Hello,
i did run mercat2 and got followed errors:
Runnnig mercat2 with fastqsanger files and -prod flag produced followed error:
2025-02-24 11:59:15,333 WARNING services.py:1832 -- WARNING: The object store is using /tmp/tmpwxtzbi9v/tmp instead of /dev/shm because /dev/shm has only 67108864 bytes available. This will harm performance! You may be able to free up space by deleting files in /dev/shm. If you are inside a Docker container, you can increase /dev/shm size by passing '--shm-size=5.05gb' to 'docker run' (or add it to the run_options list in a Ray cluster config). Make sure to set this to more than 30% of available RAM.
2025-02-24 11:59:15,333 INFO worker.py:1612 -- Started a local Ray instance. View the dashboard at �[1m�[32m127.0.0.1:8265 �[39m�[22m
Traceback (most recent call last):
File "/usr/local/bin/mercat2.py", line 508, in <module>
mercat_main()
File "/usr/local/bin/mercat2.py", line 471, in mercat_main
figPlots = mercat2_figures.plot_sample_metrics(samples[sample_type], tsv_out)
File "/usr/local/lib/python3.10/site-packages/mercat2_lib/mercat2_figures.py", line 185, in plot_sample_metrics
dfMetrics.sort_values(by='Length', ascending=False, inplace=True)
File "/usr/local/lib/python3.10/site-packages/pandas/core/frame.py", line 7176, in sort_values
k = self._get_label_or_level_values(by[0], axis=axis)
File "/usr/local/lib/python3.10/site-packages/pandas/core/generic.py", line 1910, in _get_label_or_level_values
raise KeyError(key)
KeyError: 'Length'
using the -fgs flag produce followed error:
2025-02-24 11:53:07,132 WARNING services.py:1832 -- WARNING: The object store is using /tmp/tmpwxtzbi9v/tmp instead of /dev/shm because /dev/shm has only 67108864 bytes available. This will harm performance! You may be able to free up space by deleting files in /dev/shm. If you are inside a Docker container, you can increase /dev/shm size by passing '--shm-size=5.05gb' to 'docker run' (or add it to the run_options list in a Ray cluster config). Make sure to set this to more than 30% of available RAM.
2025-02-24 11:53:07,132 INFO worker.py:1612 -- Started a local Ray instance. View the dashboard at �[1m�[32m127.0.0.1:8265 �[39m�[22m
Traceback (most recent call last):
File "/usr/local/bin/mercat2.py", line 508, in <module>
mercat_main()
File "/usr/local/bin/mercat2.py", line 403, in mercat_main
ret = ray.get(ready[0])
File "/usr/local/lib/python3.10/site-packages/ray/_private/auto_init_hook.py", line 24, in auto_init_wrapper
return fn(*args, **kwargs)
File "/usr/local/lib/python3.10/site-packages/ray/_private/client_mode_hook.py", line 103, in wrapper
return func(*args, **kwargs)
File "/usr/local/lib/python3.10/site-packages/ray/_private/worker.py", line 2524, in get
raise value.as_instanceof_cause()
ray.exceptions.RayTaskError(PermissionError): �[36mray::orf_call_fgs()�[39m (pid=126, ip=172.17.0.2)
File "/usr/local/bin/mercat2.py", line 394, in orf_call_fgs
return mercat2_fasta.orf_call_fgs(basename, file, outpath)
File "/usr/local/lib/python3.10/site-packages/mercat2_lib/mercat2_fasta.py", line 259, in orf_call_fgs
fgs.extractall(PATH_FGS)
File "/usr/local/lib/python3.10/tarfile.py", line 2264, in extractall
self._extract_one(tarinfo, path, set_attrs=not tarinfo.isdir(),
File "/usr/local/lib/python3.10/tarfile.py", line 2331, in _extract_one
self._handle_fatal_error(e)
File "/usr/local/lib/python3.10/tarfile.py", line 2327, in _extract_one
self._extract_member(tarinfo, os.path.join(path, tarinfo.name),
File "/usr/local/lib/python3.10/tarfile.py", line 2410, in _extract_member
self.makefile(tarinfo, targetpath)
File "/usr/local/lib/python3.10/tarfile.py", line 2455, in makefile
with bltn_open(targetpath, "wb") as target:
PermissionError: [Errno 13] Permission denied: '/usr/local/lib/python3.10/site-packages/mercat2_lib/FGS/FragGeneScanRs'
and the last error i get is using fastqsanger files without any other flag is that certain files are not genreted:
clean
report
tsv_nucleotide
This is the only content created by mercat2 combined_Nucleotide.tsv is missing in this case.
Is this know and if so is there any fix to this? I use the latest bioconder version of mercat2 (1.4.1) and this is the docker used
REPOSITORY TAG IMAGE ID CREATED SIZE
quay.io/biocontainers/mercat2 1.4.1--pyhdfd78af_0 4f4b48dacdfc 11 months ago 2.3GB
Hello,
i did run mercat2 and got followed errors:
Runnnig mercat2 with fastqsanger files and
-prodflag produced followed error:using the
-fgsflag produce followed error:and the last error i get is using fastqsanger files without any other flag is that certain files are not genreted:
This is the only content created by mercat2
combined_Nucleotide.tsvis missing in this case.Is this know and if so is there any fix to this? I use the latest bioconder version of mercat2 (1.4.1) and this is the docker used