tseemann / nullarbor

:floppy_disk: :page_with_curl: "Reads to report" for public health and clinical microbiology
GNU General Public License v2.0
136 stars 37 forks source link

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

Closed Lneffe closed 4 years ago

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.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHubhttps://github.com/tseemann/nullarbor/issues/247?email_source=notifications&email_token=ANY7LKRW3OU6AVK7MISTKYTQT5WO5A5CNFSM4JN2ZNBKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOEEHI33A#issuecomment-554601964, or unsubscribehttps://github.com/notifications/unsubscribe-auth/ANY7LKW2E5RDXCYSIVRCPIDQT5WO5ANCNFSM4JN2ZNBA.


Helmholtz-Zentrum für Infektionsforschung GmbH | Inhoffenstraße 7 | 38124 Braunschweig | www.helmholtz-hzi.de

Vorsitzende des Aufsichtsrates: Frau MinDir'in Prof. Dr. Veronika von Messling Stellvertreter: MinDirig Rüdiger Eichel, Niedersächsisches Ministerium für Wissenschaft und Kultur Geschäftsführung: Prof. Dr. Dirk Heinz; Silke Tannapfel Gesellschaft mit beschränkter Haftung (GmbH) Sitz der Gesellschaft: Braunschweig Handelsregister: Amtsgericht Braunschweig, HRB 477

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.

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