Error running test again

[aebaci]

Hi:
I ran the test_odp_basic, and I got an error in job 16 (unfortunately I didn't save it). I tried to run it again but I get the following error immediately, even after erasing the folders and files created in that first run:

Building DAG of jobs...
LockException:
Error: Directory cannot be locked. Please make sure that no other Snakemake process is trying to create the same files in the following directory:
/home/antonella/odp/tests/test_odp_basic
If you are sure that no other instances of snakemake are running on this directory, the remaining lock was likely caused by a kill signal or a power loss. It can be removed with the --unlock argument.

I tried running ./test_odp_basic.sh --unlock
but the same happened (not sure if that's the way to do it).

Any help would be appreciated, thanks.

[aebaci]

Thanks for the quick reply, but my Windows laptop doesn't allow me to download it. I can't copy the link to the file either to download it directly in linux ...

In the meantime, the first error was the following (I installed it in two machines, one of which is giving me the re-run error now, and the other has the same as before):

make the black dots a little lighter

All the Hydra scaffolds have been identified in a connected component, continuing
All the Urchin scaffolds have been identified in a connected component, continuing
/home/ml208s/odp/tests/test_odp_basic/../../scripts/odp:1313: UserWarning: Starting a Matplotlib GUI outside of the main thread will likely fail.

make the black dots a little lighter

All the BCnS_LGs scaffolds have been identified in a connected component, continuing
All the Urchin scaffolds have been identified in a connected component, continuing
/home/ml208s/odp/tests/test_odp_basic/../../scripts/odp:1313: UserWarning: Starting a Matplotlib GUI outside of the main thread will likely fail.

make the black dots a little lighter

QObject::killTimer: Timers cannot be stopped from another thread
Segmentation fault (core dumped)
[Wed Sep 4 14:43:08 2024]
Error in rule plot_synteny_nocolor:
jobid: 16
input: odp/step1-rbh/Hydra_Urchin_reciprocal_best_hits.D.FET.rbh, odp/step0-chromsize/analyses/Hydra_Urchin.chromsize
output: odp/step2-figures/synteny_nocolor/Hydra_Urchin_xy_reciprocal_best_hits.plotted.rbh, odp/step2-figures/synteny_nocolor/Hydra_Urchin_xy_synteny.pdf, odp/step2-figures/synteny_nocolor/Hydra_Urchin_yx_synteny.pdf

Removing output files of failed job plot_synteny_nocolor since they might be corrupted:
odp/step2-figures/synteny_nocolor/Hydra_Urchin_xy_reciprocal_best_hits.plotted.rbh, odp/step2-figures/synteny_nocolor/Hydra_Urchin_xy_synteny.pdf, odp/step2-figures/synteny_nocolor/Hydra_Urchin_yx_synteny.pdf
QObject::killTimer: Timers cannot be stopped from another thread
Segmentation fault (core dumped)
[Wed Sep 4 14:43:12 2024]
Error in rule plot_synteny_of_ALGs_plus_species:
jobid: 47
input: odp/step1-rbh/BCnS_LGs_Urchin_reciprocal_best_hits.hmm.D.FET.rbh, odp/step0-chromsize/species/Urchin.chromsize
output: odp/step2-figures/ALG-species_plots/BCnS_LGs_Urchin_xy_reciprocal_best_hits.plotted.rbh, odp/step2-figures/ALG-species_plots/BCnS_LGs_Urchin_xy_synteny.pdf, odp/step2-figures/ALG-species_plots/BCnS_LGs_Urchin_yx_synteny.pdf

Removing output files of failed job plot_synteny_of_ALGs_plus_species since they might be corrupted:
odp/step2-figures/ALG-species_plots/BCnS_LGs_Urchin_xy_reciprocal_best_hits.plotted.rbh, odp/step2-figures/ALG-species_plots/BCnS_LGs_Urchin_xy_synteny.pdf, odp/step2-figures/ALG-species_plots/BCnS_LGs_Urchin_yx_synteny.pdf
[Wed Sep 4 14:43:50 2024]
Finished job 46.
2 of 48 steps (4%) done
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-09-04T144258.989213.snakemake.log
WorkflowError:
At least one job did not complete successfully.