nohup: ignoring input
46132185 reads; of these:
  46132185 (100.00%) were paired; of these:
    28729411 (62.28%) aligned concordantly 0 times
    16861619 (36.55%) aligned concordantly exactly 1 time
    541155 (1.17%) aligned concordantly >1 times
    ----
    28729411 pairs aligned concordantly 0 times; of these:
      10416132 (36.26%) aligned discordantly 1 time
    ----
    18313279 pairs aligned 0 times concordantly or discordantly; of these:
      36626558 mates make up the pairs; of these:
        32900237 (89.83%) aligned 0 times
        1289581 (3.52%) aligned exactly 1 time
        2436740 (6.65%) aligned >1 times
64.34% overall alignment rate
./MR_rnaseq_v4_local_servre.sh: line 73: htseq-count: command not found
51054965 reads; of these:
  51054965 (100.00%) were paired; of these:
    35193826 (68.93%) aligned concordantly 0 times
    15177513 (29.73%) aligned concordantly exactly 1 time
    683626 (1.34%) aligned concordantly >1 times
    ----
    35193826 pairs aligned concordantly 0 times; of these:
      12596050 (35.79%) aligned discordantly 1 time
    ----
    22597776 pairs aligned 0 times concordantly or discordantly; of these:
      45195552 mates make up the pairs; of these:
        41030498 (90.78%) aligned 0 times
        978162 (2.16%) aligned exactly 1 time
        3186892 (7.05%) aligned >1 times
59.82% overall alignment rate
./MR_rnaseq_v4_local_servre.sh: line 73: htseq-count: command not found
36376165 reads; of these:
  36376165 (100.00%) were paired; of these:
    24221141 (66.59%) aligned concordantly 0 times
    11683525 (32.12%) aligned concordantly exactly 1 time
    471499 (1.30%) aligned concordantly >1 times
    ----
    24221141 pairs aligned concordantly 0 times; of these:
      9598677 (39.63%) aligned discordantly 1 time
    ----
    14622464 pairs aligned 0 times concordantly or discordantly; of these:
      29244928 mates make up the pairs; of these:
        26164350 (89.47%) aligned 0 times
        627847 (2.15%) aligned exactly 1 time
        2452731 (8.39%) aligned >1 times
64.04% overall alignment rate
./MR_rnaseq_v4_local_servre.sh: line 73: htseq-count: command not found
49447362 reads; of these:
  49447362 (100.00%) were paired; of these:
    27540031 (55.70%) aligned concordantly 0 times
    20539147 (41.54%) aligned concordantly exactly 1 time
    1368184 (2.77%) aligned concordantly >1 times
    ----
    27540031 pairs aligned concordantly 0 times; of these:
      20392873 (74.05%) aligned discordantly 1 time
    ----
    7147158 pairs aligned 0 times concordantly or discordantly; of these:
      14294316 mates make up the pairs; of these:
        6093020 (42.63%) aligned 0 times
        1299494 (9.09%) aligned exactly 1 time
        6901802 (48.28%) aligned >1 times
93.84% overall alignment rate
./MR_rnaseq_v4_local_servre.sh: line 73: htseq-count: command not found
45321422 reads; of these:
  45321422 (100.00%) were paired; of these:
    24936488 (55.02%) aligned concordantly 0 times
    19087004 (42.11%) aligned concordantly exactly 1 time
    1297930 (2.86%) aligned concordantly >1 times
    ----
    24936488 pairs aligned concordantly 0 times; of these:
      18580138 (74.51%) aligned discordantly 1 time
    ----
    6356350 pairs aligned 0 times concordantly or discordantly; of these:
      12712700 mates make up the pairs; of these:
        5541513 (43.59%) aligned 0 times
        1057896 (8.32%) aligned exactly 1 time
        6113291 (48.09%) aligned >1 times
93.89% overall alignment rate
./MR_rnaseq_v4_local_servre.sh: line 73: htseq-count: command not found
47461364 reads; of these:
  47461364 (100.00%) were paired; of these:
    23087684 (48.65%) aligned concordantly 0 times
    23075909 (48.62%) aligned concordantly exactly 1 time
    1297771 (2.73%) aligned concordantly >1 times
    ----
    23087684 pairs aligned concordantly 0 times; of these:
      16929321 (73.33%) aligned discordantly 1 time
    ----
    6158363 pairs aligned 0 times concordantly or discordantly; of these:
      12316726 mates make up the pairs; of these:
        5699542 (46.27%) aligned 0 times
        1085286 (8.81%) aligned exactly 1 time
        5531898 (44.91%) aligned >1 times
94.00% overall alignment rate
./MR_rnaseq_v4_local_servre.sh: line 73: htseq-count: command not found
mv: target './alignment': Not a directory