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[Errno 30] Read-only file system: '/usr/local/lib/python3.10/dist-packages/quast_libs/bwa/make.log' #255
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Long story short, two workarounds:
In more detail: |
Unfortunately I keep having issues with the installation of the tool. Even if it seems to work, at some point it gets stuck. 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: 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 Reference: Contigs: 2023-11-16 17:07:45 I also want to show you the Dockerfile I used to install it:
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The error appears when options parameters have been used. If I run QUAST just by giving in input only the assembly, everything works properly.
For more details:
[Errno 30] Read-only file system: '/usr/local/lib/python3.10/dist-packages/quast_libs/bwa/make.log'
Traceback (most recent call last):
File "/usr/local/bin/quast.py", line 309, in
return_code = main(sys.argv[1:])
File "/usr/local/bin/quast.py", line 118, in main
bed_fpath, cov_fpath, physical_cov_fpath = reads_analyzer.do(ref_fpath, contigs_fpaths,
File "/usr/local/lib/python3.10/dist-packages/quast_libs/reads_analyzer.py", line 928, in do
if not compile_reads_analyzer_tools(logger):
File "/usr/local/lib/python3.10/dist-packages/quast_libs/ra_utils/misc.py", line 115, in compile_reads_analyzer_tools
if compile_bwa(logger, only_clean) and compile_bedtools(logger, only_clean) and compile_minimap(logger, only_clean):
File "/usr/local/lib/python3.10/dist-packages/quast_libs/ra_utils/misc.py", line 86, in compile_bwa
return bwa_fpath('bwa') or compile_tool('BWA', bwa_dirpath, ['bwa'], only_clean=only_clean, logger=logger)
File "/usr/local/lib/python3.10/dist-packages/quast_libs/qutils.py", line 886, in compile_tool
open(make_logs_basepath + '.log', 'w').close()
OSError: [Errno 30] Read-only file system: '/usr/local/lib/python3.10/dist-packages/quast_libs/bwa/make.log'
By changing the permissions, the error keeps showing.
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