fasta2homozygous fails for --identity 0.33 --overlap 0.51

[lpryszcz]

~/src/redundans/fasta2homozygous.py -i redundans/MAGSPI*/contigs.fa --identity 0.33 --overlap 0.33

Homozygous assembly/ies will be written with input name + '.homozygous.fa.gz'

file name genome size contigs heterozygous size [%] heterozygous contigs [%] identity [%] possible joins homozygous size [%] homozygous contigs [%]

[ERROR] seq21018_len7789_cov189 (('seq1_len104_cov121', 104, 0, 70, 'seq9735_len101_cov148', 101, 31, 101, '+', 0.8285714285714286, 0.693069306930693, 46)) not in contigs!
[ERROR] seq26477_len7324_cov148 (('seq1_len104_cov121', 104, 0, 81, 'seq9735_len101_cov148', 101, 20, 101, '+', 0.7777777777777778, 0.801980198019802, 45)) not in contigs!
[ERROR] seq20577_len9015_cov141 (('seq3_len238_cov168', 238, 0, 238, 'seq10_len238_cov189', 238, 0, 238, '+', 0.9831932773109243, 1.0, 230)) not in contigs!
[ERROR] seq19649_len8979_cov175 (('seq3_len238_cov168', 238, 0, 84, 'seq16825_len172_cov141', 172, 88, 172, '+', 1.0, 0.4883720930232558, 84)) not in contigs!
[ERROR] seq20482_len6873_cov155 (('seq8_len6349_cov128', 6349, 588, 743, 'seq27924_len149_cov114', 149, 0, 149, '+', 0.8456375838926175, 1.0, 103)) not in contigs!
[ERROR] seq20999_len4731_cov189 (('seq8_len6349_cov128', 6349, 5653, 5935, 'seq5386_len269_cov141', 269, 0, 269, '+', 0.6505576208178439, 1.0, 81)) not in contigs!
[ERROR] seq24053_len5120_cov168 (('seq8_len6349_cov128', 6349, 4540, 4646, 'seq27404_len104_cov189', 104, 0, 104, '+', 0.8653846153846154, 1.0, 77)) not in contigs!
[ERROR] seq24131_len10134_cov155 (('seq8_len6349_cov128', 6349, 6249, 6349, 'seq7853_len154_cov296', 154, 0, 100, '+', 0.84, 0.6493506493506493, 68)) not in contigs!
[ERROR] seq25312_len13069_cov148 (('seq8_len6349_cov128', 6349, 419, 679, 'seq5386_len269_cov141', 269, 0, 269, '+', 0.620817843866171, 1.0, 65)) not in contigs!
[ERROR] seq18534_len7476_cov148 (('seq8_len6349_cov128', 6349, 5849, 5999, 'seq27924_len149_cov114', 149, 0, 149, '+', 0.6912751677852349, 1.0, 57)) not in contigs!
[ERROR] seq24935_len5793_cov162 (('seq8_len6349_cov128', 6349, 493, 613, 'seq14809_len119_cov94', 119, 0, 119, '+', 0.6890756302521008, 1.0, 45)) not in contigs!
Traceback (most recent call last):
File "/home/lpryszcz/src/redundans/fasta2homozygous.py", line 234, in
main()
File "/home/lpryszcz/src/redundans/fasta2homozygous.py", line 228, in main
libraries, limit, o.threads, o.joinOverlap, o.endTrimming, o.verbose)
File "/home/lpryszcz/src/redundans/fasta2homozygous.py", line 122, in fasta2homozygous
contig2skip, identity = hits2skip(hits, faidx, verbose)
File "/home/lpryszcz/src/redundans/fasta2homozygous.py", line 74, in hits2skip
if contig2skip[q]:
KeyError: 'seq18807_len4442_cov148'

[lpryszcz]

This is most likely due to corrupted .fai file, try rerunning after: rm redundans/MAGSPI*/contigs.fa.*

[lpryszcz]

FastaIndex.py now should recognise and repair corrupted .fai.