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cluster detected 1 threads available to it
cluster reported completion
The following command failed with exit code 1
rm -rf /media/crlkims/Data_Vol_1/ROSE/Wghole_genome_sequencing_pneumoniae/RawDat…
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Hello, here is the output of the fimH_typing.txt in my analysis:
CR18000822 FimH type - E.coli
CR18000822b FimH type - E.coli
ATCC25922one FimH type: fimH30
ATCC25922nor FimH type: fimH30
And…
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Hi, I get the following error message when running PneumoCat with several samples:
```
Settings:
Output files: "out/SNP_based_serotyping/54_S8_L001_R1_001_tmp/reference.fasta.*.bt2"
Line rate:…
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Hi,
I've got several samples with a coverage > 90 % for a given Serotype, which are reported as "Failed", such as the following example:
```
…
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Great idea for a program, much more accessible than the alternatives for Ecoli serotyping.
I got the following using multi_serotyper.py
This happens when it gets about half way through my list of ge…
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I have got an isolate with top hit to M84642|6,7,14,[54]|C1 for wzx (97.904% pident; 100% coverage) and 17|gb|11|F for wzy (97.5% pident; 100% coverage). So it gives serogroup C1 for serogroup_predict…
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* this will let us compare (in a more general fashion, given differing cpu usage at the time) different modules, for example two serotyping modules
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Hi,
I just run a wgs-contig file with Sistr.
I am running the program with multiple _Salmonella_ wgs contig files. However, their species/variety names are unknown.
I run the following comman…
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I have converted the SerotypeFinder and EcOH (SRST2) databases for E. coli serotyping to Abricate format. Are you interested in such databases to be made generally available? I am happy to share.