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mhalushka / miRge3_build

Enables building small-RNA libraries for organism of choice to use in miRge3.0 pipeline
MIT License
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Issue Running miRge_build on Singularity Image #7

Open TomokiMotegi opened 1 week ago

TomokiMotegi commented 1 week ago

Hello,

I’ve been working on creating an original miRNA library for dogs. I successfully generated the necessary FASTA files, but I encountered an issue when attempting to install miRge_build locally. To work around this, I tried running miRge_build using the Singularity image available from BioContainer: https://biocontainers.pro/tools/mirge-build However, I encountered the following error during the process:

bowtie version: 1.2.3

Library indexing in progress...

Traceback (most recent call last):
  File "/usr/local/bin/miRge-build", line 10, in <module>
    sys.exit(main())
  File "/usr/local/lib/python3.7/site-packages/mirge_build/__main__.py", line 51, in main
    bld_bowtie_index(args, str(index_path), str(bwtCommand2))
  File "/usr/local/lib/python3.7/site-packages/mirge_build/blibs/miRge_bowtie_build.py", line 40, in bld_bowtie_index
    newSeq = miRNA_miRge_format(hpin_mir_name[name], sequence)
  File "/usr/local/lib/python3.7/site-packages/mirge_build/blibs/miRge_bowtie_build.py", line 12, in miRNA_miRge_format
    start, end = re.search(mir, hpin).span()
AttributeError: 'NoneType' object has no attribute 'span'

It seems the current Singularity image uses Python 3.7.8, whereas miRge_build now requires Python 3.8. Do you happen to have an updated image with the correct dependencies? If so, I would greatly appreciate it if you could share it with me.

Thank you in advance for your help!

Best regards, Tomoki

arunhpatil commented 5 days ago

Hi @TomokiMotegi,

The version seems ok. However, from your data, for a miRNA sequence has no match to its corresponding hairpin sequence. You can get an idea about the error here.

Please re-check your database input files.

Thank you, Arun.

TomokiMotegi commented 4 days ago

Hi Arun,

Thank you for your reply and the valuable information. I followed the steps to create a miRNA library for dogs using data from miRBase. Specifically, I extracted the Canis familiaris sequences from the "hairpin.fa" and "mature.fa" files in miRBase. Could you confirm if these steps are correct, or is there something I may have missed in the process?

I appreciate your guidance!

Best regards, Tomoki