This is nullarbor-report.pl 2.0.20191013/ Making folder --> no report

Lneffe commented 4 years ago

Hi! After running the nullarbor pipeline no report is generated and the report folder is empty:

[13:05:32] This is nullarbor-report.pl 2.0.20191013 [13:05:32] Send complaints to Torsten Seemann [13:05:32] Making folder --outdir /vol/projects/..... But nothing happens?!

How can I proceed?

Many thanks in advance!

tseemann commented 4 years ago

Please attach the nullarbor.log file.

Lneffe commented 4 years ago

Please find the log file attached.

Thanks, Lisa

Von: Torsten Seemann notifications@github.com Gesendet: Samstag, 16. November 2019 05:05 An: tseemann/nullarbor nullarbor@noreply.github.com Cc: Neffe, Lisa Lisa.Neffe@helmholtz-hzi.de; Author author@noreply.github.com Betreff: Re: [tseemann/nullarbor] This is nullarbor-report.pl 2.0.20191013/ Making folder --> no report (#247)

Please attach the nullarbor.log file.

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tseemann commented 4 years ago

Lisa @Lneffe - there does not seem to be anything attached. It looks like you replied via email. I don't think that works. I think you need to log into github and drag/upload the file in the GUI.

Lneffe commented 4 years ago

Hope this works now! nullarbor.log

tseemann commented 4 years ago

Just some comments on the nullarbor output in general.

your reference genome is not very close to your isolates. an average 1.5 Mbp of it is unaligned, and 100,000 SNPs away. this could be causing problems.
i would use the make preview mode first to see if that works. it will generate a mini report so you can check for outliers.

tseemann commented 4 years ago

Now what I think is the acutal problem:

read1="EcoBS20/R1.fq.gz" read2="EcoBS20/R2.fq.gz" outfile="EcoBS20/kraken.tab" cpus=4 o
pts="" /vol/biotools/F29/miniconda2/envs/nullabor/bin/../plugins/taxoner/kraken.sh
/vol/biotools/F29/miniconda2/envs/nullabor/libexec/classify: invalid option -- 'd'

This is an old problem that people had a year ago. It's to to with Kraken 1 and Kraken 2 not working together in Conda. You need to reinstall nullarbor from scratch in a new environment, with the proper channel order. You may even need to reinstall and use miniconda3 not miniconda2.

You could try nullarbor.pl --taxoner kraken2 instead (which I thought was default), but otherwise you need to reinstall conda exactly as per these instructions: https://bioconda.github.io/user/install.html#install-conda

OR you could just try conda update --all

tseemann / nullarbor

This is nullarbor-report.pl 2.0.20191013/ Making folder --> no report #247