I'm getting an error in the output files when I call IlluminaBasecallsToSam
java -Xmx40g -jar IlluminaBasecallsToSam.jar \
BASECALLS_DIR=/MyFolder/Data/Intensities/BaseCalls \
BARCODES_DIR=/MyFolder/MyDir \
LANE=1 \
READ_STRUCTURE="101T8B101T" \
LIBRARY_PARAMS=/MyFolder/library_params.txt \
RUN_BARCODE=MY_BARCODE \
NUM_PROCESSORS=4 \
ADAPTERS_TO_CHECK="PAIRED_END" \
MAX_READS_IN_RAM_PER_TILE=100000 \
MAX_RECORDS_IN_RAM=100000 \
FORCE_GC=false
If I specify .bam format in the library_params.txt I get an error:
Exception in thread "main" htsjdk.samtools.util.RuntimeIOException:
Terminator block not found after closing BGZF file /MyFolder/my_sample.bam
at htsjdk.samtools.util.BinaryCodec.close(BinaryCodec.java:610)
at htsjdk.samtools.BAMFileWriter.finish(BAMFileWriter.java:136)
at htsjdk.samtools.SAMFileWriterImpl.close(SAMFileWriterImpl.java:205)
...
If I specify .sam format in the library_params.txt I don't get any errors
when I check the log:
INFO 2014-11-20 11:16:49 IlluminaBasecallsConverter All work is complete.
[Thu Nov 20 11:16:50 EST 2014] picard.illumina.IlluminaBasecallsToSam done.
Elapsed time: 56.49 minutes.
Runtime.totalMemory()=14310244352
But the header of the sam file is corrupt:
hexdump /MyFolder/my_sample.sam | head -n5
0000000 0000 0000 0000 0000 0000 0000 0000 0000
*
33ff00000 4354 4347 4341 5443 4341 4343 4143 4347
33ff00010 4141 5443 4143 4141 5454 4143 4343 4341
33ff00020 5443 4209 3a3a 4442 4646 4846 4847 4748
The asterisk means that all lines between 0000000 and 33ff00000 are
identical to the first line (all zeros).
Any ideas what might be going on?
------------------------------------------------------------------------------
Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
from Actuate! Instantly Supercharge Your Business Reports and Dashboards
with Interactivity, Sharing, Native Excel Exports, App Integration & more
Get technology previously reserved for billion-dollar corporations, FREE
http://pubads.g.doubleclick.net/gampad/clk?id=157005751&iu=/4140/ostg.clktrk
_______________________________________________
Samtools-help mailing list
Samtools-help@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/samtools-help
