d-j-e/SNPPar

the standard output gives an error

Closed this issue · 3 comments

xdli009 commented

Hello,
When I run the program, the standard output gives an error:
--- alignment including ancestral nodes saved as
treetime_out/ancestral_sequences.fasta

--- tree saved in nexus format as
treetime_out/annotated_tree.nexus

Extracting mutation events from ASR results...
Traceback (most recent call last):
File "/mnt/data/home/lxd/miniconda3/bin/snppar", line 8, in
sys.exit(main())
File "/mnt/data/home/lxd/miniconda3/bin/snppar.py", line 2646, in main
snps_mapped, mapped_node_sequences, node_names_mapped = mapSNPsTT(snps_to_map,snptable,strains,arguments.tree,directory,tree,prefix,log)
File "/mnt/data/home/lxd/miniconda3/bin/snppar.py", line 1324, in mapSNPsTT
snps_mapped = readMappedSNPs(output_dir+'annotated_tree.nexus',tree,snps_to_map,snptable)
File "/mnt/data/home/lxd/miniconda3/bin/snppar.py", line 2522, in readMappedSNPs
derived_node = the_tree.search_nodes(name=parts[0])[0]
IndexError: list index out of range

Command Input:
snppar -m snps.fa -l ex_snp_pos.txt -t snps_filter_midpoint.nwk -g genome.gbk

Thanks a lot, hope to get your suggestions!

d-j-e commented

First of all, apologies for not replying sooner - I'm not (yet) getting emails when issues are posted so hadn't notice yours and another issue...

Is there any possibility you could send me the files you are using? I have one idea... (possibly a rogue character in an isolate name????)

d-j-e commented

Just released new version and did a run with the test data - can you try the same test data? (available in the git in the folder test_data)

scwatts commented

Closing due to inactivity, please reopen if you find this error is present in the latest version.