bug in pointfinder/phenotype2genotype

[Daniel Mende]

Dear ResFinder DevTeam,

First of all: Thank you for developing ResFinder and PointFinder.

I have used them to annotate some metagenomes dominated by specific species. The ResFinder runs ran perfectly but for a few of the PointFinder runs I ran into a couple of errors. I also ran the analysis for 2 samples on the webserver where they completed giving some warning, I copied the jobids below.

I also attempted to attach the fastq file to this issue but the files were too large.

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jobid = 5FC0E0480000356D76206AA3

python3 /home/dmende/bin/resfinder/resfinder/run_resfinder.py -o /project/mendecol/MUS/results_resfinder_test/MS_1756 -s "Escherichia coli" -l 0.6 -t 0.8 --point -ifq /home/dmende/data/MUS/all_split/MS_1756_*_*.fq.gz
Traceback (most recent call last):
  File "/home/dmende/bin/resfinder/resfinder/run_resfinder.py", line 554, in <module>
    type="seq_variations")
  File "/home/dmende/bin/resfinder/resfinder/cge/phenotype2genotype/isolate.py", line 134, in load_finder_results
    res_feature = self.new_res_mut(feat_info, unique_id, ab_class)
  File "/home/dmende/bin/resfinder/resfinder/cge/phenotype2genotype/isolate.py", line 162, in new_res_mut
    ab_class=ab_class)
  File "/home/dmende/bin/resfinder/resfinder/cge/phenotype2genotype/feature.py", line 205, in __init__
    premature_stop=premature_stop, frameshift=frameshift)
  File "/home/dmende/bin/resfinder/resfinder/cge/phenotype2genotype/feature.py", line 95, in __init__
    self.set_mut_str_del()
  File "/home/dmende/bin/resfinder/resfinder/cge/phenotype2genotype/feature.py", line 169, in set_mut_str_del
    ref_right=self.ref_aa_right.upper()))
AttributeError: 'NoneType' object has no attribute 'upper'

‌

The following second error has been reported previously but I wanted to repost it in case it couldn’t be reproduced yet.

jobid = 5FC0E55B0000499D62BB9DA5

python3 /home/dmende/bin/resfinder/resfinder/run_resfinder.py -o /project/mendecol/MUS/results_resfinder_test/MS_1039 -s "Enterococcus faecalis" -l 0.6 -t 0.8 --point -ifq /home/dmende/data/MUS/all_split/MS_1039_*_*.fq.gz
Traceback (most recent call last):
  File "/home/dmende/bin/resfinder/resfinder/run_resfinder.py", line 521, in <module>
    "PointFinder")
  File "/home/dmende/bin/resfinder/resfinder/cge/standardize_results.py", line 346, in standardize_results
    res_collection, mismatch, gene_results, ref_db_name)
  File "/home/dmende/bin/resfinder/resfinder/cge/standardize_results.py", line 27, in __init__
    region_name = region_results[0]["ref_id"]
IndexError: list index out of range

Thank you for looking into this.

[CGE Helpdesk]

Dear Daniel,

Thank you very much for the interest in ResFinder.

Which version of ResFinder did you use? The Readme instructions for installing ResFinder has just been updated recently (a couple of hours ago). Before, the ResFinder 4.0 was installed if the instructions were followed, but the command has been updated, meaning that the newest version will be cloned instead. The new version should be equivalent to the one on the webpage.

Please let me know, if this does not solve your issue.

Kind regards,

Malene, CGE helpdesk.

[Daniel Mende]

Thank you! With the latest update, those problems disappear.

Best wishes!

[CGE Helpdesk]

I am glad to hear that. Please let us know if any problems or questions arise.

Best,

Malene, CGE helpdesk

[Daniel Mende]

Hi Malene,

I think this issue can be closed.

I have one more question though: Even though Klebsiella seems to be part of the pointfinder database I get the following message:

Warning: No panel was detected for the species: klebsiella pneumoniae

Am I doing something wrong? I tried to update the db_pointfinder but it was already up to date.

Thank you and best wishes!

[Alfred Ferrer Florensa]

Hello Daniel,

‌

I believe you are using ”Klebsiella pneumoniae”, but you should use “klebsiella” only.

‌

Alfred