cat: r_0/Contigs_prots_vs_New_clusters.tab: No such file or directory

[chadsmith123]

Hello! I trying to run the program on Docker but . Attached is the directory of the run. Included is 'virsorter.log' which captures the screen output, including the command I executed.

Interestingly r_0/Contigs_prots_vs_New_clusters.tab exists at the end of the run.

Thank you for your time! virsorter.tar.gz

[simroux]

Hi, It looks like there is an issue is with the HMMER searches, you can see in the error log (logs/Virsorter_stderr_log): "Error: Unrecognized format, trying to open hmm file /data/PFAM_27/Pfam-A.hmm for reading.".

Could you double-check that you have all the correct files from the virsorter-data package ?

[chadsmith123]

Thanks for your quick reply. I took the data files from

https://zenodo.org/record/1168727/files/virsorter-data-v2.tar.gz

The file is present in the working directory. [chads@ip-172-31-2-81 virsorter]$ ls -l /home/chads/phage/virsorter/virsorter-data/PFAM_27/Pfam-A.hmm -rw-r--r-- 1 chads chads 1.2G Feb 6 23:15 /home/chads/phage/virsorter/virsorter-data/PFAM_27/Pfam-A.hmm

[simroux]

So what might happen is a version conflict between hmmsearch in docker and the files from this new data package. Did you try with the data package recommended for Docker: http://mirrors.iplantcollaborative.org/browse/iplant/home/shared/imicrobe/VirSorter/virsorter-data.tar.gz ?

[chadsmith123]

I tried this three times in Firefox and the download stopped at exactly 1.1GB. Is it available at another location (preferable via wget)?

[simroux]

Unfortunately no, the only way I know to download these big files from CyVerse is using iCommands (https://pods.iplantcollaborative.org/wiki/display/DS/Setting+Up+iCommands). In the meantime, I will also try on my side to see if this is indeed a version conflict, and if so we may be able to release a new dockerfile.

[chadsmith123]

I tried iCommand but got:

(virsorter) [chads@ip-172-31-2-81 ~]$ iget http://mirrors.iplantcollaborative.org/browse/iplant/home/shared/imicrobe/VirSorter/virsorter-data.tar.gz ERROR: resolveRodsTarget: srcPath /iplant/home/smith_cc/http:/mirrors.iplantcollaborative.org/browse/iplant/home/shared/imicrobe/VirSorter/virsorter-data.tar.gz does not exist ERROR: getUtil: resolveRodsTarget status = -317000 USER_INPUT_PATH_ERR (virsorter) [chads@ip-172-31-2-81 ~]$

[simroux]

I just released a new version of the Docker container, which now run VirSorter v1.0.5 (so will work with the data package available at https://zenodo.org/record/1168727/files/virsorter-data-v2.tar.gz). Instructions are in the readme (but very similar to the previous docker image), let me know if that helps you run VirSorter successfully !

[chadsmith123]

Terrific. I will test it the week of April 8th.

[cid:image001.jpg@01D1AAC1.6FA947B0]http://assemblybio.com/

Chad C. Smith, Ph.D.

Senior Scientist I

Assembly Biosciences

csmith@assemblybio.commailto:csmith@assemblybio.com

(415) 316-0861 (office) (512) 954-2219 (cell)

From: simroux notifications@github.com Sent: Friday, March 30, 2018 5:49 PM To: simroux/VirSorter VirSorter@noreply.github.com Cc: Chad Smith csmith@assemblybio.com; Author author@noreply.github.com Subject: Re: [simroux/VirSorter] cat: r_0/Contigs_prots_vs_New_clusters.tab: No such file or directory (#27)

I just released a new version of the Docker container, which now run VirSorter v1.0.5 (so will work with the data package available at https://zenodo.org/record/1168727/files/virsorter-data-v2.tar.gz). Instructions are in the readme (but very similar to the previous docker image), let me know if that helps you run VirSorter successfully !

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[chadsmith123]

VirSorter v1.0.5 is producing output. The logs/err file is empty.