run_pipeline_test.sh gives error: ERROR: Sequence file FindORFS/in/soapdenovo.55.asm.contig does not exist

[nortex]

Hi all,

I am trying to install metAMOS on CentOS 6.5, after installing all the program and dependencies guide suggesting to check if the program is installed well. To do that, i was asked to run run_pipeline_test.sh from Test folder inside metAMOS. While running that script, i receive the next error:

During findorfs, the following command failed with return code 1:

/metAMOS/1.5rc3/Utilities/cpp/Linux-x86_64/FragGeneScan -s /metAMOS/1.5rc3/Test/test1/FindORFS/in/soapdenovo.55.asm.contig -o /metAMOS/1.5rc3/Test/test1/FindORFS/out/soapdenovo.55.orfs -w 0 -t complete

Last 10 lines of output (/metAMOS/1.5rc3/Test/test1/Logs/FINDORFS.log) [complete] for complete genomic sequences or short sequence reads without sequencing error [sanger_5] for Sanger sequencing reads with about 0.5% error rate [sanger_10] for Sanger sequencing reads with about 1% error rate [454_5] for 454 pyrosequencing reads with about 0.5% error rate [454_10] for 454 pyrosequencing reads with about 1% error rate [454_30] for 454 pyrosequencing reads with about 3% error rate [illumina_5] for Illumina sequencing reads with about 0.5% error rate [illumina_10] for Illumina sequencing reads with about 1% error rate

ERROR: Sequence file [/metAMOS/1.5rc3/Test/test1/FindORFS/in/soapdenovo.55.asm.contig] does not exist

Can anyone help me solving that problem if it is really a problem?

Thanks, Igor

[nortex]

UPDATE:

Problem fixed by adding -W imetamos flag to the run_pipeline_test.sh initpipline line.