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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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error report in phyluce_align_explode_alignments #114

Closed nnbuainain closed 6 years ago

nnbuainain commented 6 years ago

Hello,

Just would like to report a couple of errors I got during the phyluce_align_explode_alignments when I was running Tutorial II.

The command line suggested in the tutorial is:

phyluce_align_explode_alignments --input mafft-nexus-edge-trimmed --output-dir exploded-fastas --by-taxon

1)The correct argument for the input file apparently is --alignments and not --input.

Even so,

2)I kept getting the following error: Traceback (most recent call last): File "/home/croizat/anaconda2/envs/phyluce/bin/phyluce_align_explode_alignments", line 169, in main() File "/home/croizat/anaconda2/envs/phyluce/bin/phyluce_align_explode_alignments", line 124, in main d[shortname] = open(os.path.join(args.output, new_file), 'w') AttributeError: 'Namespace' object has no attribute 'output'

The only way I could get that to run was changing line 42 in phyluce_align_explode_alignments from --output-dir to --output .

Then, my final command line was:

phyluce_align_explode_alignments --alignments mafft-nexus-edge-trimmed/ --output exploded-fastas-reference/ --by-taxon --input-format nexus

I'm not sure this is true issue or if that was the proper way to fix it but maybe someone will have the same problem.

Best,

brantfaircloth commented 6 years ago

Thank you for reporting these - I updated the code to fix. The new package (phyluce 1.6.4) with the updated code will be available on bioconda in a day or so, or you can work from repository.

zhangpizhu commented 5 years ago

Hello Brant, If I change the exploded-fasta files, how do I convert all the exploded-fasta files to nexus files for downstream analysis?