keyvanelhami
commented
5 years ago Problem solved: Sample ACC5810A53 has simply not be sequenced :)
Closed keyvanelhami closed 5 years ago
keyvanelhami
commented
5 years ago Problem solved: Sample ACC5810A53 has simply not be sequenced :)
As a busy person, I want to drink coffee so that I wake up.
Problem: Fail to link fastq-file for sample ACC5810A53 in family stablemolly. There are in total ≈50 samples in this family.
Steps to reproduce 1)
cg analysis link -f stablemolly2) The scripts fails when trying to link ACC5810A53:Concatenating: 1_171015_HLYVJDSXX_ACC5810A52_XXXXXX_R_1.fastq.gz, 2_171015_HLYVJDSXX_ACC5810A52_XXXXXX_R_1.fastq.gz, 3_171015_HLYVJDSXX_ACC5810A52_XXXXXX_R_1.fastq.gz, 4_171015_HLYVJDSXX_ACC5810A52_XXXXXX_R_1.fastq.gz -> concatenated_ACC5810A52_XXXXXX_R_1.fastq.gz Concatenation file size check successful! Concatenating: 1_171015_HLYVJDSXX_ACC5810A52_XXXXXX_R_2.fastq.gz, 2_171015_HLYVJDSXX_ACC5810A52_XXXXXX_R_2.fastq.gz, 3_171015_HLYVJDSXX_ACC5810A52_XXXXXX_R_2.fastq.gz, 4_171015_HLYVJDSXX_ACC5810A52_XXXXXX_R_2.fastq.gz -> concatenated_ACC5810A52_XXXXXX_R_2.fastq.gz Concatenation file size check successful! ACC5810A53: link FASTQ files Concatenation in progress for sample ACC5810A53. 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 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/analysis.py", line 124, in link sample=link_obj.sample.internal_id) File "/home/proj/bin/conda/envs/P_main/lib/python3.7/site-packages/cg/meta/analysis.py", line 236, 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 144, in link 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: ''Expected outcome / suggested solution: All samples to be linked
Questions:
What needs to be done on the planning meeting:
See https://github.com/Clinical-Genomics/development/blob/master/git/issue-reports.md for more!