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SouthGreenPlatform / culebrONT

A snakemake pipeline to assembly, polishing, correction and quality check from Oxford nanopore reads.

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Error in SystemExit

yi-tingho opened this issue · comments

commented

Hi,

I am trying to run culebrONT for my Oxford Nanopore Technologies reads but I keep running into this error in the Snakefile:
expected str, bytes or os.PathLike object, not bool
SystemExitin line 21 of /home/hxxyit001/culebrONT/lib/python3.9/site-packages/culebrONT/snakefiles/Snakefile. File "/home/hxxyit001/culebrONT/lib/python3.9/site-packages/culebrONT/snakefiles/Snakefile", line 21, in <module> expected str, bytes or os.PathLike object, not bool

How do I debug this error?
Thanks in advance.

commented

Hi can you send Log file please?

commented

Ok the workflow crash because i think something is wrong on your file /scratch/hxxyit001/hins/hinsolens_config.yaml
Can you send your file please.
You install on Local mode I think, but you only mount home as binding and file is in scratch, please also make sure singularity can access to /scratch

commented

I run an sbatch command to run my hins_run.sh file (attached as hins_run.txt) and attached is my .yaml file. I did add a cd function to allow it to access /scratch.
hins_run.txt
hinsolens_config.txt

commented

Thanks,
I see the illumina key was remove, you must keep all key on yaml file but you can leave empty like ILLUMINA: ''
can you change your file /home/hxxyit001/culebrONT/lib/python3.9/site-packages/culebrONT/snakefiles/Snakefile line 12

# GLOBAL VARIABLES
version_CulebrONT = get_version()
try:
    culebront = CulebrONT(workflow, config)
    #pp(culebront)

except Exception as e:
    logger.logger.fatal(e, exc_info=False)
    logging.shutdown()
    raise SystemExit()

TO

# GLOBAL VARIABLES
version_CulebrONT = get_version()
culebront = CulebrONT(workflow, config)
pp(culebront)

The log capture is not full, I want to see where is error on your class CulebrONT

then run again job
you can also remove

  snakemake --nolock --use-singularity --singularity-args "--bind $HOME" \
    --cores -p -s /home/hxxyit001/culebrONT/lib/python3.9/site-packages/culebrONT/snakefiles/Snakefile \
    --latency-wait 6000000 --keep-going --restart-times 0 --rerun-incomplete --configfile /scratch/hxxyit001/hins/hinsolens_config.yaml

from your file hins_run.sh

commented

I added the ILLUMINA: field back in and edited the lines you suggested. See the log file.
SystemExit error w traceback.txt

commented

I think the error happened when path_value (Inside SnakeWrapper._check_dir_or_string) has a falsey value, so using an empty string or False would automatically throw that error

image

commented

No the error is you activate PILON but for PILON you need illumina !!! (mandatory=["KAT", "PILON", "FLAGSTATS"])
please make pilon to false and run again.
sorry normally the error should be more explicit, I will look at the problem.

commented

I deactivated PILON and it ran after including all parameters even those not activated. I did run into another issue error_jobrulegraph.txt. Here is my sh file
run_culebrONT_test.txt. I ran the snakemake command as it also showed that the directory is locked:

Error in rule rule_graph:
jobid: 19
output: /scratch/hxxyit001/test/culebrONT_OUTPUT/FINAL_REPORT/dag.png
log: /scratch/hxxyit001/test/culebrONT_OUTPUT/FINAL_REPORT/LOGS/GRAPH.o, /scratch/hxxyit001/test/culebrONT_OUTPUT/FINAL_REPORT/LOGS/GRAPH.e (check log file(s) for error message)
shell:

    (snakemake -s /home/hxxyit001/culebrONT/lib/python3.9/site-packages/culebrONT/snakefiles/Snakefile --use-singularity   --rulegraph --configfile /scratch/hxxyit001/test/culebrONT_OUTPUT/config_corrected.yaml > /scratch/hxxyit001/test/culebrONT_OUTPUT/FINAL_REPORT/dag.tmp
    dot -Tpng /scratch/hxxyit001/test/culebrONT_OUTPUT/FINAL_REPORT/dag.tmp > /scratch/hxxyit001/test/culebrONT_OUTPUT/FINAL_REPORT/dag.png) 1>/scratch/hxxyit001/test/culebrONT_OUTPUT/FINAL_REPORT/LOGS/GRAPH.o 2>/scratch/hxxyit001/test/culebrONT_OUTPUT/FINAL_REPORT/LOGS/GRAPH.e
    
    (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Logfile /scratch/hxxyit001/test/culebrONT_OUTPUT/FINAL_REPORT/LOGS/GRAPH.o:

Logfile /scratch/hxxyit001/test/culebrONT_OUTPUT/FINAL_REPORT/LOGS/GRAPH.e:
Building DAG of jobs...
Error: Directory cannot be locked. This usually means that another Snakemake instance is running on this directory. Another possibility is that a previous run exited unexpectedly.
/usr/bin/bash: line 2: dot: command not found

Please advise. Thanks in advance.

commented

Hello, the output directory is locked by snakemake. see https://snakemake.readthedocs.io/en/stable/project_info/faq.html#how-does-snakemake-lock-the-working-directory to unlock
the second error is culebrONT need graphviz to build graph.