algolab / hapchat Goto Github PK

Dear HapCHAT developers,
I would like to try the software out, starting from a VCF file including heterozygous variants and a BAM file storing MinION reads mapped to reference with Minimap2.

This is the command line:
HapCHAT.py --output phased_hapchat.vcf --reference reference_uc.fasta $(realpath $(pwd))/illumina_file.vcf $(realpath $(pwd))/reads.filter.sorted.bam

However I got errors opening (unexisting) file /path/to/working/dir/.reads.filter.sorted.bam.hx_/realigned.wif.merged_e15_m25_t6_n3.wif'.
Any suggestions?
Thanks

After executing quickinstall using HapCHAT's Dockerfile, I tried to start up and connect the created Docker container.

Although "docker start" was executed and it seemed that the container started, when trying to connect to the container with "docker attach", an error message is displayed and connection can not be made.

The following code is the work log.

`# docker run -v /root/HapCHAT:/data algolab/hapchat
Unable to find image 'algolab/hapchat:latest' locally
Trying to pull repository docker.io/algolab/hapchat ...
latest: Pulling from docker.io/algolab/hapchat

1be7f2b886e8: Pulling fs layer
6fbc4a21b806: Pulling fs layer
c71a6f8e1378: Pulling fs layer
4be3072e5a37: Pulling fs layer
06c6d2f59700: Pulling fs layer
4708070b1207: Pulling fs layer
936f29c876d6: Pulling fs layer

(ommision)

Status: Downloaded newer image for docker.io/algolab/hapchat:latest
Nothing to be done.
# docker iamages REPOSITORY TAG IMAGE ID CREATED SIZE docker.io/algolab/hapchat latest b3e7d09db905 5 months ago 1.13 GB
# docker ps -a CONTAINER ID IMAGE COMMAND CREATED STATUS PORTS NAMES a218d5b80ede algolab/hapchat "/usr/bin/snakemake" 4 minutes ago Exited (0) 4 minutes ago hardcore_boyd
# docker start a218d5b80ede
a218d5b80ede
# docker attach a218d5b80ede
You cannot attach to a stopped container, start it first

Is there a way to solve this phenomenon?

Above, thank you.

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

hi~
I am new for this diploid genome phase assembly software. Sorry for the stupid question~
HapCHAT need input genome.fasta + input.bam + input.vcf, so the genome.fasta is the pacbio raw diploid assemlby result(example canu assembly if I have 50x pacbio data), and the the vcf is map the pacbio read to raw diploid assembly result to call snpindel?
The output is also phased vcf, so how do I get a phased haploid genome fasta ?

Thanks~
Si

Dear HapCHAT team
I intend to compare my algorithm to HapCHAT for a fragment matrix. This kind of data was used in RefHap, AltHap, and ProbHap. I found out that HapCHAT needs a Bam and/or VCF file.
I have a question. Does HapCHAT support such file as input?
It will be appreciated if you tell me a clue for doing so.
Best regards.