[ome-users] Negative position error with bfconvert

[Frank Pennekamp]

Dear all,

I use the bio-formats command line tools (version 5.1.0) to convert 
large cxd files (> 60GB) into avi files. However, the processing stops 
after about 500 planes with an error message 
java.lang.IllegalArgumentException: Negative position. This threads was 
the only related information I could find and suggest its maybe a bug. 
Any suggestions how to circumvent this problem?

Many thanks,

    Frank



Please find the terminal output here:
ieu0825-petchey:1 - raw Frank$ 
/Users/Frank/Documents/Postdoc/Software/bftools/bfconvert 
20150331_jg_para_didin_trials00001.cxd out.avi
20150331_jg_para_didin_trials00001.cxd
PCIReader initializing 20150331_jg_para_didin_trials00001.cxd
[Compix Simple-PCI] -> out.avi [Audio Video Interleave]
     Converted 16/18000 planes (0%)
     Converted 37/18000 planes (0%)
     Converted 57/18000 planes (0%)
     Converted 78/18000 planes (0%)
     Converted 98/18000 planes (0%)
     Converted 107/18000 planes (0%)
     Converted 122/18000 planes (0%)
     Converted 137/18000 planes (0%)
     Converted 152/18000 planes (0%)
     Converted 167/18000 planes (0%)
     Converted 182/18000 planes (1%)
     Converted 196/18000 planes (1%)
     Converted 210/18000 planes (1%)
     Converted 224/18000 planes (1%)
     Converted 238/18000 planes (1%)
     Converted 252/18000 planes (1%)
     Converted 266/18000 planes (1%)
     Converted 280/18000 planes (1%)
     Converted 294/18000 planes (1%)
     Converted 307/18000 planes (1%)
     Converted 320/18000 planes (1%)
     Converted 333/18000 planes (1%)
     Converted 346/18000 planes (1%)
     Converted 359/18000 planes (1%)
     Converted 372/18000 planes (2%)
     Converted 384/18000 planes (2%)
     Converted 401/18000 planes (2%)
     Converted 417/18000 planes (2%)
     Converted 433/18000 planes (2%)
     Converted 450/18000 planes (2%)
     Converted 467/18000 planes (2%)
     Converted 483/18000 planes (2%)
     Converted 495/18000 planes (2%)
     Converted 507/18000 planes (2%)
Exception in thread "main" java.lang.IllegalArgumentException: Negative 
position
     at sun.nio.ch.FileChannelImpl.read(FileChannelImpl.java:600)
     at 
loci.common.NIOByteBufferProvider.allocateDirect(NIOByteBufferProvider.java:127)
     at 
loci.common.NIOByteBufferProvider.allocate(NIOByteBufferProvider.java:112)
     at loci.common.NIOFileHandle.buffer(NIOFileHandle.java:600)
     at loci.common.NIOFileHandle.seek(NIOFileHandle.java:291)
     at 
loci.common.RandomAccessInputStream.seek(RandomAccessInputStream.java:174)
     at loci.formats.out.AVIWriter.setId(AVIWriter.java:257)
     at loci.formats.ImageWriter.setId(ImageWriter.java:433)
     at 
loci.formats.tools.ImageConverter.testConvert(ImageConverter.java:521)
     at loci.formats.tools.ImageConverter.main(ImageConverter.java:822)