Ariba fails when using virulencefinder db

[Camilsek]

Thanks for a nice programme.
We have used Ariba With both Card and Resfinder database and it Works well.
Today I have also tested the virulencefinder db and get the following error Message (see below).
I've also run With resfinder today as well and it Works fine.
Do you have any idea what's going wrong? And if there is there anything you could do to help I would be very Grateful.
Best regards, Camilla

[E::hts_idx_push] Unsorted positions on sequence #1: 16 followed by 2
Traceback (most recent call last):
File "/work/projects/nn9305k/src/anaconda3/bin/ariba", line 298, in
args.func(args)
File "/work/projects/nn9305k/src/anaconda3/lib/python3.6/site-packages/ariba/tasks/run.py", line 65, in run
c.run()
File "/work/projects/nn9305k/src/anaconda3/lib/python3.6/site-packages/ariba/clusters.py", line 602, in run
self._run()
File "/work/projects/nn9305k/src/anaconda3/lib/python3.6/site-packages/ariba/clusters.py", line 627, in _run
self._init_and_run_clusters()
File "/work/projects/nn9305k/src/anaconda3/lib/python3.6/site-packages/ariba/clusters.py", line 424, in _init_and_run_clusters
reference_names=self.cluster_ids[cluster_name],
KeyError: ''

[Asutu]

I'm getting (almost) exactly the same error with virulencefinder database. This doesn't seem to happen to all data, as for some isolates (read pairs) I was able to finish Ariba on virulencefinder and obtain results. The other databases seem to be working OK.

Any idea what the problem is and/or how to solve it?

  [E::hts_idx_push] Unsorted positions on sequence #1: 1009 followed by 101
  Traceback (most recent call last):
    File "/scratch/scratch/ucjucoe/Software/bacterialGenomics/ariba/bin/ariba", line 298, in <module>
      args.func(args)
    File "/scratch/scratch/ucjucoe/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/ariba/tasks/run.py", line 65, in run
      c.run()
    File "/scratch/scratch/ucjucoe/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/ariba/clusters.py", line 602, in run
      self._run()
    File "/scratch/scratch/ucjucoe/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/ariba/clusters.py", line 613, in _run
      self._map_and_cluster_reads()
    File "/scratch/scratch/ucjucoe/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/ariba/clusters.py", line 276, in _map_and_cluster_reads
      log_fh=filehandle
    File "/scratch/scratch/ucjucoe/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/ariba/read_store.py", line 19, in __init__
      self._compress_and_index_file(self.outprefix, log_fh)
    File "/scratch/scratch/ucjucoe/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/ariba/read_store.py", line 35, in _compress_and_index_file
      pysam.tabix_index(infile + '.gz', seq_col=0, start_col=1, end_col=1)
    File "pysam/libctabix.pyx", line 1025, in pysam.libctabix.tabix_index
  OSError: building of index for virulencefinder/read_store.gz failed

Cheers,
Pedro

[martinghunt]

Thanks for reporting this @Csekse and @Asutu.

After a little digging I found a badly formatted FASTA file in the virulencefinder download. ariba will fix it when running getref, so you'll need to rerun getref and prepareref. The fix is in the new release 2.11.2. Could you please try it? I am hoping that it will stop the crashes that you found on your data.

[Asutu]

Thanks for trying to sort things out. Unfortunately, I'm still getting the same error message as above with Ariba 2.11.2.

[E::hts_idx_push] Unsorted positions on sequence #1: 1009 followed by 101
 Traceback (most recent call last):
   File "/scratch/scratch/ucjucoe/Software/bacterialGenomics/ariba/bin/ariba", line 298, in <module>
     args.func(args)
   File "/scratch/scratch/ucjucoe/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/ariba/tasks/run.py", line 65, in run
     c.run()
   File "/scratch/scratch/ucjucoe/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/ariba/clusters.py", line 602, in run
     self._run()
   File "/scratch/scratch/ucjucoe/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/ariba/clusters.py", line 613, in _run
     self._map_and_cluster_reads()
   File "/scratch/scratch/ucjucoe/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/ariba/clusters.py", line 276, in _map_and_cluster_reads
     log_fh=filehandle
   File "/scratch/scratch/ucjucoe/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/ariba/read_store.py", line 19, in __init__
     self._compress_and_index_file(self.outprefix, log_fh)
   File "/scratch/scratch/ucjucoe/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/ariba/read_store.py", line 35, in _compress_and_index_file
     pysam.tabix_index(infile + '.gz', seq_col=0, start_col=1, end_col=1)
   File "pysam/libctabix.pyx", line 1025, in pysam.libctabix.tabix_index
 OSError: building of index for virulencefinder/read_store.gz failed

Here's the output of running ariba version:

ARIBA version: 2.11.2

External dependencies:
bowtie2	2.3.2	/home/pmca/Software/ngs/bowtie2/2.3.2-legacy/bowtie2
cdhit	4.7	/home/pmca/Software/bio-misc/cd-hit/4.6.8/cd-hit-est
nucmer	3.1	/home/pmca/Software/alignments/mummer/3.23-64bits/nucmer
spades	3.11.1	/home/pmca/Software/assemblers/SPAdes/SPAdes-3.11.1-Linux/bin/spades.py

External dependencies OK: True

Python version:
3.6.3 (default, Oct 10 2017, 15:11:55) 
[GCC 4.9.2]

Python packages:
ariba	2.11.2	/home/pmca/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/ariba/__init__.py
bs4	4.6.0	/home/pmca/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/bs4/__init__.py
dendropy	4.3.0	/home/pmca/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/dendropy/__init__.py
pyfastaq	3.17.0	home/pmca/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/pyfastaq/__init__.py
pymummer	0.10.3	/home/pmca/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/pymummer/__init__.py
pysam	0.14.1	/home/pmca/Software/bacterialGenomics/ariba/lib/python3.6/site-packages/pysam/__init__.py

Python packages OK: True

Everything looks OK: True

[martinghunt]

@Asutu could you try the latest release 2.12.0?

[ys4]

@martinghunt It appears that the getref command in 2.12.0 release

ariba getref virulencefinder out.virulencefinder

points to the plasmidfinder data instead.

[martinghunt]

@ys4 thank you for reporting! It's fixed in the new release 2.12.1.