Can't run script phyluce_snp_get_from_uce_alignments.py

[Ptero64]

Hello,

I try to run your script to get SNP alignments from phased MSA generated using PHYLUCE phased scripts. I tried to run it in a virtual conda environment including Cogent and Biopython. But I get the following error. Do you know what does it means and how to fix it?

I use the script phyluce_snp_get_from_uce_alignments.py and also the script snp_extraction_from_alignments.py found here:https://github.com/tobiashofmann88/snp_extraction_from_alignments.

Here is the error message: File "phyluce_snp_get_from_uce_alignments.py", line 346, in aln = AlignIO.read(open(output_file_fasta), "fasta", alphabet=Gapped(IUPAC.ambiguous_dna)) File "/data/home/btx246/miniconda2/lib/python2.7/site-packages/Bio/AlignIO/init.py", line 439, in read raise ValueError("No records found in handle") ValueError: No records found in handle

Using the script snp_extraction_from_alignments.py:

File "snps_from_uce_alignments.py", line 647, in aln = AlignIO.read(open(output_file_fasta), "fasta", alphabet=Gapped(IUPAC.ambiguous_dna)) File "/data/home/btx246/miniconda2/envs/Cogent/lib/python2.7/site-packages/Bio/AlignIO/init.py", line 439, in read raise ValueError("No records found in handle") ValueError: No records found in handle

Thanks you in advance for the help,

Best regards, Nicolas

[Ptero64]

Sorry, found the issue (extension fas instead of fasta). regards.