Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:11505:26824:7988 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:11505:26824:7988 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:11602:20384:14835 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:11602:20384:14835 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:13602:12343:17487 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:13602:12343:17487 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:21502:9741:3446 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:21502:9741:3446 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:23611:12896:3926 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:23611:12896:3926 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:11503:4414:9351 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:11503:4414:9351 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:21603:22402:16667 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:21603:22402:16667 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:22504:5736:7067 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:22504:5736:7067 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:11112:4403:13147 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:11112:4403:13147 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:11303:4346:10323 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:11303:4346:10323 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:21111:16664:13163 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:21111:16664:13163 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:21209:26384:10183 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:21209:26384:10183 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:21310:8087:4956 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:21310:8087:4956 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:11311:3059:2857 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:11311:3059:2857 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:13205:18784:5531 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:13205:18784:5531 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:21102:26108:12870 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:21102:26108:12870 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:21110:2892:10485 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:21110:2892:10485 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:22211:9684:15403 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:22211:9684:15403 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:23302:26679:3600 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:23302:26679:3600 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:11402:6266:17983 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:11402:6266:17983 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:12404:7501:8511 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:12404:7501:8511 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:12508:21380:9020 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:12508:21380:9020 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:21407:14191:8191 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:21407:14191:8191 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:21504:9207:18298 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:21504:9207:18298 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:23403:19319:7740 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:23403:19319:7740 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:3:11612:13710:3273 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:3:11612:13710:3273 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:3:12606:7026:19625 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:3:12606:7026:19625 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:3:13503:26613:2999 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:3:13503:26613:2999 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:11112:7861:11446 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:11112:7861:11446 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:21109:11939:8919 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:21109:11939:8919 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:12108:10290:10627 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:12108:10290:10627 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:13104:5372:17206 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:13104:5372:17206 2:N:0:CTCTACTT' because it was < 2 characters long
6166784 reads; of these:
  6166784 (100.00%) were paired; of these:
    4411675 (71.54%) aligned concordantly 0 times
    1696437 (27.51%) aligned concordantly exactly 1 time
    58672 (0.95%) aligned concordantly >1 times
    ----
    4411675 pairs aligned concordantly 0 times; of these:
      137405 (3.11%) aligned discordantly 1 time
    ----
    4274270 pairs aligned 0 times concordantly or discordantly; of these:
      8548540 mates make up the pairs; of these:
        7736761 (90.50%) aligned 0 times
        787217 (9.21%) aligned exactly 1 time
        24562 (0.29%) aligned >1 times
37.27% overall alignment rate
