Problem running chromosomer: error

Question

[biomagician]

Hi,

I am trying to use Chromosomer (https://github.com/gtamazian/chromosomer), in vain.

I have aligned my contigs to a reference and the result is in bristolSorted.bam. I then got the FASTA sequences out of the alignment so that 'chromosomer fastalength' can use it to calculate the sequence lengths. I then use the 'chromosomer fragmentmap' command and that's where it fails:

samtools fasta bristolSorted.bam > bristolSorted.fa

chromosomer fastalength bristolSorted.fa bristolSortedChromosomer.txt

chromosomer fragmentmap bristolSorted.bam 1000 bristolSortedChromosomer.txt map.txt
[M::bam2fq_mainloop] discarded 0 singletons
[M::bam2fq_mainloop] processed 128 reads
Traceback (most recent call last):
  File "/Users/cr517/anaconda/envs/python2env/bin/chromosomer", line 11, in <module>
    sys.exit(chromosomer())
  File "/Users/cr517/anaconda/envs/python2env/lib/python2.7/site-packages/chromosomer/cli.py", line 269, in chromosomer
    alignments, args.ratio_threshold)
  File "/Users/cr517/anaconda/envs/python2env/lib/python2.7/site-packages/chromosomer/fragment.py", line 349, in blast
    for alignment in blast_alignments.alignments():
  File "/Users/cr517/anaconda/envs/python2env/lib/python2.7/site-packages/bioformats/blast.py", line 48, in alignments
    for self.__line_parts in self.__reader:
_csv.Error: line contains NULL byte

Can anybody help, please?

Best, Thanks. C.

Answer 1

[biomagician]

OK, so it seems I was not using the right alignment format. I need a BLAST tabular format, as the creator explains here: https://github.com/gtamazian/chromosomer/issues/14