cctyper dies with missing files

[jnesme]

Hi Jakob,

I was running cctyper (fresh conda install) on a large fasta file (7.7GB) and it seems that it runs smoothly until minced step where it's trying to locate a missing file. Any idea on what might be the issue ?

Joseph.

cctyper -t 64 m64241e_210617_232502.hifi_reads.fasta cctyper.m64241e_210617_232502.hifi_reads.out
[2021-06-25 12:22:40] INFO: Running CRISPRCasTyper version 1.4.1
[2021-06-25 12:23:23] INFO: Predicting ORFs with prodigal
[2021-06-25 13:31:06] INFO: Running HMMER against Cas profiles
100%|█████████████████████████████████████████████████████████████████████████████████████████████████████████████████████| 693/693 [13:06:04<00:00, 68.06s/it]
[2021-06-26 07:21:47] INFO: Parsing HMMER output
[2021-06-26 07:21:48] INFO: Subtyping putative operons
[2021-06-26 07:28:48] INFO: Predicting CRISPR arrays with minced
Traceback (most recent call last):
  File "/projects/codon_0000/apps/miniconda3/envs/cctyper/bin/cctyper", line 86, in <module>
    crispr_obj.run_minced()
  File "/projects/codon_0000/apps/miniconda3/envs/cctyper/lib/python3.9/site-packages/cctyper/minced.py", line 79, in run_minced
    self.write_spacers()
  File "/projects/codon_0000/apps/miniconda3/envs/cctyper/lib/python3.9/site-packages/cctyper/minced.py", line 156, in write_spacers
    f = open(self.out+'spacers/{}.fa'.format(crisp.crispr), 'w')
FileNotFoundError: [Errno 2] No such file or directory: 'cctyper.m64241e_210617_232502.hifi_reads.out/spacers/m64241e_210617_232502/165939000/ccs_1.fa'

[Russel88]

Hi Joseph

That's odd. How does your fasta headers look like?

[jnesme]

They look like this, and that's probably these "/" that cause the issue, I'll try editing and run again :'(

>m64241e_210617_232502/20/ccs
>m64241e_210617_232502/6686011/ccs
>m64241e_210617_232502/14681679/ccs
>m64241e_210617_232502/22611689/ccs
>m64241e_210617_232502/30213142/ccs
>m64241e_210617_232502/37619981/ccs
>m64241e_210617_232502/45156585/ccs
>m64241e_210617_232502/52627283/ccs
>m64241e_210617_232502/60162622/ccs
>m64241e_210617_232502/67700160/ccs

[Russel88]

Yeah, definitely the '/' that are messing things up.

[zh8008]

I'm glad you like the tool! But I had some issues about minced. Traceback (most recent call last): File "/project/hz/.conda/envs/AcaFinder/bin/cctyper", line 91, in crispr_obj.run_minced() File "/project/hz/.conda/envs/AcaFinder/lib/python3.8/site-packages/cctyper/minced.py", line 75, in run_minced subprocess.run(['minced', File "/project/hz/.conda/envs/AcaFinder/lib/python3.8/subprocess.py", line 493, in run with Popen(*popenargs, **kwargs) as process: File "/project/hz/.conda/envs/AcaFinder/lib/python3.8/subprocess.py", line 858, in init self._execute_child(args, executable, preexec_fn, close_fds, File "/project/hz/.conda/envs/AcaFinder/lib/python3.8/subprocess.py", line 1720, in _execute_child raise child_exception_type(errno_num, err_msg, err_filename) FileNotFoundError: [Errno 2] No such file or directory: 'minced'