External MBEDTLS version mismatch with Julia but not with bash
Hello
I am running a shell script that launches blastx. From terminal it works but launching the script from Julia gives this error:
julia> x_blast = read(pipeline(`.../fetcher.sh`), String)
Critical: [blastx] External MBEDTLS version mismatch: 2.16.0 headers vs. 2.16.2 runtime
would you know what it is about?
• 2,209 views
•
link
updated
by
Biostar
•
written
by
marongiu.luigi
•
written
by
marongiu.luigi
0 answers
No answers yet.
Log in to answer this question.
More posts like this
-
Tutorial: ABodyBuilder2 on macOS: OMP Error #15 libomp.dylib already initialized (Abort trap: 6)
written by parthivrajesh •
-
GATK BQSR error — Reference and BAM file chromosome name mismatch (“chr” vs. no “chr”)
written by iamsmor •
-
MISO Sorted BAM file header mismatch
written by bimeva5703 •
-
remote command line BLAST job ends in CPU error and gives MBEDTLS version mismatch
written by janneken0210 •
-
Building a BLAST database with the python subprocess module
written by timothy.kirkwood •
-
Error running blastn on Linux: Critical [blastn] External MBEDTLS version mismatch: 2.16.2 headers …
written by 2jackcummins •
-
Tutorial: How to run CWL with Nextflow
written by steve
-
Error in the "autoNoise0" stage while doing de novo assembly of Bionano data
written by Ritu •
-
Passing multiple arguments to external programs in a Pipeline with Python
written by barslmn •
-
Tutorial: Minimum Standards For Bioinformatics Command Line Tools
written by Medhat
Most commands that "work when run on the shell but don't work when a wrapper is added" probably stop working because they rely on one of the dot file settings. In your case, probably, there is a
PATHvariable that needs to be read in for the command to find the right version of a tool.Try running the same command using
bash --noprofile -c "<command>"and if that fails, you'll know that the problem is caused by a dotfile setting.I tried with
Try running the
bash --noprofilecommand from the shell, not from within Julia. You're debugging a dot file related problem and trying to do that while maintaining a wrapper, which makes no sense. Please try and understand what you're doing before you try to do it.is this correct
.../?it is the short for the real path, which is a bit long.
I guess
...is aliased to../../. That could be causing a problem too, but doesn't look like it.Do you set or modify any environment variable before running the script on the command line? Do you have to load something with
module load xxx-yyy? What is the content of thefetch.shscript?You can speed up a lot the process of getting help if you are more careful and detailed when asking questions.