error loading file and segmentation fault about tripal_blast

[laceysanderson]

The Tripal Daemon sometimes has issues with caching. I always try stopping and restarting the daemon when I run into problems with jobs -especially after an update or change.

I've never seen those errors before. There is a known issue with simplexml and very large blast resultsets... Can you check in [your drupal root]/sites/default/files/tripal/tripal_blast for the associated files from the error message. Is the .xml file really empty? and is the .tsv with the same name empty?

[kyrenya]

hi, if it helps, when I stop the daemon and run the job via drush, it occures the same issue.
I tried running the command manually for the blastn job again same database, and it works.
Respect to the files:
the files:
-rw-rw-r-- 1 ubi ubi 0 mar 8 15:52 2019Mar08_155222.blast.tsv
-rw-rw-r-- 1 ubi ubi 0 mar 8 15:52 2019Mar08_155222.blast.xml

[kyrenya]

so, after a lot of trying to debug it, I rebuilt the nucleotide blastdatabase, and despite the steps followed and the input file and output files be exactly the same, (at least they seem so), now it works.
Issue can be closed I guess!

[laceysanderson]

Glad you got it working! Thank you for checking back and letting us know ❤️