Segmentation fault when running tcoffee from website
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I have a script that first generates several files with dna sequences and then iterates over them and calculates a multiple sequence alignment using tcoffee.
This script is started from a website using php with shell_exec
I get the error:
generateSequences.sh: line 29: 8736 Segmentation fault (core dumped) t_coffee -seq $file -n_core 4
However, when I log into the user www-data and start the script with the same command from there, it executes just fine.
In both cases I started the script as
bash generateSequences.sh <options>
I'm guessing there is some apache configuration that I have to change, but I don't know which.
The sequence generation part works even when started from the website, only the call to t_coffee inside of the script results in an error.
I already set the memory_limit to 20GB
Thank you for your help
segmentation-fault apache2 shell-exec
asked Nov 8 at 10:38
alex
445
add a comment |
up vote
0
down vote
favorite
I have a script that first generates several files with dna sequences and then iterates over them and calculates a multiple sequence alignment using tcoffee.
This script is started from a website using php with shell_exec
I get the error:
generateSequences.sh: line 29: 8736 Segmentation fault (core dumped) t_coffee -seq $file -n_core 4
However, when I log into the user www-data and start the script with the same command from there, it executes just fine.
In both cases I started the script as
bash generateSequences.sh <options>
I'm guessing there is some apache configuration that I have to change, but I don't know which.
The sequence generation part works even when started from the website, only the call to t_coffee inside of the script results in an error.
I already set the memory_limit to 20GB
Thank you for your help
segmentation-fault apache2 shell-exec
asked Nov 8 at 10:38
alex
445
add a comment |
up vote
0
down vote
favorite
up vote
0
down vote
favorite
I have a script that first generates several files with dna sequences and then iterates over them and calculates a multiple sequence alignment using tcoffee.
This script is started from a website using php with shell_exec
I get the error:
generateSequences.sh: line 29: 8736 Segmentation fault (core dumped) t_coffee -seq $file -n_core 4
However, when I log into the user www-data and start the script with the same command from there, it executes just fine.
In both cases I started the script as
bash generateSequences.sh <options>
I'm guessing there is some apache configuration that I have to change, but I don't know which.
The sequence generation part works even when started from the website, only the call to t_coffee inside of the script results in an error.
I already set the memory_limit to 20GB
Thank you for your help
segmentation-fault apache2 shell-exec
asked Nov 8 at 10:38
alex
445
I have a script that first generates several files with dna sequences and then iterates over them and calculates a multiple sequence alignment using tcoffee.
This script is started from a website using php with shell_exec
I get the error:
generateSequences.sh: line 29: 8736 Segmentation fault (core dumped) t_coffee -seq $file -n_core 4
However, when I log into the user www-data and start the script with the same command from there, it executes just fine.
In both cases I started the script as
bash generateSequences.sh <options>
I'm guessing there is some apache configuration that I have to change, but I don't know which.
The sequence generation part works even when started from the website, only the call to t_coffee inside of the script results in an error.
I already set the memory_limit to 20GB
Thank you for your help
segmentation-fault apache2 shell-exec
segmentation-fault apache2 shell-exec
asked Nov 8 at 10:38
alex
445
asked Nov 8 at 10:38
alex
445
asked Nov 8 at 10:38
alex
445
asked Nov 8 at 10:38
alex
445
asked Nov 8 at 10:38
alex
445
445
add a comment |
add a comment |
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