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
Error occured when processing GFF file (line 1 of file hp_index.gff):
  [Errno 2] No such file or directory: 'hp_index.gff'
  [Exception type: FileNotFoundError, raised in __init__.py:47]
Error occured when processing GFF file (line 1 of file hp_index.gff):
  [Errno 2] No such file or directory: 'hp_index.gff'
  [Exception type: FileNotFoundError, raised in __init__.py:47]
Error occured when processing GFF file (line 1 of file hp_index.gff):
  [Errno 2] No such file or directory: 'hp_index.gff'
  [Exception type: FileNotFoundError, raised in __init__.py:47]
Error occured when processing GFF file (line 1 of file hp_index.gff):
  [Errno 2] No such file or directory: 'hp_index.gff'
  [Exception type: FileNotFoundError, raised in __init__.py:47]
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’

The following objects are masked from ‘package:parallel’:

    clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
    clusterExport, clusterMap, parApply, parCapply, parLapply,
    parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

    IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

    anyDuplicated, append, as.data.frame, basename, cbind, colnames,
    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’

The following object is masked from ‘package:base’:

    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’

The following objects are masked from ‘package:Biobase’:

    anyMissing, rowMedians

Loading required package: BiocParallel

Attaching package: ‘DelayedArray’

The following objects are masked from ‘package:matrixStats’:

    colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges

The following objects are masked from ‘package:base’:

    aperm, apply, rowsum

Error in read.table(file.path(directory, fn), fill = TRUE) : 
  no lines available in input
Calls: DESeqDataSetFromHTSeqCount -> lapply -> lapply -> FUN -> read.table
Execution halted
