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FunctionLab / sei-framework

code to run sei and obtain sei and sequence class predictions
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Error Kindly help #11

Closed amitpande74 closed 1 year ago

amitpande74 commented 1 year ago

Hi, I ran the sh script like this sh 1_sequence_prediction.sh /home/amit/Desktop/lingo1/regions/gain.HS.TEs.bed /home/amit/Desktop/lingo1/hg19/hg19.fa /home/amit/Desktop/lingo1/regions/TE_predict 1_sequence_prediction.sh: 20: set: Illegal option -o pipefail Kindly help

kathyxchen commented 1 year ago

It might be a difference in os / shell you are using - can you try removing

set -o errexit
set -o pipefail
set -o nounset

in any of the scripts you use from the repo?

amitpande74 commented 1 year ago

HI, I was able to install the code in an environment with python=3.6. Here is the command I ran

sh 1_sequence_prediction.sh /home/amit/Desktop/lingo1/regions/gain.HS.TEs.bed /home/amit/Desktop/lingo1/regions/TE_predict genome=resources/hg19 Input argments: /home/amit/Desktop/lingo1/regions/gain.HS.TEs.bed genome=resources/hg19 /home/amit/Desktop/lingo1/regions/TE_predict use_cuda: False Traceback (most recent call last):

le "1_sequence_prediction.py", line 72, in <module>
    raise ValueError("--genome=<hg> must be 'hg19' or 'hg38'")
ValueError: --genome=<hg> must be 'hg19' or 'hg38'
kathyxchen commented 1 year ago

You should run it using

sh 1_sequence_prediction.sh /home/amit/Desktop/lingo1/regions/gain.HS.TEs.bed hg19 /home/amit/Desktop/lingo1/regions/TE_predict

I would strongly recommend you run this on a GPU node if you have access to one though. If your BED file is small, you may be able to run it on your computer but it will take a long time.