skoren
commented
8 years ago Your soap assembly looks like it is failing. Do you have soap installed as part of metAMOS or was it already available in your path? Is the soapdenovo.55.asm.contig file empty? What is the output in ASSEMBLE.log
Hi all,
Without getting any help with the previous problem, trying my luck on another problem that getting on the postinstall process:
I'm trying to get a successful run of the run_pipeline_test.sh test from the Test suite.
OS: CentOS 6.5 Linux.
The error that i have now is:
[***** ****ERROR****** During findorfs, the following command failed with return code 2:
****DETAILS****** Last 10 commands run before the error (/data/apps/metAMOS/1.5rc3/Test/test1/Logs/COMMANDS.log) |2016-02-16 09:36:42| cat /data/apps/metAMOS/1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates >> /data/apps/metAMOS/1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr |2016-02-16 09:36:43| cp /data/apps/metAMOS/1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.hdr /data/apps/metAMOS/1.5rc3/Test/test1/Assemble/out/soapdenovo.55.lib1.mappedmates |2016-02-16 09:36:43| /data/apps/metAMOS/1.5rc3/Utilities/cpp/Linux-x86_64/bowtie-build -o 2 /data/apps/metAMOS/1.5rc3/Test/test1/Assemble/out/velvet.55.asm.contig /data/apps/metAMOS/1.5rc3/Test/test1/Assemble/out/velvet.55.IDX |2016-02-16 09:36:43| /data/apps/metAMOS/1.5rc3/Utilities/cpp/Linux-x86_64/bowtie -p 15 -f -l 25 -e 140 --best --strata -m 10 -k 1 --un /data/apps/metAMOS/1.5rc3/Test/test1/Assemble/out/velvet.55.lib1.unaligned.fasta /data/apps/metAMOS/1.5rc3/Test/test1/Assemble/out/velvet.55.IDX /data/apps/metAMOS/1.5rc3/Test/test1/Preprocess/out/lib1.seq > /data/apps/metAMOS/1.5rc3/Test/test1/Assemble/out/lib1.bout |2016-02-16 09:36:45| cat /data/apps/metAMOS/1.5rc3/Test/test1/Assemble/out/velvet.55.lib1.mappedmates >> /data/apps/metAMOS/1.5rc3/Test/test1/Assemble/out/velvet.55.lib1.hdr |2016-02-16 09:36:45| cp /data/apps/metAMOS/1.5rc3/Test/test1/Assemble/out/velvet.55.lib1.hdr /data/apps/metAMOS/1.5rc3/Test/test1/Assemble/out/velvet.55.lib1.mappedmates |2016-02-16 09:36:47|# [FINDORFS] |2016-02-16 09:36:47| unlink /data/apps/metAMOS/1.5rc3/Test/test1/FindORFS/in/soapdenovo.55.asm.contig |2016-02-16 09:36:47| ln /data/apps/metAMOS/1.5rc3/Test/test1/Assemble/out/soapdenovo.55.asm.contig /data/apps/metAMOS/1.5rc3/Test/test1/FindORFS/in/soapdenovo.55.asm.contig |2016-02-16 09:36:48| /data/apps/metAMOS/1.5rc3/Utilities/cpp/Linux-x86_64/prokka/bin/prokka --fast --outdir /data/apps/metAMOS/1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.prokka --prefix soapdenovo.55 --force /data/apps/metAMOS/1.5rc3/Test/test1/FindORFS/in/soapdenovo.55.asm.contig
Last 10 lines of output (/data/apps/metAMOS/1.5rc3/Test/test1/Logs/FINDORFS.log) [09:36:48] Determined minced version is 1.6 [09:36:48] Looking for 'parallel' - found /data/apps/metAMOS/1.5rc3/Utilities/cpp/Linux-x86_64/prokka/bin/../binaries/linux/../common/parallel [09:36:48] Determined parallel version is 20140322 [09:36:48] Looking for 'prodigal' - found /data/apps/metAMOS/1.5rc3/Utilities/cpp/Linux-x86_64/prokka/bin/../binaries/linux/prodigal [09:36:48] Determined prodigal version is 2.60 [09:36:48] Looking for 'sed' - found /bin/sed [09:36:48] Looking for 'tbl2asn' - found /data/apps/metAMOS/1.5rc3/Utilities/cpp/Linux-x86_64/prokka/bin/../binaries/linux/tbl2asn [09:36:48] Determined tbl2asn version is 24.3 [09:36:48] Using genetic code table 11. [09:36:48] '/data/apps/metAMOS/1.5rc3/Test/test1/FindORFS/in/soapdenovo.55.asm.contig' is not a readable non-empty FASTA file
Please veryify input data and restart MetAMOS. If the problem persists please contact the MetAMOS development team.
Hope for some help!
Igor