crushed when "Splicing in phased SVs"

[yekaizhou]

Hi,

crossstitch will break out in the the stage of splicing in phased SVs, using my data of 8X ONT reads-generated BAM, VCF etc. The memory usage was largely beneath the capacity.

[Ocean-Lyu]

Hi, thanks for developing crossstitch!
I`m having the same issue, and the final.splice.log file outputs like:

-cat final.spliced.log
Reading phased SNPs
Exception in thread "main" java.lang.OutOfMemoryError: Java heap space
at java.base/java.nio.HeapCharBuffer.toString(HeapCharBuffer.java:598)
at java.base/java.nio.CharBuffer.toString(CharBuffer.java:1506)
at java.base/java.util.regex.Matcher.toMatchResult(Matcher.java:274)
at java.base/java.util.Scanner.match(Scanner.java:1399)
at java.base/java.util.Scanner.nextLine(Scanner.java:1652)
at PhaseSVs.runSplicing(PhaseSVs.java:194)
at PhaseSVs.main(PhaseSVs.java:80)

Could you possibly help with this?

[mschatz]

You will need to rerun with more memory. For this you will need to edit crossstitch.sh to increase the memory for the PhaseSV stage with something like: java -Xmx400000m -cp $BINDIR PhaseSVs $PHASEDSNPS $OUTPREFIX.scrubbed.vcf $OUTPREFIX.hairs $OUTPREFIX.spliced.vcf $GENOME >& $OUTPREFIX.spliced.log Good luck! Mike

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On Fri, Dec 15, 2023 at 10:26 PM Ocean-Lyu ***@***.***> wrote: Hi, thanks for developing crossstitch! I`m having the same issue, and the final.splice.log file outputs like: -cat final.spliced.log Reading phased SNPs Exception in thread "main" java.lang.OutOfMemoryError: Java heap space at java.base/java.nio.HeapCharBuffer.toString(HeapCharBuffer.java:598) at java.base/java.nio.CharBuffer.toString(CharBuffer.java:1506) at java.base/java.util.regex.Matcher.toMatchResult(Matcher.java:274) at java.base/java.util.Scanner.match(Scanner.java:1399) at java.base/java.util.Scanner.nextLine(Scanner.java:1652) at PhaseSVs.runSplicing(PhaseSVs.java:194) at PhaseSVs.main(PhaseSVs.java:80) Could you possibly help with this? — Reply to this email directly, view it on GitHub <#14 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AABP3442QFRNXI5ZOMZPBF3YJUIHVAVCNFSM5CHURL5KU5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBVHA3DSOJUGEZA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[Ocean-Lyu]

Thanks for your timely reply! My problem is now solved!