lanl001
ERROR: Failed to run HALC:Unknown error 35584
Hi guys,
I've been trying to use Halc for hybrid error correction of PacBio reads. The program has split my raw PB reads into 80 chunks and has successfully finished steps 1 and 2 of the pipeline. While running step3 on the 80 batches, the program finishes the first 7 batches correctly and then crashes with the 8th one. I have repeated the command and can see that the error always happens at the same point. Unfortunately the error output is not very informative and the actual error inside the step3 directory looks like an incomplete file, so I have no clue what seems to be the problem.
The content of HALC_8.err is the following:
boundary = 4
coverage = auto
width = 4
threads = 32
out = ./temp/step3/
prefix = pb-008
repeatfree = false
Making hashmap for long reads...
Running time: 0h 0min 1s
Making hashmap for contigs...
Running time: 0h 0min 45s
Reading map result...
Running time: 0h 0min 29s
Preprocessing...
Running time: 0h 1min 14s
Generating subcontigs...
Running time: 0h 0min 2s
Building graph...
Any suggestions would be more than welcome.
Kind regards,
Juan Montenegro
Dear Juan, I am having exactly the same problem with the majority of my 800+ jobs. Have you been able to find a solution? Thanks, Mark
Hi Marc, Unfortunately I haven't and went back to using prooveread for hybrid error correction. Cheers, Juan D.
On Sun, 10 Jun 2018, 4:03 AM MarkChristianHarrison [email protected] wrote:
Dear Juan, I am having exactly the same problem with the majority of my 800+ jobs. Have you been able to find a solution? Thanks, Mark
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