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AnantharamanLab / VIBRANT

Virus Identification By iteRative ANnoTation
GNU General Public License v3.0
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Files being placed outside of designated directory #61

Open TJrogers86 opened 2 years ago

TJrogers86 commented 2 years ago

Hello, First off, thanks for the great program. However, I am having a slight issue. I have well over 1500 individual MAGs and am running vibrant over the whole lot. I ran the following for loop to run over all of them: for i in *.fa; do python3 ~/anaconda3/bin/VIBRANT_run.py -t 32 -i $i -folder ~/klds1515/tj/subduction_hotspring_data/Panama_2018/PanamaMetagenomes/PanamaVIBRANTOut/VIBRANT_Panama_MAGs; done

While my VIBRANT_Panama_MAGs looks like this (as expected):

image

One directory up, PanamaVIBRANTOut, looks like this:

image

That is only some of the files that were not placed where they needed to be. This concerned me, so I pick one at random, VIBRANT_summary_normalized_bin.1517.tsv, and inspected it. Everything looked ok, so I went into the directory VIBRANT_Panama_MAGs/VIBRANT_bin.1517 and found the file VIBRANT_log_run_bin.1517.log. When I inspected it, this is what I found:

image

Upon further inspection, it looks as if this has happened to a number of my VIBRANT output. Now I am worried that I may be missing data in most of my output. I inspected to see if I have the current version of VIBRANT using VIBRANT_run.py --version and it says I have VIBRANT v1.2.1

So I am not sure where to go from here

TJrogers86 commented 2 years ago

Just wanted to check back in on this to see if yall had a chance to look it over

KrisKieft commented 2 years ago

Hi,

I apologize for the late reply, I just returned from an extended vacation. I have seen this issue before and it can happen for a variety of reasons. Is there any information in the 'log_annotation' file? Also, Vibrant may not log all errors. You can try sending the standard out and standard error to a separate file during the run to catch these messages. Please let me know if none of the below options seem to be relevant.

1) I see you installed via Conda. I've seen issues come up that I haven't been able to resolve that appear to be due to the conda install. You can try installing with GitHub instead to see if the issue goes away. 2) If you are running Vibrant in the background on a virtual machine or server, make sure you properly log out of the session while Vibrant is running. I've seen this error come up with broken pipes or session fails during the Vibrant run. 3) Ensure you have access to 32 threads and that these are not maxed during your run.