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:11512:15404:4939 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:11512:15404:4939 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:13607:18913:1846 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:13607:18913:1846 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:23512:21841:15075 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:23512:21841:15075 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:11410:26496:8317 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:11410:26496:8317 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:11602:21795:16120 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:11602:21795:16120 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:13607:16302:13382 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:13607:16302:13382 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:12212:24558:12850 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:12212:24558:12850 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:21201:2862:5744 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:21201:2862:5744 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:11107:19812:9790 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:11107:19812:9790 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:11503:16027:20042 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:11503:16027:20042 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:21610:9163:16301 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:21610:9163:16301 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:11304:18025:10013 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:11304:18025:10013 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:13107:26784:3746 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:13107:26784:3746 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:22305:19719:8460 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:22305:19719:8460 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:11208:26245:19481 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:11208:26245:19481 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:12210:6002:2088 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:12210:6002:2088 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:21106:10577:13328 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:21106:10577:13328 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:21112:15826:19549 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:21112:15826:19549 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:23112:6452:12216 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:23112:6452:12216 2:N:0:CTCTACTT' because it was < 2 characters long
4982146 reads; of these:
  4982146 (100.00%) were paired; of these:
    3465048 (69.55%) aligned concordantly 0 times
    1472918 (29.56%) aligned concordantly exactly 1 time
    44180 (0.89%) aligned concordantly >1 times
    ----
    3465048 pairs aligned concordantly 0 times; of these:
      114795 (3.31%) aligned discordantly 1 time
    ----
    3350253 pairs aligned 0 times concordantly or discordantly; of these:
      6700506 mates make up the pairs; of these:
        6023936 (89.90%) aligned 0 times
        659412 (9.84%) aligned exactly 1 time
        17158 (0.26%) aligned >1 times
39.54% overall alignment rate
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:12106:19691:14582 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:12106:19691:14582 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:13403:16126:13254 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:13403:16126:13254 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:23601:23414:1927 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:23601:23414:1927 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:12207:11238:14485 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:12207:11238:14485 2:N:0:CTCTACTT' because it was < 2 characters long
627905 reads; of these:
  627905 (100.00%) were paired; of these:
    512199 (81.57%) aligned concordantly 0 times
    112214 (17.87%) aligned concordantly exactly 1 time
    3492 (0.56%) aligned concordantly >1 times
    ----
    512199 pairs aligned concordantly 0 times; of these:
      9193 (1.79%) aligned discordantly 1 time
    ----
    503006 pairs aligned 0 times concordantly or discordantly; of these:
      1006012 mates make up the pairs; of these:
        960521 (95.48%) aligned 0 times
        44432 (4.42%) aligned exactly 1 time
        1059 (0.11%) aligned >1 times
23.51% overall alignment rate
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:11505:15256:10601 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:11505:15256:10601 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:11608:22658:11759 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:11608:22658:11759 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:23507:15456:13096 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:4:23507:15456:13096 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:12602:11592:3170 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:12602:11592:3170 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:13512:4691:2268 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:13512:4691:2268 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:21503:19544:7765 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:21503:19544:7765 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:21604:11417:5374 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:21604:11417:5374 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:22604:1100:10316 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:22604:1100:10316 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:23401:18460:19264 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:23401:18460:19264 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:23412:16764:4281 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:23412:16764:4281 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:23603:4254:5989 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:4:23603:4254:5989 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:11312:4255:5673 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:11312:4255:5673 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:12310:16273:12889 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:12310:16273:12889 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:22310:10003:6709 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:22310:10003:6709 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:23106:7878:13610 