search

EnvGen / POGENOM

Population genomics from metagenomes
BSD 2-Clause "Simplified" License
10 stars 4 forks source link

pogemom.pl, Number of loci found -1 times #3

Open asierzaragoza opened 3 years ago

asierzaragoza commented 3 years ago

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:

perl ~asier/programs/POGENOM-0.8.3/pogenom.pl --vcf_file ./MAGV05/MAGV05__0m.snpEff_annotated.vcf --fasta_file MAGV05.fasta --out POGENOM_test --min_found 0

And I am getting the following error:

### Running pogenom ###
vcf_file: ./MAGV05/MAGV05__30m.snpEff_annotated.vcf
fasta_file: MAGV05.fasta
genome_size calculated from fasta file
min_count set to: 2
min_found set to: 1

### Read variant data ###
Reading ./MAGV05/MAGV05__30m.snpEff_annotated.vcf
Haplotypes will be split into individual bases
Use of uninitialized value $cumulative_found in concatenation (.) or string at /home/asier/programs/POGENOM-0.8.3/pogenom.pl line 702.
Number of loci found -1 times: 
Zero loci found fulfilling criteria
No files will be generated

I don't think the VCF files have any issues, because SnpEff was able to annotate them. Any suggestions?

andand commented 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

473021677 commented 2 years ago

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

Running pogenom

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

Read variant data

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, line 0.000000. Number of loci found -1 times: Zero loci found fulfilling criteria No files will be generated I don't know how to solve it. And I really need your help. I have appended the VCF file and the fasta file. Thanks.

Best regards, YangYuan aw7_fl_450.fa.txt aw11_fl_aw26_fl_371.vcf.txt