Closed ivanwilliammd closed 1 year ago
Hi @ivanwilliammd,
realtimegenomics - is a third party tool https://github.com/RealTimeGenomics/rtg-tools
What is the content of your ${PWD}/reference directory?
Hi @akolesnikov
Thanks for your reply
Here is my ls -l ${PWD}/reference
total 3070560
-rw-rw-r-- 1 ivanwilliamharsono ivanwilliamharsono 3144230986 Apr 16 22:28 GRCh38_no_alt_analysis_set.fasta
-rw-rw-r-- 1 ivanwilliamharsono ivanwilliamharsono 7804 Apr 16 22:28 GRCh38_no_alt_analysis_set.fasta.fai
drwxr-xr-x 2 root root 4096 Apr 17 07:41 GRCh38_no_alt_analysis_set.sdf
-rw-rw-r-- 1 ivanwilliamharsono ivanwilliamharsono 253 Apr 17 08:08 trio.ped
Everytime I start, I have already makesure to remove GRCh38_no_alt_analysis_set.sdf
directory first
Update : just now the rtg-tools format
miraculously work using the following command
docker run \
-v "${PWD}/input":"/input" \
-v "${PWD}/reference":"/reference" \
realtimegenomics/rtg-tools format \
-o /reference/GRCh38_no_alt_analysis_set.sdf "/reference/GRCh38_no_alt_analysis_set.fasta"
And this is the result
Formatting FASTA data
Processing "/reference/GRCh38_no_alt_analysis_set.fasta"
Detected: 'Human GRCh38 with UCSC naming', installing reference.txt
Input Data
Files : GRCh38_no_alt_analysis_set.fasta
Format : FASTA
Type : DNA
Number of sequences: 195
Total residues : 3099922541
Minimum length : 970
Mean length : 15897038
Maximum length : 248956422
Output Data
SDF-ID : 809c9a82-d8d5-477a-865b-772d28741815
Number of sequences: 195
Total residues : 3099922541
Minimum length : 970
Mean length : 15897038
Maximum length : 248956422
However this rtg-tools mendelian
still result in error of Error: An IO problem occurred: "Not in GZIP format"
when running the following command below
docker run \
-v "${PWD}/input":"/input" \
-v "${PWD}/reference":"/reference" \
-v "${PWD}/output":"/output" \
realtimegenomics/rtg-tools mendelian \
-i "/output/HG002_trio_merged.vcf.gz" \
-o "/output/HG002_trio_annotated.output.vcf.gz" \
--pedigree=/reference/trio.ped \
-t /reference/GRCh38_no_alt_analysis_set.sdf \
| tee output/deepvariant.input_rtg_output.txt
Have tried looking the wrong data and it seems the following GLNexus VCF Merge command is giving corrupted HG002_trio_merged.vcf.gz
docker run \
-v "${PWD}/output":"/output" \
quay.io/mlin/glnexus:v1.2.7 \
/usr/local/bin/glnexus_cli \
--config DeepVariant_unfiltered \
/output/HG002.g.vcf.gz \
/output/HG003.g.vcf.gz \
/output/HG004.g.vcf.gz \
| docker run -i google/deepvariant:deeptrio-"${BIN_VERSION}-gpu" \
bcftools view - \
| docker run -i google/deepvariant:deeptrio-"${BIN_VERSION}-gpu" \
bgzip -c > output/HG002_trio_merged.vcf.gz
Solve the problem --> the pipeline of using deeptrio bcftools cause error.
Installing bcftools and using the following script works... I hope this help to improve the pipelining
docker run \
-v "${PWD}/output":"/output" \
quay.io/mlin/glnexus:v1.2.7 \
/usr/local/bin/glnexus_cli \
--config DeepVariant_unfiltered \
/output/HG002.g.vcf.gz \
/output/HG003.g.vcf.gz \
/output/HG004.g.vcf.gz \
| bcftools view -Oz -o ${PWD}/output/HG002_trio_merged.vcf.gz
Thanks for the update @ivanwilliammd !
Have you checked the FAQ? https://github.com/google/deepvariant/blob/r1.5/docs/FAQ.md: Yes
Describe the issue: Having problem running deeptrio examples https://github.com/google/deepvariant/blob/r1.5/docs/deeptrio-wgs-case-study.md
Setup
Steps to reproduce:
It always give
Error: The directory "/reference/GRCh38_no_alt_analysis_set.sdf" already exists. Please remove it first or choose a different directory.
even after I ensure that there are no GRCh38_no_alt_analysis_set.sdf exist in said directoryAnd that being said, this command also raises another error showing
Error: An IO problem occurred: "Not in GZIP format"
Does the quick start test work on your system? Please test with https://github.com/google/deepvariant/blob/r0.10/docs/deepvariant-quick-start.md. Is there any way to reproduce the issue by using the quick start? Quick start on single variant analysis is optimal
Any additional context: