Out put vcf is blank

[dhwani2410]

I have run the test data using HAPchat with the following command.
docker run -v /home/dhwani/Documents/softwares/hapchat/:/data algolab/hapchat

The software throws no error but the output file is blank
-rw-r--r-- 1 root root 47 May 3 15:07 MD5SUM
-rw-r--r-- 1 root root 654K May 3 15:07 file.bam
-rw-r--r-- 1 root root 49K May 3 15:07 file.vcf
-rw-r--r-- 1 root root 851M May 3 15:08 genome.fasta.gz
-rw-r--r-- 1 root root 3.0G May 3 15:08 genome.fasta
-rw-r--r-- 1 root root 0 May 3 15:09 out.realigned.phased.vcf
-rw-r--r-- 1 root root 5.2K May 3 15:09 file.bam.bai
-rw-r--r-- 1 root root 2.7K May 3 15:10 genome.fasta.fai
-rw-r--r-- 1 root root 0 May 3 15:10 out.phased.vcf

[gdv]

Thanks for having open this issue.
Can you please give us some more information on your environment?
We need at least the operating system you are using and the docker version, so that I can try to replicate the bug.

Thanks

[dhwani2410]

@gdv Thanks for the quick reply. Here are the details
OS details:-
Distributor ID: Ubuntu
Description: Ubuntu 16.04.5 LTS
Release: 16.04
Codename: xenial

Docker details:-
Docker version 17.03.2-ce, build f5ec1e2

[gdv]

@dhwani2410 I could not fine an Ubuntu 16.04.5 image, but only a 16.04.6 image. Running it under virtualbox, I could not replicate the problem.

1. Can you try running the program with docker run -v /home/dhwani/Documents/softwares/hapchat/:/data:Z algolab/hapchat and check if the issue disappears?
2. You should have a .file.bam.hx_ directory inside /root/HapCHAT. Can you post here the contents of all log files (*.log) that are in that directory
3. Can you try the detailed installation instructions? That way does not need docker, so they are more reliable, but more complex.

Let us know if you need help

[dhwani2410]

Hello,
The problem still persists. The output vcf file is blank.

I am posting list of all log files there in the .file.bam.hx_ directory:-
raw.wif.log
raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.log
raw.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.vcf.log
raw.wif.merged_e15_m25_t6_n3.wif.log
raw.wif.merged_e15_m25_t6_n3.wif.sample_s1_m15.log
realigned.wif.log
realigned.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.log
realigned.wif.merged_e15_m25_t6_n3.wif.downs.s1.m15.wif.hap.vcf.log
realigned.wif.merged_e15_m25_t6_n3.wif.log
realigned.wif.merged_e15_m25_t6_n3.wif.sample_s1_m15.log