Closed shameem356 closed 5 years ago
Hi,
Looks like Ragout can't find hal executables. Maybe your .bashrc was not loaded? Please check the output of which halStats
and also echo $PATH
to make sure the environment was loaded properly. You can also apply export
commands directly into the current bash session to check if it's working properly.
Best, Mikhail
Hello @fenderglass ,
I checked .bashrc file and it is loaded properly . I checked which halStats and also echo $PATH after getting the "hal is not installed" error message (See below).And still the problem remain.I have the following list of hal executable files in my PATH.Please let me know if I missed any hal executable file which causing the error
Hal Executable file :
Ragout]$ bin/ragout -s hal --refine hal_example/hal_example/cholerae.rcp -o out [09:56:58] INFO: Starting Ragout v2.2 [09:56:58] ERROR: An error occured while running Ragout: [09:56:58] ERROR: "hal" is not installed.
which halStats /data/labs/genomics_lab/shared/apps/HAL/hal/bin/halStats
echo $PATH /data/labs/genomics_lab/shared/apps/HAL/hal/bin:/data/apps/software/perl-5.26.0/site/bin:/data/apps/software/perl-5.26.0/bin:/data/apps/software/R-3.4.4/bin/Rscript:/data/apps/software/R-3.4.4/bin:/data/apps/software/java/jdk1.8.0_191/bin:/data/apps/software/samtools-1.3/bin:/data/labs/genomics_lab/shared/apps/hdf5-1.10.1/hdf5/bin:/opt/advcomp/bin:/usr/lib64/openmpi/bin:/usr/lib64/nagios/plugins:/usr/lpp/mmfs/bin:/opt/bin:/opt/sbin:/usr/local/bin:/usr/bin:/usr/local/sbin:/usr/sbin:/opt/ibutils/bin:/data/labs/genomics_lab/shared/shameem/apps/php-5.6/sapi/cli
Thank you! It seems that halStats
and hal2fasta
are indeed in your PATH. Could you also double check they are executable by invoking them? (sometimes file permissions could be messed up).
Also, I don't see hal2mafMP.py
script in your PATH - I think this might be the issue. I think it should be placed in the hal/bin
directory, but maybe the location has changed in the recent HAL releases? Which version are you using?
I tried with HAL V2.1 and V2.0. Both are having same problem. Please can you check the ragout running status with these versions of HAL.OR please let me know which HAL version will be suitable of Ragout ?
I am using HAL 2.1.
Please double check that hal is properly installed by invoking halStats
, hal2fasta
and hal2mafMP.py
commands and post the output of all three commands here.
solved the file. Actual problem was related to hal2mafMP.py. In HAL installation , hal2mafMP.py was located in maf folder. I copied hal2mafMP.py file to bin folder from maf and it solved the problem.
@fenderglass : Thank you so much your time and quick helps.
Hello Team & @fenderglass
I tried to run ragout with hal option. But I am getting the following error. I have properly installed hal software and added the PATH and PYTHONPTH in ~/.bashrc file.
Ragout command : bin/ragout -s hal --refine hal_example/hal_example/cholerae.rcp -o out
PATH setting command in bashrc export PYTHONPATH=/data/labs/genomics_lab/shared/apps/HAL/hal/:$PYTHONPATH export PATH=/data/labs/genomics_lab/shared/apps/HAL/hal/bin/:$PATH
Error Message :
[15:56:26] INFO: Starting Ragout v2.2 [15:56:26] ERROR: An error occured while running Ragout: [15:56:26] ERROR: "hal" is not installed.
Please can you let me know how to solve this issue.