I'm seeing this error:
ERROR: Failed to open output file '/projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/001/000013.ovb.WORKING.gz': Function not implemented
I'm running this command:
runCA -d celera -p celegans celera/c-elegans_LongRead_500_1499nt.frg celera/c-elegans_LongRead.frg
I also see a similar error if I attempt to assemble fastq.gz files. I'm thinking that perhaps support for reading/writing compressed files is missing. Any thoughts on how to troubleshoot this issue?
Cheers,
Shaun
Which OS and filesystem? We're using popen() to call gzip, and it seems popen isn't supported. I got lots of hits for "popen function not implemented". Unfortunately, short of recoding to use libz (not going to happen), you're stuck.
ABySS also uses fork/exec to uncompress files rather than zlib. I'm happy to see that another assembler uses this approach as well. I thought I was the only one. Now that I know where to look, I'll try some troubleshooting with popen.
Celera Assembler 8.2
glibc 2.19
Linux 2.6.18
CentOS 5.10
Cheers,
Shaun
The file system is NFS.