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HYPHY Package >> HyPhy feedback >> HYPHY MPI for GARD http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1331860115 Message started by ricardoab on Mar 15th, 2012 at 6:08pm |
Title: HYPHY MPI for GARD Post by ricardoab on Mar 15th, 2012 at 6:08pm
Hello,
We trying to use HyPhy for detect recombinants. We install HYPHY in a cluster with open MPI. We call HYPHY $mpirun -np 4 /usr/local/bin/HYPHYMPI and then display the next message /HYPHY 2.1020120130beta(MPI) for Linux on x86_64\ ***************** TYPES OF STANDARD ANALYSES ***************** We choose 11 and after that, We choose 1 for Screen an alignment using GARD. We choose an alignment (we can not download the example file) in fasta or phy. and then we choose the Batch File: SingleBreakpointRecomb.bf And the next error message is: -------------------------------------------------------------------------- MPI_ABORT was invoked on rank 0 in communicator MPI_COMM_WORLD with errorcode 1. NOTE: invoking MPI_ABORT causes Open MPI to kill all MPI processes. You may or may not see output from other processes, depending on exactly when Open MPI kills them. -------------------------------------------------------------------------- /usr/local/lib/hyphy/TemplateBatchFiles/Nucleotide file to screen::Error: Master node received an error:The format of the sequence file has not been recognized and may be invalid Function call stack 1 : Read Data Set ds from file PROMPT_FOR_FILE ------- -------------------------------------------------------------------------- mpirun has exited due to process rank 0 with PID 23329 on node biosistemas1.ira.cinvestav.mx exiting without calling "finalize". This may have caused other processes in the application to be terminated by signals sent by mpirun (as reported here). -------------------------------------------------------------------------- Do you have any idea about What we are doing wrong? Thankyou for your help. Cheers, Ricardo I. |
Title: Re: HYPHY MPI for GARD Post by Sergei on Mar 18th, 2012 at 9:04pm
Hi there,
In Quote:
you seem to be supplying GARD.bf as the input sequence file to process. Instead of seqs.fasta on the previous line, please try entering the absolute path (e.g. /home/user/directory/seqs.fasta) instead. HyPhy is not finding your alignment and prompting for it twice -- the second time it read GARD.bf as the input file and was not able to do much with it. Sergei |
Title: Re: HYPHY MPI for GARD Post by ricardoab on Mar 20th, 2012 at 3:10pm
Dear Sergei,
Thanks for your help, we knew that we were doing something wrong, but we never thought about the path. Sorry for the inconveniences, Kind regards! Ricardo I. |
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