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mozack / abra

Assembly Based ReAligner
MIT License
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No contigs assembled: no space left on device #43

Closed toddcreasy closed 5 years ago

toddcreasy commented 5 years ago

I'm getting the below error when running ABRA1. The command is also below. Has anyone seen this before? There is sufficient disk space in the directory so I'm not sure why I'm getting this java error.

java -Xmx16G -jar abra-0.97.jar --in normal.bam,tumor.bam --out normal_ABRA.bam,tumor_ABRA.bam --ref hg38.fa --bwa-ref BWAIndex/hg38 --targets Regions.hg38.bed --threads 8 --working abra_temp_dir --sv abra.sv.txt

Mon Nov 26 14:17:42 EST 2018 : WARNING! No contigs assembled. Just making a copy of input converting to/from SAM/BAM as appropriate. Exception in thread "main" htsjdk.samtools.util.RuntimeIOException: java.io.IOException: No space left on device at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:245) at htsjdk.samtools.util.SortingCollection.add(SortingCollection.java:165) at htsjdk.samtools.SAMFileWriterImpl.addAlignment(SAMFileWriterImpl.java:180) at abra.ReAligner.copySam(ReAligner.java:384) at abra.ReAligner.reAlign(ReAligner.java:229) at abra.ReAligner.run(ReAligner.java:1240) at abra.Abra.main(Abra.java:12) Caused by: java.io.IOException: No space left on device at java.io.FileOutputStream.writeBytes(Native Method) at java.io.FileOutputStream.write(FileOutputStream.java:326) at java.io.BufferedOutputStream.flushBuffer(BufferedOutputStream.java:82) at java.io.BufferedOutputStream.flush(BufferedOutputStream.java:140) at java.io.FilterOutputStream.close(FilterOutputStream.java:158) at htsjdk.samtools.util.SortingCollection.spillToDisk(SortingCollection.java:236) ... 6 more

toddcreasy commented 5 years ago

Nevermind. I was able to successfully use ABRA2