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jinghuazhao / PW-pipeline

A Pathway Analysis pipeline
https://jinghuazhao.github.io/PW-pipeline/
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Need help to solve : 'Command not found error' #1

Open Manonanthini opened 3 years ago

Manonanthini commented 3 years ago

Hi Jinghuazhao, Thanks for the pipeline. I have been trying to run MAGENTA tool for pathway analysis. I could not find the reason for the error. input_pipeline.sumstats: line 1: SNP: command not found input_pipeline.sumstats: line 2: rs10875231: command not found Please help me to find the reason for the error and to run the tool.

regards Mano

jinghuazhao commented 3 years ago

I haven't worked on this for a while -- MAGENTA requires matlab to be functional; maybe that is the reason?

Manonanthini commented 3 years ago

Thanks for your reply. I have installed the latest version of MATLAB 2020b. I will try with 2017 version also.

On Mon, 1 Feb 2021, 22:19 jinghuazhao, notifications@github.com wrote:

I haven't worked on this for a while -- MAGENTA requires matlab to be functional; maybe that is the reason?

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/jinghuazhao/PW-pipeline/issues/1#issuecomment-771165411, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACPEQJEGVOWD44ZEDLMGDLDS44LFRANCNFSM4W5E6MPA .

jinghuazhao commented 3 years ago

I changed string replacement by sed as with the order of the modified and unmodified files for MAGENTA and it seemed working on the interactive session (in a new environment). I can check for the SLURM part once this is OK.

Manonanthini commented 3 years ago

Ok, thanks. I will also try. Thanks for your support.

On Thu, 4 Feb 2021, 16:07 jinghuazhao, notifications@github.com wrote:

I changed string replacement by sed as with the order of the modified and unmodified files for MAGENTA and it seemed working on the interactive session (in a new environment). I can check for the SLURM part once this is OK.

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/jinghuazhao/PW-pipeline/issues/1#issuecomment-773378338, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACPEQJB5IDXXJVZOSUHDKY3S5KZ4XANCNFSM4W5E6MPA .

jinghuazhao commented 3 years ago

I just revised calls to SLURM but these may be system-specific, e.g., MAGENTA/magenta.slurm.

!/usr/bin/bash

SBATCH --job-name=MAGENTA

SBATCH --account ACCOUNT

SBATCH --partition PARTITION

SBATCH --qos=PARTITION

SBATCH --mem=28800

SBATCH --time=5-00:00:00

SBATCH --output=magenta.out

SBATCH --error=magenta.err

SBATCH --export ALL

matlab -nodisplay -nodesktop -nosplash -nojvm -r "Run_MAGENTA_vs2_July_2011, exit"

Manonanthini commented 3 years ago

Hi Jinghuazhao,

Thanks a lot, I'll check it out. Thank you so much for your time.

Best regards, Mano

On Fri, 5 Feb 2021, 10:24 jinghuazhao, notifications@github.com wrote:

I just revised calls to SLURM but these may be system-specific, e.g., MAGENTA/magenta.slurm.

!/usr/bin/bash

SBATCH --job-name=MAGENTA

SBATCH --account ACCOUNT

SBATCH --partition PARTITION

SBATCH --qos=PARTITION

SBATCH --mem=28800

SBATCH --time=5-00:00:00

SBATCH --output=magenta.out

SBATCH --error=magenta.err

SBATCH --export ALL

matlab -nodisplay -nodesktop -nosplash -nojvm -r "Run_MAGENTA_vs2_July_2011, exit"

— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://github.com/jinghuazhao/PW-pipeline/issues/1#issuecomment-773908336, or unsubscribe https://github.com/notifications/unsubscribe-auth/ACPEQJFXUO4Z6TI5GYQIUXLS5O2OTANCNFSM4W5E6MPA .