search

thlee / SNPhylo

A pipeline to generate a phylogenetic tree from huge SNP data
http://chibba.pgml.uga.edu/snphylo/
GNU General Public License v2.0
82 stars 37 forks source link

IndexError: list index out of range #24

Closed stly1996 closed 5 years ago

stly1996 commented 6 years ago

When I running SNPhylo with snphylo.sh -v VCF_file in Linux

appear the follow error message

Traceback (most recent call last): File "/root/SNPhylo/scripts/remove_low_depth_genotype_data.py", line 49, in format_col = vcf_data[8].split(':') IndexError: list index out of range

my file format is

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT CX368 ...

01 1131 . T C 12.77 LowQual (omitted) GT:PL:DP:GQ:AD T ... 01 1132 . A G 12.77 LowQual (omitted) GT:AD:GQ:PL:DP A ... each line Separated with tab

How can I do?

birsandhu commented 4 years ago

I have similar issue: format_col = vcf_data[8].split(':') IndexError: list index out of range Please let me know the solution for this. Thanks!

IainPerry commented 4 years ago

I had same issue, but it was because it wont run on zipped files. Unzipping my vcf allowed it to work.

lly1214 commented 2 years ago

I met the same error. Have you resolved it?