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enasequence / webin-cli

Webin command line submission program.
Apache License 2.0
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java.lang.OutOfMemoryError when submitting read data submissions (Fastq) #34

Open tuxskar opened 4 years ago

tuxskar commented 4 years ago

I was trying to submit a read data with the same user and password I used to be doing it in the past but I got an error java.lang.OutOfMemoryError pointing that I should review the files at validate folder.

Checking the folder, I can see a single file but it is empty, I'm sharing the trace execution of the command here:

INFO : Your application version is 3.1.0
INFO : For SARS-CoV-2 data submissions, users should contact us in advance of submission at virus-dataflow@ebi.ac.uk for specific advice on options and to access the highest levels of support.
INFO : Creating report file: C:\Users\user\webin\Lecturas\.\webin-cli.report
INFO : Field "INSTRUMENT" value "Illumina miSeq" was corrected to "Illumina MiSeq". [manifest file: C:\Users\user\webin\Lecturas\manifest.txt, line number: 4, field: INSTRUMENT, value: Illumina miSeq]
INFO : Submission has not been validated previously.
ERROR: Submission validation failed because of a system error: java.lang.OutOfMemoryError: Java heap space. Please check validation reports for further information: C:\Users\user\webin\Lecturas\reads\RawReads_EAR8\validate

I also tried increasing the allocated memory to my local JVM to 2 GB but during the execution of the command I can't see any pressure increase on it so I guess this error in on the submission server side.

Could I please get some help?

raskoleinonen commented 3 years ago

Apologies for this very late answer. The:

java.lang.OutOfMemoryError

is caused by Webin-CLI on the client side running out of memory and increasing the JVM memory should help with this.