marbl / canu

A single molecule sequence assembler for genomes large and small.
http://canu.readthedocs.io/
644 stars 177 forks source link

Something goes wrong when I use canu. Help me plz #2315

Closed helloworldABCD1234 closed 1 month ago

helloworldABCD1234 commented 1 month ago

Something goes wrong when I use canu. Help me plz

-- Detected Java(TM) Runtime Environment '18.0.2.1' (from '/APP/apps/jdk/18.0.2.1/bin/java') without -d64 support.
-- WARNING:  Failed to run gnuplot using command 'gnuplot'.
-- WARNING:  Plots will be disabled.

-- Stages to run:
-- assemble HiFi reads.
-- Correction skipped; not enabled.
-- Trimming skipped; not enabled.

3.
sbatch: error: Batch job submission failed: Invalid account or account/partition combination specified
----------------------------------------
ERROR:
ERROR:  Failed with exit code 1.  (rc=256)
ERROR:
-- Failed to submit Canu executive.  Delay 10 seconds and try again.
----------------------------------------

What should I do.

1 2 3

skoren commented 1 month ago

It's a good idea to check other issues and the documentation for similar cases (e.g. #1810, #1330). As listed on the FAQ: https://canu.readthedocs.io/en/latest/faq.html#how-do-i-run-canu-on-my-slurm-sge-pbs-lsf-torque-system, Canu will not request specific partitions/queues and will try to submit to the default partition. It looks like your cluster requires something else, you have whatever account/partition you want Canu to use yourself using gridOptions (e.g. `gridOptions="<however your grid requires you to specify account/partition>".

As for the gnuplot, it is optional and canu will run fine without it, you just won't get some plots in your outputs.

skoren commented 1 month ago

Idle