bamqc out of memory with 38G of java-mem-size

[Esther Kockelmans]

Hey there,

I am using qualimap for analyzing an alignment I made using minimap2.

Although, with every --java-mem-size possible, I get an "out of memory" warning.

This is the command line I use:

/home/hsl_s1101570/software/qualimap_v2.2.1/qualimap \
bamqc -bam alignment_bs_sf.sorted.bam --java-mem-size=38G -outdir qualimap_results

and this is the error (that occurs with every mem size):

Java memory size is set to 38G
Launching application...

OpenJDK 64-Bit Server VM warning: ignoring option MaxPermSize=1024m; support was removed in 8.0
QualiMap v.2.2.1
Built on 2016-10-03 18:14

Selected tool: bamqc
Available memory (Mb): 32
Max memory (Mb): 36268
Mon Nov 22 13:14:28 CET 2021            WARNING Output folder already exists, the results will be saved there

Starting bam qc....
Loading sam header...
Loading locator...
Loading reference...
Number of windows: 400, effective number of windows: 1881
Chunk of reads size: 1000
Number of threads: 16
Processed 188 out of 1881 windows...
Processed 376 out of 1881 windows...
Processed 564 out of 1881 windows...
Processed 752 out of 1881 windows...
Processed 940 out of 1881 windows...
Processed 1128 out of 1881 windows...
Processed 1316 out of 1881 windows...
Processed 1504 out of 1881 windows...
Processed 1692 out of 1881 windows...
Processed 1880 out of 1881 windows...
Total processed windows:1881
Number of reads: 7435
Number of valid reads: 5262
Number of correct strand reads:0

Inside of regions...
Num mapped reads: 5262
Num mapped first of pair: 0
Num mapped second of pair: 0
Num singletons: 0
Time taken to analyze reads: 176
Computing descriptors...
numberOfMappedBases: 7324977
referenceSize: 691780295
numberOfSequencedBases: 7092255
numberOfAs: 1654269
Computing per chromosome statistics...
Computing histograms...
Overall analysis time: 239
end of bam qc
Computing report...

WARNING: out of memory!
Qualimap allows to set RAM size using special argument: --java-mem-size
Check more details using --help command or read the manual.

Also, the output doesn't come with an html page, only a "genome_results.txt" file.

Do you know how I can fix this?

Hope to hear from you soon.

Kind regards,
Esther