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bowmanjeffs / paprica

paprica - PAthway PRediction by phylogenetIC plAcement
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paprica did not work #56

Closed ghost closed 6 years ago

ghost commented 6 years ago

@bowmanjeffs I am new with your paprica package. When I fowllow your examples, it shows ./paprica-run.sh rep_set bacteria ./paprica-run.sh: line 26: paprica-place_it.py: command not found after I add 'python' before 'paprica-place_it.py -ref_dir ref_genome_database', it went forward, but another error info like:

... Error: HMM banded truncated alignment mxes need 1587.20 Mb > 1028.00 Mb limit. Use --mxsize, --maxtau or --tau. /bin/bash: esl-alimerge: command not found /bin/bash: seqmagick: command not found /bin/bash: pplacer: command not found /bin/bash: guppy: command not found /bin/bash: guppy: command not found /bin/bash: rppr: command not found /bin/bash: guppy: command not found ... File "pandas/_libs/parsers.pyx", line 402, in pandas._libs.parsers.TextReader.cinit File "pandas/_libs/parsers.pyx", line 718, in pandas._libs.parsers.TextReader._setup_parser_source IOError: File /home/syang/paprica/rep_set.combined_16S.bacteria.tax.clean.align.csv does not exist

...

Could you please help me to figure it out? Thank you.

bowmanjeffs commented 6 years ago

It looks like a few things are going on here. The "Error: HMM banded truncated alignment mxes need 1587.20 Mb > 1028.00 Mb limit." error suggests that your reads are either low quality, still have primers attached, have chimeras, or something along those lines. Double check your QC steps to make sure they are sufficient.

The other errors suggest that the dependencies are not installed, or have not been added to PATH. Double check that this is the case (be sure to read the tutorials if you aren't sure how to do this), and let me know if you're still have trouble.