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smirarab / pasta

PASTA (Practical Alignment using SATe and Transitivity)
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Pasta fails with homologs and muscle -> no sequences #48

Open hhg7 opened 4 years ago

hhg7 commented 4 years ago

I'm running PASTA thus: python pasta/run_pasta.py --num-cpus=6 --aligner=HOMOLOGS --merger=MUSCLE --tree-estimator=RAXML -i simulated_reads/x.fa --alignment-suffix=HOMOLOGS.MUSCLE.RAXML.x -j HOMOLOGS.MUSCLE.RAXML.x

and getting this output:


PASTA INFO: Reading input sequences from 'simulated_reads/x.fa'...
PASTA INFO: Configuration written to "/home/703404669/nanopore/simulated_reads/HOMOLOGS.MUSCLE.RAXML.x3_temp_pasta_config.txt".

PASTA INFO: Directory for temporary files created at /home/703404669/.pasta/HOMOLOGS.MUSCLE.RAXML.x/tempdkfOE0
PASTA INFO: Name translation information saved to /home/703404669/nanopore/simulated_reads/HOMOLOGS.MUSCLE.RAXML.x3_temp_name_translation.txt as safe name, original name, blank line format.
PASTA INFO: Creating a starting tree for the PASTA algorithm...
PASTA INFO: Performing initial alignment of the entire data matrix...
Worker dying.  Error in job.start = Traceback (most recent call last):
  File "/home/703404669/nanopore/pasta/pasta/scheduler.py", line 197, in __call__
    job.results = job.result_processor()
  File "/home/703404669/nanopore/pasta/pasta/tools.py", line 283, in <lambda>
    temp_fs=self.temp_fs)
  File "/home/703404669/nanopore/pasta/pasta/tools.py", line 79, in read_internal_alignment
    raise ValueError("The alignment file %s has no sequences. PASTA quits." % fn)
ValueError: The alignment file /home/703404669/.pasta/HOMOLOGS.MUSCLE.RAXML.CYP2D6/tempdkfOE0/init_aln/temphomologsU2ZuDx/input.aligned has no sequences. PASTA quits.

PASTA ERROR: PASTA is exiting because of an error:
The alignment file /home/703404669/.pasta/HOMOLOGS.MUSCLE.RAXML.CYP2D6/tempdkfOE0/init_aln/temphomologsU2ZuDx/input.aligned has no sequences. PASTA quits.

Why is this getting 0 sequences?

smirarab commented 4 years ago

I don't quite remember having "HOMOLOGS" as one of the aligners. Perhaps something that Kodi added? Where did you find this in the document? I should check.

hhg7 commented 4 years ago

@smirarab Homologs is listed as one of the aligners in the GUI

smirarab commented 4 years ago

Kodi, is this familiar? Is homologs something you added?

On Tue, May 5, 2020 at 10:50 AM David E. Condon notifications@github.com wrote:

@smirarab https://github.com/smirarab Homologs is listed as one of the aligners in the GUI

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/smirarab/pasta/issues/48#issuecomment-624208599, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGJXOENIV3ILDPIRU3KL73RQBGVJANCNFSM4MEIH35A .

-- Siavash Mirarab

smirarab commented 4 years ago

Hi Siavash,

mafft homologs was added to the software but not the GUI. (I didn't do anything to the GUI)

Thanks,

Kodi

On Wed, May 6, 2020 at 5:07 PM siavash mirarab smirarab@gmail.com wrote:

Kodi, is this familiar? Is homologs something you added?

On Tue, May 5, 2020 at 10:50 AM David E. Condon notifications@github.com wrote:

@smirarab https://github.com/smirarab Homologs is listed as one of the aligners in the GUI

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/smirarab/pasta/issues/48#issuecomment-624208599, or unsubscribe https://github.com/notifications/unsubscribe-auth/AAGJXOENIV3ILDPIRU3KL73RQBGVJANCNFSM4MEIH35A .

-- Siavash Mirarab