Issues with the installation

[ChiaraCampanelli]

Unfortunately I keep having issues with the installation of the tool. Even if it seems to work, at some point it gets stuck.
This is the .log file and the part of the process where quast stops:

136541_shasta_racon_trimmed.fastq -r GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -o quast_haploid --threads 18

Version: 5.2.0

System information:
OS: Linux-4.18.0-425.13.1.el8_7.x86_64-x86_64-with-glibc2.35 (linux_64)
Python version: 3.10.12
CPUs number: 72

Started: 2023-11-16 17:05:20

Logging to /lustre1/project/stg_00124/Chiara/tmp/df/3cdbd1d92d786ea20cdfbbfa7da3e4/quast_haploid/quast.log

CWD: /lustre1/project/stg_00124/Chiara/tmp/df/3cdbd1d92d786ea20cdfbbfa7da3e4
Main parameters:
MODE: default, threads: 18, min contig length: 500, min alignment length: 65, min alignment IDY: 95.0,
ambiguity: one, min local misassembly length: 200, min extensive misassembly length: 1000

Reference:
GCA_000001405.15_GRCh38_no_alt_analysis_set.fna ==> GCA_000001405.15_GRCh38_no_alt_analysis_set

Contigs:
Pre-processing...
polished_assembly.fasta ==> polished_assembly

2023-11-16 17:07:45
Running Reads analyzer...
Logging to files /lustre1/project/stg_00124/Chiara/tmp/df/3cdbd1d92d786ea20cdfbbfa7da3e4/quast_haploid/reads_stats/reads_stats.log and /lustre1/project/stg_00124/Chiara/tmp/df/3cdbd1d92d786ea20cdfbbfa7da3e4/quast_haploid/reads_stats/reads_stats.err...
Will not search Structural Variations (needs paired-end reads)
Pre-processing reads...
Running BWA...
Pre-processing reads...
Running BWA for reference...

I also want to show you the Dockerfile I used to install it:

FROM ubuntu:latest

ENV DEBIAN_FRONTEND noninteractive
RUN chmod ugo+rwx -R /usr/
RUN apt-get update
RUN apt-get install -y apt-utils make wget bzip2 gcc git libncurses5-dev bzip2 libhts-dev libbz2-dev liblzma-dev zlib1g-dev pkg-config libfreetype6-dev libpng-dev python3-matplotlib wget git python3-pip

RUN wget https://github.com/ablab/quast/releases/download/quast_5.2.0/quast-5.2.0.tar.gz
RUN tar -xzf quast-5.2.0.tar.gz
RUN ln -s  /usr/lib/x86_64-linux-gnu/libidn2.so.0.3.7 /usr/lib/x86_64-linux-gnu/libidn11.so
RUN apt install python-is-python3

WORKDIR /quast-5.2.0
RUN python3 ./setup.py install_full

RUN sed -i 's/const uint8_t rle_auxtab/extern const uint8_t rle_auxtab/' /usr/local/lib/python3.10/dist-packages/quast-5.2.0-py3.10.egg/quast_libs/bwa/rle.h
WORKDIR /usr/local/lib/python3.10/dist-packages/quast-5.2.0-py3.10.egg/quast_libs/bwa
RUN make

WORKDIR /usr/local/lib/python3.10/dist-packages/quast-5.2.0-py3.10.egg/quast_libs/bedtools
RUN make

RUN sed -i 's/const uint8_t rle_auxtab/extern const uint8_t rle_auxtab/' /quast-5.2.0/quast_libs/bwa/rle.h
WORKDIR /quast-5.2.0/quast_libs/bwa
RUN make

WORKDIR /quast-5.2.0/quast_libs/bedtools
RUN make

WORKDIR /quast-5.2.0

Originally posted by @ChiaraCampanelli in #255 (comment)