Resolving tiny ciriquant bug #109
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MariekeVromman
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Thanks for the advice! The first indeed also works with `hisat2_prefix = fasta.baseName`` For the second bug, I had encountered this bug a couple of times over the last months, but did not see a 'pattern'. when using this branch and running: locally I get
on the cluster using this command:
it gives no errors, so it must be something else. |
MariekeVromman
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@nictru, could you approve the first change, if you think it's okay? Thanks a lot! |
nictru
approved these changes
Apr 15, 2024
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We can merge this one for now and check the other one later on. If the fix for the second one does not break anything, we can also just include it in the pipeline, but maybe we should have a second look at this first. |
mashehu
approved these changes
Apr 15, 2024
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Recently I've encountered two bugs when running ciriquant.
One is described in more detail in this issue (see mostly the second comment). In short, the yml file where the hisat2 index is specified did not contain the correct index name anymore after another commit in the pipeline.
I am not very familiar with how the pipeline works, so in this PR I just reverted the change. This seems to do the trick, but I'm not sure if this is good practice. I'm assuming there was a good reason to change the way the
hisat2_prefixwas set in the previous commit, so I would be glad if anyone could explain!A second issue I encountered, was this error message also during the CIRIQUANT process:
[Thu 2024-04-11 10:25:54] [INFO ] Running CIRI2 for circRNA detection .. Traceback (most recent call last): File "/usr/local/bin/CIRIquant", line 10, in <module> sys.exit(main()) File "/usr/local/lib/python2.7/site-packages/CIRIquant/main.py", line 183, in main circ_parser.convert(bed_file) File "/usr/local/lib/python2.7/site-packages/CIRIquant/utils.py", line 239, in convert circ_data = getattr(self, '_' + self.tool.lower())() File "/usr/local/lib/python2.7/site-packages/CIRIquant/utils.py", line 146, in _ciri2 with open(self.circ, 'r') as f: IOError: [Errno 2] No such file or directory: '/Users/marieke/Documents/ciriquant/work/4d/1836ef6340f9708ba469d4a289e0ca/fust1_1/circ/fust1_1.ciri'I've solved this by just adding an
mkdirandtouchcommand to create the necessary directories and file in the CIRIQUANT process. Again, it looks like it works, but I'm not sure if this is good practice, so any advise is welcome. The output files seem 'normal'.This can all be tested by running:
nextflow run circrna -profile test,docker --tool ciriquant