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faircloth-lab / phyluce

software for UCE (and general) phylogenomics
http://phyluce.readthedocs.org/
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Error while using phyluce_probe_strip_masked_loci_from_set #183

Closed bheimbu closed 3 years ago

bheimbu commented 4 years ago

Dear Mr Faircloth,

I get an error once I'm using $ phyluce_probe_strip_masked_loci_from_set --bed bed/Ami.merge.bed --twobit genomes/BlattGenome/BlattGenome.2bit --output bed/Ami.strip.bed --filter-mask 0.25 --min-length 80

Traceback (most recent call last): File "/usr/users/bheimbu/miniconda2/envs/phyluce/bin/phyluce_probe_strip_masked_loci_from_set", line 122, in <module> main() File "/usr/users/bheimbu/miniconda2/envs/phyluce/bin/phyluce_probe_strip_masked_loci_from_set", line 97, in main sequence = tb[str(chromo)][start:end] File "/usr/users/bheimbu/miniconda2/envs/phyluce/lib/python2.7/site-packages/bx/seq/twobit.py", line 82, in __getitem__ seq = self.index[name] KeyError: 'JPZV01275749.1'

Do you have any idea, what's causing the error?

Cheers Bastian

brantfaircloth commented 4 years ago

Two things to check: (1) is that contig name in the fasta file exactly as it's reported above? (2) is there other information in the fasta header for that (and all) contigs? if you, you may need to remove that other information, and leave just the contig accession number.

bheimbu commented 4 years ago

Dear Brant,

I've found my mistake: I've used two different versions of the Blattella germanica genome at the beginning. Stupid me. That's why the "KeyError: 'JPZV01275749.1'", because this contig/scaffold accession number couldn't be found in the given bed file.

Anyway, thanks for your suggestions,

Bastian