Generating checksum for /gscratch/srlab/sam/data/metagenomics/P_generosa/assemblies/20190103-mgm-nucleotides.fa
Finished generating checksum for /gscratch/srlab/sam/data/metagenomics/P_generosa/assemblies/20190103-mgm-nucleotides.fa

83562471 reads; of these:
  83562471 (100.00%) were paired; of these:
    59860834 (71.64%) aligned concordantly 0 times
    23681668 (28.34%) aligned concordantly exactly 1 time
    19969 (0.02%) aligned concordantly >1 times
    ----
    59860834 pairs aligned concordantly 0 times; of these:
      2461673 (4.11%) aligned discordantly 1 time
    ----
    57399161 pairs aligned 0 times concordantly or discordantly; of these:
      114798322 mates make up the pairs; of these:
        96107615 (83.72%) aligned 0 times
        18470469 (16.09%) aligned exactly 1 time
        220238 (0.19%) aligned >1 times
42.49% overall alignment rate
[bam_sort_core] merging from 56 files and 28 in-memory blocks...
82486730 reads; of these:
  82486730 (100.00%) were paired; of these:
    59313713 (71.91%) aligned concordantly 0 times
    23147103 (28.06%) aligned concordantly exactly 1 time
    25914 (0.03%) aligned concordantly >1 times
    ----
    59313713 pairs aligned concordantly 0 times; of these:
      2489002 (4.20%) aligned discordantly 1 time
    ----
    56824711 pairs aligned 0 times concordantly or discordantly; of these:
      113649422 mates make up the pairs; of these:
        95401139 (83.94%) aligned 0 times
        18012903 (15.85%) aligned exactly 1 time
        235380 (0.21%) aligned >1 times
42.17% overall alignment rate
[bam_sort_core] merging from 56 files and 28 in-memory blocks...
88941440 reads; of these:
  88941440 (100.00%) were paired; of these:
    77155153 (86.75%) aligned concordantly 0 times
    11779619 (13.24%) aligned concordantly exactly 1 time
    6668 (0.01%) aligned concordantly >1 times
    ----
    77155153 pairs aligned concordantly 0 times; of these:
      1220728 (1.58%) aligned discordantly 1 time
    ----
    75934425 pairs aligned 0 times concordantly or discordantly; of these:
      151868850 mates make up the pairs; of these:
        142400546 (93.77%) aligned 0 times
        9399906 (6.19%) aligned exactly 1 time
        68398 (0.05%) aligned >1 times
19.95% overall alignment rate
[bam_sort_core] merging from 56 files and 28 in-memory blocks...
72142506 reads; of these:
  72142506 (100.00%) were paired; of these:
    47853133 (66.33%) aligned concordantly 0 times
    24269120 (33.64%) aligned concordantly exactly 1 time
    20253 (0.03%) aligned concordantly >1 times
    ----
    47853133 pairs aligned concordantly 0 times; of these:
      2506119 (5.24%) aligned discordantly 1 time
    ----
    45347014 pairs aligned 0 times concordantly or discordantly; of these:
      90694028 mates make up the pairs; of these:
        73156096 (80.66%) aligned 0 times
        17332802 (19.11%) aligned exactly 1 time
        205130 (0.23%) aligned >1 times
49.30% overall alignment rate
[bam_sort_core] merging from 56 files and 28 in-memory blocks...
73610508 reads; of these:
  73610508 (100.00%) were paired; of these:
    50339250 (68.39%) aligned concordantly 0 times
    23249420 (31.58%) aligned concordantly exactly 1 time
    21838 (0.03%) aligned concordantly >1 times
    ----
    50339250 pairs aligned concordantly 0 times; of these:
      2592614 (5.15%) aligned discordantly 1 time
    ----
    47746636 pairs aligned 0 times concordantly or discordantly; of these:
      95493272 mates make up the pairs; of these:
        77320029 (80.97%) aligned 0 times
        17931931 (18.78%) aligned exactly 1 time
        241312 (0.25%) aligned >1 times
47.48% overall alignment rate
[bam_sort_core] merging from 56 files and 28 in-memory blocks...
88314076 reads; of these:
  88314076 (100.00%) were paired; of these:
    60950288 (69.02%) aligned concordantly 0 times
    27338793 (30.96%) aligned concordantly exactly 1 time
    24995 (0.03%) aligned concordantly >1 times
    ----
    60950288 pairs aligned concordantly 0 times; of these:
      2829776 (4.64%) aligned discordantly 1 time
    ----
    58120512 pairs aligned 0 times concordantly or discordantly; of these:
      116241024 mates make up the pairs; of these:
        96024383 (82.61%) aligned 0 times
        19970563 (17.18%) aligned exactly 1 time
        246078 (0.21%) aligned >1 times
45.63% overall alignment rate
[bam_sort_core] merging from 56 files and 28 in-memory blocks...