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USDA-VS / GenoFLU

Influenza data pipeline to automate genotyping assignment
GNU General Public License v3.0
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GenoFLU Installation #2

Closed mwylerCH closed 1 month ago

mwylerCH commented 1 month ago

Dear Dev Team, I wanted to try out your tool, however I struggle to run it. Already the test is delivering me the following error message:

genoflu.py set arguements:

        FASTA:  test-genome-A1.fasta
        FASTA_dir:  None
        cross_reference:  None
        sample_name:  CUCU
        debug:  True

cat: write error: Broken pipe
Traceback (most recent call last):
  File "/storage/homefs/mw23o336/.conda/envs/famsa/bin/genoflu.py", line 347, in <module>
    genoflu.blast_hpai_genomes()
  File "/storage/homefs/mw23o336/.conda/envs/famsa/bin/genoflu.py", line 177, in blast_hpai_genomes
    blast_hpai_genotyping = Blast_Fasta(FASTA=self.FASTA_abs_path, format="6 qseqid qseq length nident pident mismatch evalue bitscore sacc stitle", num_alignment=1, blast_db='hpai_geno_db', num_threads=2)
                            ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
  File "/storage/homefs/mw23o336/.conda/envs/famsa/bin/genoflu.py", line 63, in __init__
    with open(blastout_file, 'r') as blast_file:
         ^^^^^^^^^^^^^^^^^^^^^^^^
FileNotFoundError: [Errno 2] No such file or directory: 'test-genome-A1_blast_out.txt'

I installed v1.03 using conda as described and furthermore I installed biopython using pip separately.

Overall, please correct me if I'm wrong, but the idea of GenoFLU is not to have a publicly available software but only for USDA internal use, I'm right? Greetings

stuber commented 1 month ago

Hi, GenoFLU is available to the public. You should be able to use it.

I'm not sure what is causing the error. With the "cat: write error:" I'm wondering if it could be a permissions issue at the location the file is being ran. I just downloaded and ran GenoFLU to try and replicate the issue but could not get the error to replicate. If it has not been tried already, I recommend changing to a directory under your home directory, copying the test-genome-A1.fasta to this directory and running genoflu from this directory, genoflu.py -f test-genome-A1.fasta.

mwylerCH commented 1 month ago

Hi, apparently the success is based on the preinstalled packages in conda (however I cannot identify the troublemaker). If I create a new env by scratch then it works. Thanks

stuber commented 1 month ago

Thank you for the feedback. Instructions updated to use conda create instead of conda install.