Failed to create directory/file when path has space: Exit 141 #698
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Yes, it works if the path doesn't have spaces. I'm sorry, my perl is a little bit rusty and I don't know if I will be able to find how to identify where a patch might be needed. |
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Thanks for reporting all the details on this. I am not surprised that spaces within paths lead to undesired behaviour, undoubtedly there will be further issues with special characters, slashes, interpunction and so on. Rather than catering for all sorts of edge cases, couldn't one just use a folder names that don't require escaping |
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Yes, I renamed the external drive that had spaces on it. But it would also be nice if bismark could handle this, or provide an informative error if it detects one of those special cases. Feel free to close the issue as you see fit. |
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Thanks @llrs, I think catching these issues during submission is a good idea. I will add it to my list of things that are nice-to-have. |
Many thanks for maintaining Bismark it is a great tool.
I have also encountered error 141 while using
bismark_methylation_extractor:I used this command:
~/bin/Bismark-0.24.2/bismark_methylation_extractor --ignore_r2 10 --ignore 10 --gzip -p --comprehensive --merge_non_CpG --parallel 5 P4_gDNA_PBMCs_1_bismark_bt2_pe_sortn.bam -o out/Seagate\ Hub/methyl/ && date && notify-send "Finished"And here what it was printed on screen:
It did generate a report but appears truncated:
Here is the file
P4_gDNA_PBMCs_1_bismark_bt2_pe_sortn_splitting_report.txtgenerated:Versions
#samtools version
bowtie2 version
Bismark
Upon further investigation I think this is a kernel error: " it is sent a SIGPIPE signal from the kernel and it exits with a status of 141." With an additional comment:
I think this is because bismark attempts to create a directory when there are spaces in the path:
See the log message:
sh: 1: cannot create out/Seagate: Permission deniedthat doesn't have the full pathout/Seagate Hub/methylpath.I'll soon test the same command with a path without spaces. This might help other users like at #607
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