pairs; of these: 6274674 (78.26%) aligned 0 times 1442757 (17.99%) aligned exactly 1 time 300287 (3.75%) aligned >1 times 81.55% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/90.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/90.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 18832038 reads; of these: 18832038 (100.00%) were paired; of these: 3869556 (20.55%) aligned concordantly 0 times 14341336 (76.15%) aligned concordantly exactly 1 time 621146 (3.30%) aligned concordantly >1 times ---- 3869556 pairs aligned concordantly 0 times; of these: 66801 (1.73%) aligned discordantly 1 time ---- 3802755 pairs aligned 0 times concordantly or discordantly; of these: 7605510 mates make up the pairs; of these: 5663468 (74.47%) aligned 0 times 1642449 (21.60%) aligned exactly 1 time 299593 (3.94%) aligned >1 times 84.96% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/91.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/91.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 13977590 reads; of these: 13977590 (100.00%) were paired; of these: 3222457 (23.05%) aligned concordantly 0 times 10341074 (73.98%) aligned concordantly exactly 1 time 414059 (2.96%) aligned concordantly >1 times ---- 3222457 pairs aligned concordantly 0 times; of these: 43818 (1.36%) aligned discordantly 1 time ---- 3178639 pairs aligned 0 times concordantly or discordantly; of these: 6357278 mates make up the pairs; of these: 5191790 (81.67%) aligned 0 times 987213 (15.53%) aligned exactly 1 time 178275 (2.80%) aligned >1 times 81.43% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/92.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/92.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 16826686 reads; of these: 16826686 (100.00%) were paired; of these: 2786345 (16.56%) aligned concordantly 0 times 13514906 (80.32%) aligned concordantly exactly 1 time 525435 (3.12%) aligned concordantly >1 times ---- 2786345 pairs aligned concordantly 0 times; of these: 66112 (2.37%) aligned discordantly 1 time ---- 2720233 pairs aligned 0 times concordantly or discordantly; of these: 5440466 mates make up the pairs; of these: 4230216 (77.75%) aligned 0 times 984125 (18.09%) aligned exactly 1 time 226125 (4.16%) aligned >1 times 87.43% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/97.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/97.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 20752442 reads; of these: 20752442 (100.00%) were paired; of these: 5053323 (24.35%) aligned concordantly 0 times 15052103 (72.53%) aligned concordantly exactly 1 time 647016 (3.12%) aligned concordantly >1 times ---- 5053323 pairs aligned concordantly 0 times; of these: 70232 (1.39%) aligned discordantly 1 time ---- 4983091 pairs aligned 0 times concordantly or discordantly; of these: 9966182 mates make up the pairs; of these: 7955493 (79.82%) aligned 0 times 1327714 (13.32%) aligned exactly 1 time 682975 (6.85%) aligned >1 times 80.83% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/98.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/98.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 15638736 reads; of these: 15638736 (100.00%) were paired; of these: 3551230 (22.71%) aligned concordantly 0 times 11578442 (74.04%) aligned concordantly exactly 1 time 509064 (3.26%) aligned concordantly >1 times ---- 3551230 pairs aligned concordantly 0 times; of these: 60653 (1.71%) aligned discordantly 1 time ---- 3490577 pairs aligned 0 times concordantly or discordantly; of these: 6981154 mates make up the pairs; of these: 5322377 (76.24%) aligned 0 times 1276422 (18.28%) aligned exactly 1 time 382355 (5.48%) aligned >1 times 82.98% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/99.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/99.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 14831891 reads; of these: 14831891 (100.00%) were paired; of these: 2642826 (17.82%) aligned concordantly 0 times 11673051 (78.70%) aligned concordantly exactly 1 time 516014 (3.48%) aligned concordantly >1 times ---- 2642826 pairs aligned concordantly 0 times; of these: 54044 (2.04%) aligned discordantly 1 time ---- 2588782 pairs aligned 0 times concordantly or discordantly; of these: 5177564 mates make up the pairs; of these: 3746236 (72.36%) aligned 0 times 1213673 (23.44%) aligned exactly 1 time 217655 (4.20%) aligned >1 times 87.37% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/RESUB-116.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/RESUB-116.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 15298692 reads; of these: 15298692 (100.00%) were paired; of these: 2473006 (16.16%) aligned concordantly 0 times 12251334 (80.08%) aligned concordantly exactly 1 time 574352 (3.75%) aligned concordantly >1 times ---- 2473006 pairs aligned concordantly 0 times; of these: 56742 (2.29%) aligned discordantly 1 time ---- 2416264 pairs aligned 0 times concordantly or discordantly; of these: 4832528 mates make up the pairs; of these: 3518468 (72.81%) aligned 0 times 1128164 (23.35%) aligned exactly 1 time 185896 (3.85%) aligned >1 times 88.50% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/RESUB-156.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/RESUB-156.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 13976653 reads; of these: 13976653 (100.00%) were paired; of these: 2170025 (15.53%) aligned concordantly 0 times 11340828 (81.14%) aligned concordantly exactly 1 time 465800 (3.33%) aligned concordantly >1 times ---- 2170025 pairs aligned concordantly 0 times; of these: 46767 (2.16%) aligned discordantly 1 time ---- 2123258 pairs aligned 0 times concordantly or discordantly; of these: 4246516 mates make up the pairs; of these: 3153891 (74.27%) aligned 0 times 935327 (22.03%) aligned exactly 1 time 157298 (3.70%) aligned >1 times 88.72% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/RESUB-36.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/RESUB-36.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 13765029 reads; of these: 13765029 (100.00%) were paired; of these: 2845054 (20.67%) aligned concordantly 0 times 10551586 (76.66%) aligned concordantly exactly 1 time 368389 (2.68%) aligned concordantly >1 times ---- 2845054 pairs aligned concordantly 0 times; of these: 49682 (1.75%) aligned discordantly 1 time ---- 2795372 pairs aligned 0 times concordantly or discordantly; of these: 5590744 mates make up the pairs; of these: 4365880 (78.09%) aligned 0 times 1058784 (18.94%) aligned exactly 1 time 166080 (2.97%) aligned >1 times 84.14% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/RESUB-76.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/RESUB-76.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ... 15623530 reads; of these: 15623530 (100.00%) were paired; of these: 2777932 (17.78%) aligned concordantly 0 times 12296661 (78.71%) aligned concordantly exactly 1 time 548937 (3.51%) aligned concordantly >1 times ---- 2777932 pairs aligned concordantly 0 times; of these: 57320 (2.06%) aligned discordantly 1 time ---- 2720612 pairs aligned 0 times concordantly or discordantly; of these: 5441224 mates make up the pairs; of these: 3917313 (71.99%) aligned 0 times 1325486 (24.36%) aligned exactly 1 time 198425 (3.65%) aligned >1 times 87.46% overall alignment rate Warning: [Errno 2] No such file or directory: '../output/05-cod-RNAseq-trimming/trimmed-reads/RESUB-94.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' (ERR): Read file '../output/05-cod-RNAseq-trimming/trimmed-reads/RESUB-94.flexbar_trim.R_2.fastq.gz.flexbar_trim.R_1.fastq.gz' doesn't exist Exiting now ...