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mikolmogorov / Ragout

Chromosome-level scaffolding using multiple references
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ERROR: "hal" is not installed. #45

Closed shameem356 closed 5 years ago

shameem356 commented 5 years ago

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.

mikolmogorov commented 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

shameem356 commented 5 years ago

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

mikolmogorov commented 5 years ago

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?

shameem356 commented 5 years ago

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 ?

mikolmogorov commented 5 years ago

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.

shameem356 commented 5 years ago

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.