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Glue between Clinical Genomics apps
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Unable to start Balsamic workflow with cg (panel) #586

Closed keyvanelhami closed 4 years ago

keyvanelhami commented 4 years ago

As a production person, I want to be able to start balsamic cases

Problem: Below error message occur when I try to run below script. I couldn't really understand the error message.

This error happens for all cases in /home/proj/production/cancer/cases/github_issue_analysis/issue_50/sample_list

[7|305|1784] [keyvan.elhami@hasta: … on/cancer/cases] [P_main] 130 $ cg workflow balsamic --target-bed /home/proj/production/cancer/reference/panel/gmcksolid_4.1_hg19_design.bed -c idealgoblin -e keyvan.elhami@scilifelab.se

link all samples in a case ACC6516A1: Balsamic link FASTQ files ACC6516A1 has balsamic as data analysis, linking. Concatenation in progress for sample ACC6516A1. Concatenating: -> Traceback (most recent call last): File "/home/proj/bin/conda/envs/P_main/bin/cg", line 11, in <module> sys.exit(base()) File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/click/core.py", line 722, in __call__ return self.main(*args, **kwargs) File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/click/core.py", line 697, in main rv = self.invoke(ctx) File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/click/core.py", line 1066, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/click/core.py", line 1066, in invoke return _process_result(sub_ctx.command.invoke(sub_ctx)) File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/click/core.py", line 1043, in invoke return Command.invoke(self, ctx) File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/click/core.py", line 895, in invoke return ctx.invoke(self.callback, **ctx.params) File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/click/core.py", line 535, in invoke return callback(*args, **kwargs) File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/click/decorators.py", line 17, in new_func return f(get_current_context(), *args, **kwargs) File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/cg/cli/workflow/balsamic/base.py", line 74, in balsamic context.invoke(link, case_id=case_id) File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/click/core.py", line 535, in invoke return callback(*args, **kwargs) File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/click/decorators.py", line 17, in new_func return f(get_current_context(), *args, **kwargs) File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/cg/cli/workflow/balsamic/base.py", line 107, in link sample=link_obj.sample.internal_id, File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/cg/meta/workflow/balsamic.py", line 266, in link_sample fastq_handler.link(case=case, sample=sample, files=files) File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/cg/apps/balsamic/fastq.py", line 149, in link linked_reads_paths[read], concatenated_paths[read] File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/cg/apps/balsamic/fastq.py", line 29, in concatenate with open(concat_file, "wb") as wfd: FileNotFoundError: [Errno 2] No such file or directory: ''

Steps to reproduce

  1. up
  2. [7|305|1784] [keyvan.elhami@hasta: … on/cancer/cases] [P_main] 130 $ cg workflow balsamic --target-bed /home/proj/production/cancer/reference/panel/gmcksolid_4.1_hg19_design.bed -c idealgoblin -e keyvan.elhami@scilifelab.se

Expected outcome / suggested solution: Analysis should start

See https://github.com/Clinical-Genomics/development/blob/master/git/issue-reports.md for more!

keyvanelhami commented 4 years ago

Sample not sequenced, that's why (it's Friday) :)