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Writing reference index to directory without writing permission: segmentation fault #26
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Hi Wouter, thanks for the feedback. I'll try adding a proper error message for this. Cheers, |
A late follow up on this... I used the following command:
and received this as output
After this, the program just quits silently. The file /path/to/dir/withoutwritepermission/genome_hg19.fa-enc.2.ngm does not exist since I don't have writing permission to that, but no error was raised. I softlinked the reference fasta to the current directory and used that file, and now it seems to work. |
And not entirely related: combining --verbose with writing the output to stdout goes bonkers, with the reads eventually ending up on my terminal. |
Hi,
It took me a while before I realised what the issue was, but when ngmlr tries to write the index
("Writing encoded reference to ...") to a directory to which I don't have writing permission I get a segmentation fault (core dumped) error.
Perhaps this problem could get a nicer error message? Or perhaps an option to specify where to write the index to. It's obviously easy to fix by making a symbolic link of the reference fasta to the current directory.
Cheers,
Wouter
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