#10 Exit code of Scalpel is 0 when child process fails or when external application (samtools, bcftools) fails.

[Luobin Yang]

When samtools or bcftools fail, Scalpel does not exit and report any error code and continues running. Also when Microassembler fails, Scalpel only generates a log message saying child process exit with an error code but it keeps running. In such cases, the log file has to be examined very carefully to determine if Scalpel really finished succesfully or actually failed.

[Giuseppe Narzisi]

Hi Loubin,

thank you for reporting the bug!
I recently become aware of this issue as well.
I plan to address it in the next version of the code, but, at this time, I don't have a release date schedule any time soon.

[Luobin Yang]

Hi, Giuseppe,

Thank you so much for the reply and glad to hear that you will address the
issue in future release! One thing I noticed that is when Microassembler
fails, the error message generate by Microassembler is not printed out to
standard error nor log file. I have to run Microassembler command manually
to figure out what caused the error. It would be nice if the error message
is printed out to standard error and/or log file.

Thanks,
Luobin

On Thu, Mar 16, 2017 at 4:03 PM, Giuseppe Narzisi gnarzisi@users.sf.net
wrote:

Hi Loubin,

thank you for reporting the bug!
I recently become aware of this issue as well.
I plan to address it in the next version of the code, but, at this time, I
don't have a release date schedule any time soon.

---

• [bugs:#10] https://sourceforge.net/p/scalpel/bugs/10/ Exit code of
  Scalpel is 0 when child process fails or when external application
  (samtools, bcftools) fails.*

Status: open
Milestone: 1.0
Created: Thu Mar 16, 2017 06:57 PM UTC by Luobin Yang
Last Updated: Thu Mar 16, 2017 06:57 PM UTC
Owner: nobody

When samtools or bcftools fail, Scalpel does not exit and report any error
code and continues running. Also when Microassembler fails, Scalpel only
generates a log message saying child process exit with an error code but it
keeps running. In such cases, the log file has to be examined very
carefully to determine if Scalpel really finished succesfully or actually
failed.

---

Sent from sourceforge.net because you indicated interest in
https://sourceforge.net/p/scalpel/bugs/10/

To unsubscribe from further messages, please visit
https://sourceforge.net/auth/subscriptions/