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:23106:7878:13610 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:23312:22972:12638 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:1:23312:22972:12638 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:12104:4895:14492 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:12104:4895:14492 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:21302:2617:14957 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:1:21302:2617:14957 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:21509:15589:13580 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:21509:15589:13580 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:22512:24683:11755 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:3:22512:24683:11755 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:3:12401:3772:5923 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:3:12401:3772:5923 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:3:13611:26296:8168 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:3:13611:26296:8168 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:3:23401:23386:9914 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:3:23401:23386:9914 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:3:23509:20430:1035 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:3:23509:20430:1035 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:13202:16732:4855 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:13202:16732:4855 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:23112:16411:7364 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7WFBGX7181018:HW7WFBGX7:2:23112:16411:7364 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:11310:8542:2569 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:11310:8542:2569 2:N:0:CTCTACTT' because it was < 2 characters long
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:13202:20214:17189 2:N:0:CTCTACTT' because length (1) <= # seed mismatches (0)
Warning: skipping mate #2 of read 'SL-NXC:HW7YKBGX7181017:HW7YKBGX7:2:13202:20214:17189 2:N:0:CTCTACTT' because it was < 2 characters long
4479417 reads; of these:
  4479417 (100.00%) were paired; of these:
    3465046 (77.35%) aligned concordantly 0 times
    983343 (21.95%) aligned concordantly exactly 1 time
    31028 (0.69%) aligned concordantly >1 times
    ----
    3465046 pairs aligned concordantly 0 times; of these:
      72807 (2.10%) aligned discordantly 1 time
    ----
    3392239 pairs aligned 0 times concordantly or discordantly; of these:
      6784478 mates make up the pairs; of these:
        6413875 (94.54%) aligned 0 times
        361310 (5.33%) aligned exactly 1 time
        9293 (0.14%) aligned >1 times
28.41% overall alignment rate
2240 GFF lines processed.
100000 SAM alignment record pairs processed.
200000 SAM alignment record pairs processed.
300000 SAM alignment record pairs processed.
400000 SAM alignment record pairs processed.
500000 SAM alignment record pairs processed.
600000 SAM alignment record pairs processed.
700000 SAM alignment record pairs processed.
800000 SAM alignment record pairs processed.
900000 SAM alignment record pairs processed.
1000000 SAM alignment record pairs processed.
1100000 SAM alignment record pairs processed.
1200000 SAM alignment record pairs processed.
1300000 SAM alignment record pairs processed.
1400000 SAM alignment record pairs processed.
1500000 SAM alignment record pairs processed.
1600000 SAM alignment record pairs processed.
1700000 SAM alignment record pairs processed.
1800000 SAM alignment record pairs processed.
1900000 SAM alignment record pairs processed.
2000000 SAM alignment record pairs processed.
2100000 SAM alignment record pairs processed.
2200000 SAM alignment record pairs processed.
2300000 SAM alignment record pairs processed.
2400000 SAM alignment record pairs processed.
2500000 SAM alignment record pairs processed.
2600000 SAM alignment record pairs processed.
2700000 SAM alignment record pairs processed.
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2900000 SAM alignment record pairs processed.
3000000 SAM alignment record pairs processed.
3100000 SAM alignment record pairs processed.
3200000 SAM alignment record pairs processed.
3300000 SAM alignment record pairs processed.
3400000 SAM alignment record pairs processed.
3500000 SAM alignment record pairs processed.
3600000 SAM alignment record pairs processed.
3700000 SAM alignment record pairs processed.
3800000 SAM alignment record pairs processed.
3900000 SAM alignment record pairs processed.
4000000 SAM alignment record pairs processed.
4100000 SAM alignment record pairs processed.
4200000 SAM alignment record pairs processed.
4300000 SAM alignment record pairs processed.
4400000 SAM alignment record pairs processed.
4500000 SAM alignment record pairs processed.
4600000 SAM alignment record pairs processed.
4700000 SAM alignment record pairs processed.
4800000 SAM alignment record pairs processed.
4900000 SAM alignment record pairs processed.
5000000 SAM alignment record pairs processed.
5100000 SAM alignment record pairs processed.
5200000 SAM alignment record pairs processed.
5300000 SAM alignment record pairs processed.
5400000 SAM alignment record pairs processed.
5500000 SAM alignment record pairs processed.
5600000 SAM alignment record pairs processed.
5700000 SAM alignment record pairs processed.
5800000 SAM alignment record pairs processed.
5900000 SAM alignment record pairs processed.
6000000 SAM alignment record pairs processed.
6100000 SAM alignment record pairs processed.
6166784 SAM alignment pairs processed.
2240 GFF lines processed.
100000 SAM alignment record pairs processed.
200000 SAM alignment record pairs processed.
300000 SAM alignment record pairs processed.
400000 SAM alignment record pairs processed.
500000 SAM alignment record pairs processed.
600000 SAM alignment record pairs processed.
