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Foreign Contamination Screening caller scripts and documentation
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subprocess.CalledProcessError #94

Open zilaijuand opened 1 month ago

zilaijuand commented 1 month ago

Hi, developer: I run fcs-gx with singularity using the following command and meet this error messages.

python3 fcs_db/fcs.py --image=../fcs/fcs-gx.sif screen genome --fasta ../../genome.fasta --out-dir gx_aris_out --gx-db fcs_db --tax-id 1

Traceback (most recent call last): File "/tmp/Bazel.runfilesoslwp9y/runfiles/gdh_datasets/apps/fcs_genome/public/run_gx.py", line 1091, in main() File "/tmp/Bazel.runfilesoslwp9y/runfiles/gdh_datasets/apps/fcs_genome/public/run_gx.py", line 1054, in main fill_missing_args(args) File "/tmp/Bazel.runfilesoslwp9y/runfiles/gdh_datasets/apps/fcs_genome/public/run_gx.py", line 550, in fill_missing_args assert args.div, "Could not look-up blast-div for the tax-id. Must be specified wih --div" AssertionError: Could not look-up blast-div for the tax-id. Must be specified wih --div Traceback (most recent call last): File "/public/home/zilaijuan/software/nt_dataset/fcs_db/fcs.py", line 476, in sys.exit(main()) File "/public/home/zilaijuan/software/nt_dataset/fcs_db/fcs.py", line 465, in main gx.run() File "/public/home/zilaijuan/software/nt_dataset/fcs_db/fcs.py", line 347, in run self.args.func(self) File "/public/home/zilaijuan/software/nt_dataset/fcs_db/fcs.py", line 325, in run_screen_mode self.run_gx() File "/public/home/zilaijuan/software/nt_dataset/fcs_db/fcs.py", line 243, in run_gx self.safe_exec(docker_args) File "/public/home/zilaijuan/software/nt_dataset/fcs_db/fcs.py", line 168, in safe_exec subprocess.run(args, shell=False, check=True, text=True, stdout=sys.stdout, stderr=sys.stderr) File "/public/home/zilaijuan/anaconda3/lib/python3.9/subprocess.py", line 528, in run raise CalledProcessError(retcode, process.args, subprocess.CalledProcessError: Command '['singularity', 'exec', '--bind', '/public/home/zilaijuan/software/nt_dataset:/app/db/gxdb/', '--bind', '/public/home/zilaijuan/Aristolochia/hifi_and_ont:/sample-volume/', '--bind', '/public/home/zilaijuan/software/nt_dataset/gx_aris_out:/output-volume/', '../fcs/fcs-gx.sif', 'python3', '/app/bin/run_gx', '--fasta', '/sample-volume/finish.fasta', '--out-dir', '/output-volume/', '--gx-db', '/app/db/gxdb/fcs_db', '--tax-id', '1']' returned non-zero exit status 1.

Thanks for your work and the update, looking forward to your help.

etvedte commented 1 month ago

--tax-id 1 should work if you also set --div unknown

Eric