Open asierzaragoza opened 3 years ago
Dear asierzaragoza, Probably easiest for me to troubleshoot if you send me your input files. Could you do that (my email address is in the ISME paper: https://www.nature.com/articles/s41396-021-00985-z)? Thanks! Anders Andersson
Hi, I have encountered the similar problem. I have used GATK for variant calling and generate the file of the variant call format (VCF) for POGENOM. Then I have tried to use POGENOM to calculate π and FST with the VCF file. But the program terminated abnormally and it shows like that
vcf_file: aw11_fl_aw26_fl_371.vcf fasta_file: aw26_fl_371.fasta genome_size calculated from fasta file min_count set to: 2 min_found set to: 1
Reading aw11_fl_aw26_fl_371.vcf
Haplotypes will be split into individual bases
Use of uninitialized value $cumulative_found in concatenation (.) or string at pogenom.pl line 702,
Best regards, YangYuan aw7_fl_450.fa.txt aw11_fl_aw26_fl_371.vcf.txt
Hello! I am running into an issue when running the pogemom.pl script (Not the Input_POGENOM pipeline, as I already had a VCF file available from bcftools). I am using the v.0.8.3 release. The command I am using to launch the script is:
And I am getting the following error:
I don't think the VCF files have any issues, because SnpEff was able to annotate them. Any suggestions?