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Running quast with apython or bash script: ERROR! File not found (contigs) #226

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Pepaflores56 opened this issue Sep 29, 2022 · 0 comments

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@Pepaflores56
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I am trying to develop a pipeline, and I would like to include quast for quality assembly. If I run quast with the above script, everything is good.

python ~/my_project/project_requirements/quast-5.2.0/quast.py -o ~/my_project/test_assemblies/q_results/ -L ~/my_project/test_assemblies/unicycler_assemblies/*/*.fasta -r ~/my_project/project_requirements/ref_file.fasta

However, if I try to run quast with the bash script below (sorry, the hpc I am working has an old version of quast), and the command line for script is for i in cat my_file.txt;do quash.sh ${i};done but I get an error about not finding the contings. Another approach, and the one I would like to use is a python script, which I attach but still have the same errors. Can anyone help me to solve this issue, please? Thanks

#!/bin/bash
#$ -S /bin/sh
#$ -N quast
#$ -q researchsmall.q
#$ -pe multithread 4
. /etc/profile.d/modules.sh
module purge
module load python/2.7
module load quast
quast.py -o /home/my_name/my_project/test_assemblies/q_results/ -R /home/my_name/my_project/project_requirements/ref_file.fasta  /home/my_name/my_project/unicycler_assemblies/${1}/assembly.fasta

quast.e2660653.txt
quality_quast.txt

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