IndexError: list index out of range

[jamesPet]

Running into an index out of range issue

$ maast end_to_end --min-prev 0.9 --out-dir test_out --in-dir a_few_asms/
[Warning] Total number of genomes (9) < min. number of genomes required for effective SNP calling with MAF 0.01 (100)
[Warning] Skip tag genome selection, all genomes will be used
reference genome path: a_few_asms/DRR090820_contigs_skesa.fasta
[building mash sketch]: start
[calculating mash distance]: start
[clustering] start
[clustering] done
a_few_asms/DRR090793_contigs_skesa.fasta
Running mummer4; start
reference genome path: a_few_asms/DRR090793_contigs_skesa.fasta
[paired alignment]: start
[paired alignment]: done
        DRR090793_contigs_skesa.fasta - DRR090809_contigs_skesa.fasta
        DRR090793_contigs_skesa.fasta - DRR090807_contigs_skesa.fasta
        DRR090793_contigs_skesa.fasta - DRR090793_contigs_skesa.fasta
        DRR090793_contigs_skesa.fasta - DRR090820_contigs_skesa.fasta
        DRR090793_contigs_skesa.fasta - DRR090805_contigs_skesa.fasta
        DRR090793_contigs_skesa.fasta - DRR090795_contigs_skesa.fasta
        DRR090793_contigs_skesa.fasta - DRR090797_contigs_skesa.fasta
        DRR090793_contigs_skesa.fasta - DRR090801_contigs_skesa.fasta
        DRR090793_contigs_skesa.fasta - DRR090810_contigs_skesa.fasta
Reading reference genome
   count contigs: 43
   count sites: 4529549
Initializing alignments
   count genomes: 0
Reading alignment blocks
Reading SNPs
Writing fasta
   path: test_out/temp/mummer4/a_few_asms/msa.fa

Done!
Time (s): 1.15
Running mummer4; done!
Elapsed time: 12.280270099639893
Fetching file-type-specific parser; start
Traceback (most recent call last):
  File "/home/pj/.conda/envs/maast/bin/bin/maast.py", line 1371, in <module>
    main()
  File "/home/pj/.conda/envs/maast/bin/bin/maast.py", line 1366, in main
    end2end_main(args)
  File "/home/pj/.conda/envs/maast/bin/bin/maast.py", line 1310, in end2end_main
    call_snps_main(args)
  File "/home/pj/.conda/envs/maast/bin/bin/maast.py", line 1186, in call_snps_main
    site_assembly = msa.monolithic_parse(args['msa_path'], args['msa_type'], args['max_samples'])
  File "/home/pj/.conda/envs/maast/bin/align_io/msa.py", line 17, in monolithic_parse
    return parse_control(msa_path, msa_type, max_sample)
  File "/home/pj/.conda/envs/maast/bin/align_io/msa.py", line 14, in parse_control
    return parse(msa_path, max_sample)
  File "/home/pj/.conda/envs/maast/bin/align_io/xmfa_mummer4_io.py", line 30, in parse
    cur_aln.ncols = len(cur_aln.seqs[0].seq)
IndexError: list index out of range

[zjshi]

Hi James, thanks for reporting the issue. The cause could be failure or unexpected outcome stemmed from individual alignment. Is there way that you could share these input sequences? I would like to start with reproducing the issue on my end.

[jamesPet]

You bet. See attached for the assemblies and thanks for taking a look at the issue. a_few_asms.zip

[zjshi]

Thanks for providing the sample assemblies. With those files, I have identified and fixed a bug causing this issues. It turns out to be a couple of places in the scripts did not handle assembly files with a ".fasta" suffix in the way they should have. I've pushed a patch to this repository as well as uploaded a new conda release. I will tentatively close this issue for now. Please feel free to reopen it if you still experience the similar problem.