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a-ludi / dentist

Close assembly gaps using long-reads at high accuracy.
https://a-ludi.github.io/dentist/
MIT License
47 stars 6 forks source link

MissingOutputException error #25

Open shri1984 opened 3 years ago

shri1984 commented 3 years ago

Hi, I am using HiFi data to fill the gaps in a scaffold assembly. I get this error. I changed the latency to 15s from 5s I am running it from a non-singularity source. MissingOutputException in line 984 of /scratchdata/shripathi/dentist.v2.0.0.x86_64/Snakefile: Job Missing files after 15 seconds: workdir/assembly.assembly.las This might be due to filesystem latency. If that is the case, consider to increase the wait time with --latency-wait. Job id: 13 completed successfully, but some output files are missing. 13 Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message

a-ludi commented 3 years ago

Hi, can you confirm the inexistence of that file? Is the file system accessible by both the compute node and head node? Can you check the number of blocks in the reference with cat workdir/assembly.dam?