Menu
▾
▴
#298 ERROR: Failed to open output file: Function not implemented
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
Created 13 overlap jobs. Last batch '001', last job '000013'. ----------------------------------------START CONCURRENT Fri Feb 20 00:46:59 2015 /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/overlap.sh 1 > /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/000001.out 2>&1 /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/overlap.sh 2 > /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/000002.out 2>&1 /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/overlap.sh 3 > /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/000003.out 2>&1 /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/overlap.sh 4 > /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/000004.out 2>&1 /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/overlap.sh 5 > /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/000005.out 2>&1 /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/overlap.sh 6 > /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/000006.out 2>&1 /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/overlap.sh 7 > /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/000007.out 2>&1 /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/overlap.sh 8 > /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/000008.out 2>&1 /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/overlap.sh 9 > /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/000009.out 2>&1 /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/overlap.sh 10 > /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/000010.out 2>&1 /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/overlap.sh 11 > /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/000011.out 2>&1 /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/overlap.sh 12 > /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/000012.out 2>&1 /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/overlap.sh 13 > /projects/btl/sjackman/abyss-pipeline/celegans/celera/0-overlaptrim-overlap/000013.out 2>&1 ----------------------------------------END CONCURRENT Fri Feb 20 00:46:59 2015 (0 seconds) ================================================================================ runCA failed. ---------------------------------------- Stack trace: at /gsc/btl/linuxbrew/Cellar/celera-assembler/8.2/libexec/Linux-amd64/bin/runCA line 1592, <J> line 13. main::caFailure("ERROR: Overlap job /projects/btl/sjackman/abyss-pipeline/cel"..., undef) called at /gsc/btl/linuxbrew/Cellar/celera-assembler/8.2/libexec/Linux-amd64/bin/runCA line 3842 main::checkOverlapper("trim") called at /gsc/btl/linuxbrew/Cellar/celera-assembler/8.2/libexec/Linux-amd64/bin/runCA line 3880 main::checkOverlap("trim") called at /gsc/btl/linuxbrew/Cellar/celera-assembler/8.2/libexec/Linux-amd64/bin/runCA line 4042 main::overlapTrim() called at /gsc/btl/linuxbrew/Cellar/celera-assembler/8.2/libexec/Linux-amd64/bin/runCA line 6496Which 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.