OSError: [Errno 30] Read-only file system: '/pipeline/tmp_config.json'

[c-berruto]

Start searching primer for Bacillus_subtilis
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fatal error while working on Bacillus_subtilis check logfile /home/cberruto/speciesprimer_2024_07_29.log
[Errno 30] Read-only file system: '/pipeline/tmp_config.json'
Traceback (most recent call last):
File "/pipeline/speciesprimer.py", line 4168, in main
run_pipeline_for_target(target, config)
File "/pipeline/speciesprimer.py", line 4054, in run_pipeline_for_target
newconfig = DataCollection(config).collect()
File "/pipeline/speciesprimer.py", line 645, in collect
syn, taxid = self.get_taxid(self.target)
File "/pipeline/speciesprimer.py", line 172, in get_taxid
Entrez.email = H.get_email_for_Entrez()
File "/pipeline/basicfunctions.py", line 461, in get_email_for_Entrez
email = user_input_email(email)
File "/pipeline/basicfunctions.py", line 451, in user_input_email
with open(tmp_db_path, 'w') as f:
OSError: [Errno 30] Read-only file system: '/pipeline/tmp_config.json'
Error report:
for target Bacillus_subtilis
Error 1:
fatal error while working on Bacillus_subtilis check logfile /home/cberruto/speciesprimer_2024_07_29.log

Any insight on how to fix this?

[biologger]

Hi,

It looks like you are not using docker for the run, are you running the pipeline locally or on singularity?

For singularity the problem there is that even it can run the docker image the container is read-only and in the current version of speciesprimer tries to write a temporary config file into the container.

Using docker or podman should work with the current version...

Alternativley, adding a CLI option for allowing a custom path for the tmp file for the config in the /primerdesign directory would probably fix this issue for singularity.

[wzacs1]

Alternativley, adding a CLI option for allowing a custom path for the tmp file for the config in the /primerdesign directory would probably fix this issue for singularity.

This would be amazing! I am running through Singularity now and ended here.