Menu ▾ ▴

#313 BOWTIE2 => (ERR): Could not open --un-conc mate-1 output file ... at line 402

v0.9.0
closed
nobody
None
5
2014-06-11
2014-05-19
Daniel N
No

When running Bowtie2 (versions 2.2.2) I get this error (using this command line option: --un-conc '/projects/panel/output/Vvvv-mmm-hhhh-7.1.6uM__1/rrrrr-ffllelll_ttttt/'):

(ERR): Could not open --un-conc mate-1 output file '/projects/panel/output/Vvvv-mmm-hhhh-7.1.6uM__1/rrrrr-ffllelll_ttttt/' at /tools/bowtie2/bowtie2 line 402.
Exiting now ...

BUT if one changes this:
--un-conc '/projects/panel/output/Vvvv-mmm-hhhh-7.1.6uM__1/rrrrr-ffllelll_ttttt/'
into this:
--un-conc '/projects/panel/output/ttttt/'
then Bowtie2 will run just fine (while keeping all the rest of options exactly the same)!

Discussion

  • Daniel N

    Daniel N - 2014-05-19

    It looks like this error appears if there is a dot in the path name given to "--un-conc"!

     

  • Val

    Val - 2014-05-23

    Hi Daniel,

    Thank you for letting us know about this problem. A fix will be available for the next release. Until then a fix proposal can be download it from here: https://github.com/BenLangmead/bowtie2/archive/bugs/313.zip

    thanks,
    Val

     

  • Val

    Val - 2014-06-11
    • Description has changed:

    Diff:

    --- old
+++ new
@@ -1,4 +1,3 @@
-

 When running Bowtie2 (versions 2.2.2) I get this error (using this command line option: --un-conc '/projects/panel/output/Vvvv-mmm-hhhh-7.1.6uM__1/rrrrr-ffllelll_ttttt/'):
    • status: open --> closed
     

Log in to post a comment.