File not found when running `tb-profiler update_tbdb --match_ref`

[aofarrel]

Version: staphb/tbprofiler:4.4.2 docker image

I'm hoping to run tb_profiler on some bams, but ran into an error similar to this one. My fasta file starts with >NC_000962.3 so I figured I need to run tb-profiler update_tbdb --match_ref, but I can't seem to get that working. Seems like it cannot find the fasta file I'm passing into it?

> ls -lha
drwxr-xr-x  1 root root 4.0K Mar 28 22:03 ..
drwxr-xr-x 14 root root  448 Mar 28 02:24 .git
-rw-r--r--  1 root root   66 Mar 24 01:07 .gitattributes
-rw-r--r--  1 root root  332 Mar 28 21:56 Dockerfile
-rw-r--r--  1 root root  451 Mar 26 20:14 tb_profiler.wdl
-rw-r--r--  1 root root 4.3M Mar 28 22:04 tb_seq.fasta
-rw-r--r--  1 root root   12 Mar 28 22:11 tb_seq.fasta.amb
-rw-r--r--  1 root root   46 Mar 28 22:11 tb_seq.fasta.ann
-rw-r--r--  1 root root 4.3M Mar 28 22:11 tb_seq.fasta.bwt
-rw-r--r--  1 root root   29 Mar 28 22:11 tb_seq.fasta.fai
-rw-r--r--  1 root root 1.1M Mar 28 22:11 tb_seq.fasta.pac
-rw-r--r--  1 root root 2.2M Mar 28 22:11 tb_seq.fasta.sa

.git, .gitattributes, Dockerfile, and tb_profiler.wdl are my own files from my own repo.

> tb-profiler update_tbdb --match_ref tb_seq.fasta
Running command:
set -u pipefail; git clone https://github.com/jodyphelan/tbdb.git

Running command:
set -u pipefail; git checkout master

Running command:
set -u pipefail; git pull

Running command:
set -u pipefail; tb-profiler create_db --prefix tbdb --match_ref tb_seq.fasta --load
Traceback (most recent call last):
  File "/opt/conda/bin/tb-profiler", line 693, in <module>
    args.func(args)
  File "/opt/conda/bin/tb-profiler", line 212, in main_update_tbdb
    pp.run_cmd(f"tb-profiler create_db --prefix {args.prefix} {tmp} --load")
  File "/opt/conda/lib/python3.9/site-packages/pathogenprofiler/utils.py", line 404, in run_cmd
    raise ValueError("Command Failed:\n%s\nstderr:\n%s" % (cmd,stderr.decode()))
ValueError: Command Failed:
set -u pipefail; tb-profiler create_db --prefix tbdb --match_ref tb_seq.fasta --load
stderr:
Traceback (most recent call last):
  File "/opt/conda/bin/tb-profiler", line 693, in <module>
    args.func(args)
  File "/opt/conda/bin/tb-profiler", line 232, in main_create_db
    pp.create_db(args,extra_files=extra_files)
  File "/opt/conda/lib/python3.9/site-packages/pathogenprofiler/db.py", line 584, in create_db
    chrom_conversion = match_ref_chrom_names(args.match_ref,"genome.fasta")
  File "/opt/conda/lib/python3.9/site-packages/pathogenprofiler/db.py", line 549, in match_ref_chrom_names
    source_fa = fa2dict(source)
  File "/opt/conda/lib/python3.9/site-packages/pathogenprofiler/db.py", line 63, in fa2dict
    for l in open(filename):
FileNotFoundError: [Errno 2] No such file or directory: 'tb_seq.fasta'
Cleaning up after failed run
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
  File "/opt/conda/bin/tb-profiler", line 33, in cleanup
    del args.conf['json_db']
AttributeError: 'Namespace' object has no attribute 'conf'

Cleaning up after failed run
Error in atexit._run_exitfuncs:
Traceback (most recent call last):
  File "/opt/conda/bin/tb-profiler", line 33, in cleanup
    del args.conf['json_db']
AttributeError: 'Namespace' object has no attribute 'conf'

The samtools and bwa commands mentioned here work, so this isn't a matter of the file not being mounted into the Docker image, but tb-profiler update_tbdb --match_ref is still not working. Different iterations like ./tb_seq.fasta or $(pwd)/tb_seq.fasta don't seem to be working. Am I missing a step? Does my fasta need to go somewhere specific?

[jodyphelan]

Hi Ash,

This is a bug in that version. It is fixed in the master branch, I just need to make a conda release. After running the command and seeing the error, it should have clones a git repo called tbdb. What you should do is to go into that directory and manually run the create_db step:

cd tbdb
tb-profiler create_db --prefix tbdb --match_ref tb_seq.fasta --load

Let me know if that works for you.

[aofarrel]

It seems to be working now! Thank you so much!

(If you got a notification earlier with an error message in samtools index, that was an issue on my part, sorry!)

[jodyphelan]

Great to hear it is working now!