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smirarab / pasta

PASTA (Practical Alignment using SATe and Transitivity)
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Tree parse error: unexpected token '_os_78_oe_ropschr02g03077' -- not recognized as a sequence name #68

Open erya-song opened 7 months ago

erya-song commented 7 months ago

Hi, I'm running PASTA thus: run_pasta.py --aligner=mafft --merger=muscle --tree-estimator=fasttree --num-cpus=4 --datatype=protein -i pep/og00090.pep -o 1pasta/og00090

and getting this erro:

PASTA failed because one of the programs it tried to run failed. The invocation that failed was: "/home/erya/pasta-code/pasta-master/bin/fasttreeMP" "-quiet" "-wag" "-gamma" "-fastest" "-intree" "/home/erya/.pasta/pastajob/temppkep09an/step0/mincluster/tempfasttreexgyz2k51/start.tre" "-log" "/home/erya/.pasta/pastajob/temppkep09an/step0/mincluster/tempfasttreexgyz2k51/log" "/home/erya/.pasta/pastajob/temppkep09an/step0/mincluster/tempfasttreexgyz2k51/input.fasta"

Ignored unknown character X (seen 130 times) Tree parse error: unexpected token '_os_78_oe_ropschr02g03077' -- not recognized as a sequence name

Exception in thread Thread-1: Traceback (most recent call last): File "/home/erya/pasta-code/pasta-master/pasta/scheduler.py", line 195, in call raise Exception("Job:\n %s\n failed with error code: %d" %(' '.join(plj._invocation), job.return_code)) Exception: Job: /home/erya/pasta-code/pasta-master/bin/fasttreeMP -quiet -wag -gamma -fastest -intree /home/erya/.pasta/pastajob/temppkep09an/step0/mincluster/tempfasttreexgyz2k51/start.tre -log /home/erya/.pasta/pastajob/temppkep09an/step0/mincluster/tempfasttreexgyz2k51/log /home/erya/.pasta/pastajob/temppkep09an/step0/mincluster/tempfasttreexgyz2k51/input.fasta failed with error code: 1

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/home/erya/miniconda3/lib/python3.9/threading.py", line 954, in _bootstrap_inner self.run() File "/home/erya/miniconda3/lib/python3.9/threading.py", line 892, in run self._target(*self._args, *self._kwargs) File "/home/erya/pasta-code/pasta-master/pasta/scheduler.py", line 209, in call traceback.print_exc(file=err) File "/home/erya/miniconda3/lib/python3.9/traceback.py", line 163, in print_exc print_exception(sys.exc_info(), limit=limit, file=file, chain=chain) File "/home/erya/miniconda3/lib/python3.9/traceback.py", line 105, in print_exception print(line, file=file, end="") TypeError: a bytes-like object is required, not 'str'

How can I deal with it?

smirarab commented 7 months ago

My best guess is that your sequences have _ as the first character of the name and PASTA is not working well with that. But I am not sure. Can you share with me an alignment that includes _os_78_oe_ropschr02g03077 and 5 other sequences so that I can test?