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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
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? Thanksquast.e2660653.txt
quality_quast.txt
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