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1000000 SAM alignment record pairs processed.
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1600000 SAM alignment record pairs processed.
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1800000 SAM alignment record pairs processed.
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2000000 SAM alignment record pairs processed.
2100000 SAM alignment record pairs processed.
2200000 SAM alignment record pairs processed.
2300000 SAM alignment record pairs processed.
2400000 SAM alignment record pairs processed.
2500000 SAM alignment record pairs processed.
2600000 SAM alignment record pairs processed.
2700000 SAM alignment record pairs processed.
2800000 SAM alignment record pairs processed.
2900000 SAM alignment record pairs processed.
3000000 SAM alignment record pairs processed.
3100000 SAM alignment record pairs processed.
3200000 SAM alignment record pairs processed.
3300000 SAM alignment record pairs processed.
3400000 SAM alignment record pairs processed.
3500000 SAM alignment record pairs processed.
3600000 SAM alignment record pairs processed.
3700000 SAM alignment record pairs processed.
3800000 SAM alignment record pairs processed.
3900000 SAM alignment record pairs processed.
4000000 SAM alignment record pairs processed.
4100000 SAM alignment record pairs processed.
4200000 SAM alignment record pairs processed.
4300000 SAM alignment record pairs processed.
4400000 SAM alignment record pairs processed.
4500000 SAM alignment record pairs processed.
4600000 SAM alignment record pairs processed.
4700000 SAM alignment record pairs processed.
4800000 SAM alignment record pairs processed.
4900000 SAM alignment record pairs processed.
4982146 SAM alignment pairs processed.
2240 GFF lines processed.
100000 SAM alignment record pairs processed.
200000 SAM alignment record pairs processed.
300000 SAM alignment record pairs processed.
400000 SAM alignment record pairs processed.
500000 SAM alignment record pairs processed.
600000 SAM alignment record pairs processed.
627905 SAM alignment pairs processed.
2240 GFF lines processed.
100000 SAM alignment record pairs processed.
200000 SAM alignment record pairs processed.
300000 SAM alignment record pairs processed.
400000 SAM alignment record pairs processed.
500000 SAM alignment record pairs processed.
600000 SAM alignment record pairs processed.
700000 SAM alignment record pairs processed.
800000 SAM alignment record pairs processed.
900000 SAM alignment record pairs processed.
1000000 SAM alignment record pairs processed.
1100000 SAM alignment record pairs processed.
1200000 SAM alignment record pairs processed.
1300000 SAM alignment record pairs processed.
1400000 SAM alignment record pairs processed.
1500000 SAM alignment record pairs processed.
1600000 SAM alignment record pairs processed.
1700000 SAM alignment record pairs processed.
1800000 SAM alignment record pairs processed.
1900000 SAM alignment record pairs processed.
2000000 SAM alignment record pairs processed.
2100000 SAM alignment record pairs processed.
2200000 SAM alignment record pairs processed.
2300000 SAM alignment record pairs processed.
2400000 SAM alignment record pairs processed.
2500000 SAM alignment record pairs processed.
2600000 SAM alignment record pairs processed.
2700000 SAM alignment record pairs processed.
2800000 SAM alignment record pairs processed.
2900000 SAM alignment record pairs processed.
3000000 SAM alignment record pairs processed.
3100000 SAM alignment record pairs processed.
3200000 SAM alignment record pairs processed.
3300000 SAM alignment record pairs processed.
3400000 SAM alignment record pairs processed.
3500000 SAM alignment record pairs processed.
3600000 SAM alignment record pairs processed.
3700000 SAM alignment record pairs processed.
3800000 SAM alignment record pairs processed.
3900000 SAM alignment record pairs processed.
4000000 SAM alignment record pairs processed.
4100000 SAM alignment record pairs processed.
4200000 SAM alignment record pairs processed.
4300000 SAM alignment record pairs processed.
4400000 SAM alignment record pairs processed.
4479417 SAM alignment pairs processed.
mkdir: cannot create directory ‘alignment’: File exists
mkdir: cannot create directory ‘figures’: File exists
mkdir: cannot create directory ‘kegg_analysis’: File exists
mkdir: cannot create directory ‘rnaseq_analysis’: File exists
Loading required package: S4Vectors
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

Attaching package: ‘BiocGenerics’

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    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
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    dirname, do.call, duplicated, eval, evalq, Filter, Find, get, grep,
    grepl, intersect, is.unsorted, lapply, Map, mapply, match, mget,
    order, paste, pmax, pmax.int, pmin, pmin.int, Position, rank,
    rbind, Reduce, rownames, sapply, setdiff, sort, table, tapply,
    union, unique, unsplit, which, which.max, which.min


Attaching package: ‘S4Vectors’

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    expand.grid

Loading required package: IRanges
Loading required package: GenomicRanges
Loading required package: GenomeInfoDb
Loading required package: SummarizedExperiment
Loading required package: Biobase
Welcome to Bioconductor

    Vignettes contain introductory material; view with
    'browseVignettes()'. To cite Bioconductor, see
    'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: DelayedArray
Loading required package: matrixStats

Attaching package: ‘matrixStats’

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Loading required package: BiocParallel

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    aperm, apply, rowsum

Error in DESeqDataSet(se, design = design, ignoreRank) : 
  all samples have 0 counts for all genes. check the counting script.
Calls: DESeqDataSetFromHTSeqCount -> DESeqDataSetFromMatrix -> DESeqDataSet
Execution halted
