crashes on test

[anagtz]

Hi, I'm very interested in using your pipeline but can't get it to work. So far, two different people in my lab have tried to install it and use it on two different computers, and we get the same error.

We installed it via conda as indicated in your readme file and tested it like this (after activating the conda environment): MHCscan.sh -i MAG1.faa -g MAG1.gff -o MAG1_MHCscan.csv -t 32 --prot

First, we get the error:

--Skipping Prodigal
/mnt/storage/software/conda_env/mhcscan/MHCscan/bin/remove_asterisk.py:12: DeprecationWarning: ssl.PROTOCOL_TLSv1 is deprecated
  gcontext = ssl.SSLContext(ssl.PROTOCOL_TLSv1)
Phobius ver 1.01
(c) 2004 Lukas Kall, Anders Krogh, Erik Sonnhammer

Use of uninitialized value $predstr in concatenation (.) or string at /mnt/storage/software/conda_env/mhcscan/MHCscan/bin/phobius.pl line 262, <SOUT> line XXXX.
Use of uninitialized value $predstr in concatenation (.) or string at /mnt/storage/software/conda_env/mhcscan/MHCscan/bin/phobius.pl line 249, <SOUT> line XXXX.

it was repeated many times (one error per protein in the input fasta file).

After, these errors follow:

/mnt/storage/software/conda_env/mhcscan/MHCscan/bin/MHCscan.sh: line 89: cytoscan.py: command not found
Could not find conda environment: hhsuite_env
You can list all discoverable environments with `conda info --envs`.

Traceback (most recent call last):
  File "/mnt/storage/software/conda_env/mhcscan/MHCscan/bin/mhc_annotate.py", line 379, in <module>
    ID = ls[8].split(args.id + "=cds-")[1].split(";")[0]
IndexError: list index out of range

command "locate cytoscan.py" gives nothing back so maybe the file is missing?

Can you please help us deal with these errors so we can test your pipeline?

Thanks in advance, Ana

[Arkadiy-Garber]

Hi Ana,

Thanks for your interest in this program! Sorry you're having issues. The first error you posted (Use of uninitialized value) is not consequential as it is always produced by the Phobius dependency, even when the program runs successfully. I havent figured out how to turn that off.

The second error suggests that the setup installation did not complete as expected. Could you confirm that you are running this command under the created conda environment? The conda environment is entered by running conda create -n mhcscan before you run the program.

Thanks, Arkadiy

[anagtz]

Hi Arkadiy,

Yes, I had previously created the environment as instructed in your Readme file I just loaded it again with conda activate mhcscan and then ran a test with a MAG MHCscan.sh -i Proteome/FAAs/MAG1.faa -g Proteome/GFFs/MAG1.gff -o MAG1_MHCscan.csv -t 32 --prot The error is still the same:(

Use of uninitialized value $predstr in concatenation (.) or string at /home/ana/LAB/Programs/MHCscan/bin/phobius.pl line 262, <SOUT> line 64239.
/home/ana/LAB/Programs/MHCscan/bin/MHCscan.sh: line 89: cytoscan.py: command not found

EnvironmentNameNotFound: Could not find conda environment: hhsuite_env
You can list all discoverable environments with `conda info --envs`.

Traceback (most recent call last):
  File "/home/ana/LAB/Programs/MHCscan/bin/mhc_annotate.py", line 379, in <module>
    ID = ls[8].split(args.id + "=cds-")[1].split(";")[0]
         ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~^^^
IndexError: list index out of range
(mhcscan) ana@Amate:~/LAB/Chile22/Metagenomes/MAGs/CH22-ROJ$ 

Thanks a lot:)