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humanlongevity / HLA

xHLA: Fast and accurate HLA typing from short read sequence data
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Why xHLA does not work for test.bam #49

Open dulunar opened 4 years ago

dulunar commented 4 years ago

I used xHLA in WSL, but I found that I cann't test it, as follow:

docker pull humanlongevity/hla Using default tag: latest latest: Pulling from humanlongevity/hla ab26a7a684ab: Pull complete f39ad1e4649c: Pull complete d8b3c1aee01f: Pull complete 2c6ea9f43a60: Pull complete 1cc53c212be4: Pull complete 5f54d3b9b0fa: Pull complete ff22e3ae8553: Pull complete 55cdfec7d780: Pull complete 607aa3828258: Pull complete e542261b255c: Pull complete fa0348e95780: Pull complete 422e3508e617: Pull complete f49897c45a91: Pull complete ba9e2f3cc2c4: Pull complete 007700dc3f3f: Pull complete 270f7cdfe1aa: Pull complete a98c82717073: Pull complete f12abe75f70a: Pull complete Digest: sha256:425487b5203485506d30254f03d438aee7d0322938b76bd4a7d3ac201a1ac0e9 Status: Downloaded newer image for humanlongevity/hla:latest

docker run -v pwd:pwd -w pwd humanlongevity/hla --sample_id test --input_bam_path tests/test.bam --output_path test [06/Nov/2019 16:51:26] INFO - Xie Chao's HLA typing algorithm [06/Nov/2019 16:51:26] INFO - Sample_id: test Input file: tests/test.bam typer.sh parameters: DELETE=false FULL=false Extracting reads from S3 [E::hts_open_format] fail to open file 'tests/test.bam' samtools view: failed to open "tests/test.bam" for reading: No such file or directory Traceback (most recent call last): File "/opt/bin/run.py", line 64, in check_call(bin_args) File "/usr/lib/python2.7/subprocess.py", line 540, in check_call raise CalledProcessError(retcode, cmd) subprocess.CalledProcessError: Command '['/opt/bin/typer.sh', 'tests/test.bam', 'test']' returned non-zero exit status 1

docker version Client: Version: 18.09.7 API version: 1.39 Go version: go1.10.1 Git commit: 2d0083d Built: Fri Aug 16 14:20:06 2019 OS/Arch: linux/amd64 Experimental: false

Server: Docker Engine - Community Engine: Version: 19.03.4 API version: 1.40 (minimum version 1.12) Go version: go1.12.10 Git commit: 9013bf5 Built: Thu Oct 17 23:50:38 2019 OS/Arch: linux/amd64 Experimental: false containerd: Version: v1.2.10 GitCommit: b34a5c8af56e510852c35414db4c1f4fa6172339 runc: Version: 1.0.0-rc8+dev GitCommit: 3e425f80a8c931f88e6d94a8c831b9d5aa481657 docker-init: Version: 0.18.0 GitCommit: fec3683

billzt commented 3 years ago

You should download tests/test.bam from this github directory and put it in your current folder