broadinstitute / pilon

Pilon is an automated genome assembly improvement and variant detection tool

GNU General Public License v2.0

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No output file or directory #119

Open cmaggior opened 4 years ago

cmaggior commented 4 years ago

Hello,

I'm using Pilon to polish a metagenome with the following input:

java -jar $EBROOTPILON/pilon-1.23.jar --genome contigs_500.fasta --bam S1.sorted.bam --output pilon_1pair.fa

However no output file is generated, nor a log file. Can anyone please advise?

adc0032 commented 4 years ago

Hi! I'm having the same issue as above My input: pilon -Xmx1400G --genome myassembly.fa --bam myassembly.mybarcodedreads.bam --changes --vcf --diploid --threads 35 --verbose --output myassembly_polished.fa

I'm running the job interactively and I see that the program is doing something correctly: `#fixBreak: 394826:3660-4064 L=1 R=1 S=0

fixBreak: 978:280013-280029

L=1 R=1 S=0

fixBreak: 525425:43728-44186

L=2 R=1`

But i have no output files

iremdnzl commented 1 year ago

did you solve the problem? I'm having the same issue!

cmaggior commented 1 year ago

No, I never did :/

XuhangWu commented 7 months ago

did you solve the problem? I'm having the same issue!

I tried to trouble shooting it for two days now, finally figured out the problem i have. Remember that available system memory also plays a role, so ensure that the allocated memory does not exceed the physical memory available on your machine to avoid swapping and performance degradation.

So as i have a 32G ram laptop, i had to change -Xmx50G to -Xmx32G to be able to get the output file.