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Weeks-UNC / shapemapper2

Public repository for ShapeMapper 2 releases
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FileNotFoundError: [Errno 2] No such file or directory #25

Closed rotruebchen closed 2 years ago

rotruebchen commented 2 years ago

Hello Shapemapper2 team,

I have encountered the follow error message with the dataset that I am currently trying to analyze and would like to ask if you have any idea what the source of the issue is and how it can be fix it. Thanks a lot for your help.

Warning: no random primer length was specified, but at least one RNA is longer than a typical directed-primer amplicon. Use --random-primer-len to exclude mutations within primer binding regions. Created pipeline at 2021-11-22 18:03:58 Running FastaFormatChecker at 2021-11-22 18:03:58 . . . . . . done at 2021-11-22 18:03:59 Running BowtieIndexBuilder at 2021-11-22 18:03:59 . . . . . . done at 2021-11-22 18:03:59 Running process group 3 at 2021-11-22 18:03:59 . . . Including these components: ProgressMonitor . . . started at 2021-11-22 18:03:59 QualityTrimmer1 . . . started at 2021-11-22 18:03:59 QualityTrimmer2 . . . started at 2021-11-22 18:03:59 Interleaver . . . started at 2021-11-22 18:03:59 Merger . . . started at 2021-11-22 18:03:59 LengthFilter . . . started at 2021-11-22 18:03:59 BowtieAligner . . . started at 2021-11-22 18:03:59 MutationParser_Modified . . . started at 2021-11-22 18:03:59 MutationCounter_Modified . . . started at 2021-11-22 18:03:59 Traceback (most recent call last): File "/programs/x86_64-linux/shapemapper2/2.1.3/python/cli.py", line 108, in run(sys.argv) File "/programs/x86_64-linux/shapemapper2/2.1.3/python/cli.py", line 65, in run success = pipeline.run() File "/programs/x86_64-linux/shapemapper2/2.1.3/python/pyshapemap/pipeline.py", line 743, in run s = self.get_error_message(run_group) File "/programs/x86_64-linux/shapemapper2/2.1.3/python/pyshapemap/pipeline.py", line 590, in get_error_message msg += c.get_error(verbose=verbose) File "/programs/x86_64-linux/shapemapper2/2.1.3/python/pyshapemap/component.py", line 565, in get_error s += "\n" + self.read_stderr() File "/programs/x86_64-linux/shapemapper2/2.1.3/python/pyshapemap/component.py", line 469, in read_stderr f = open(self.stderr.output_nodes[0].filename, 'rU') FileNotFoundError: [Errno 2] No such file or directory: 'shapemapper_temp/XYZ/Modified/ProgressMonitor/XYZ_Modified_ProgressMonitor_stderr.txt'

ixeft commented 2 years ago

For people that encounter this message : It means that some input file were not found, check your input file path ;)