Hey Nacho,
we are tracking your issue here:
https://github.com/broadinstitute/picard/issues/135
N
On Thu, Nov 20, 2014 at 2:55 PM, Nacho Caballero <nacho...@gmail.com> wrote:
>
> 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?
>
>
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