Add this line "fprintf(stderr, "errCode=%d\n", errCode);" in RunMatch.c. See the context (called a diff) above.
My guess is that it is not BFAST related, but related to your specific operating system configuration. This would be a good time to talk to your system administrator and/or seek bioinformatics help.
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Hi Nils,
Please bear with me for a second. I am not familiar with C at all, so could you please tell me which file (I assume RunMatch.c) and exactly where in the file (line number might be helpful) I need to add the given lines of code? The version of bfast installed on the cluster is 0.6.5a.
Thank you very much for your help with this issue.
- Boryana
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Report what the error code is. To do so, add the following to the code and re-compile:
Code:diff --git a/bfast/RunMatch.c b/bfast/RunMatch.c index d8e7de3..3cffe1a 100644 --- a/bfast/RunMatch.c +++ b/bfast/RunMatch.c @@ -853,6 +853,7 @@ int FindMatches(char **indexFileName, FindMatchesThread, /* start routine */ &data[i]); /* data to routine */ if(0!=errCode) { + fprintf(stderr, "errCode=%d\n", errCode); PrintError(FnName, "pthread_create: errCode", "C } }
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BFAST error durig match: Could not start thread
Hi,
I have been playing around with BFAST the last couple of days and I can't get past the match step as it gives me the following error message after it has checked my command line arguments:
$ bfast match -f MgIM62u.fasta -r A1.fastq > bfast.matches.MgIM62u.bmf
************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName MgIM62u.fasta.
Validating readsFileName A1.fastq.
Validating tmpDir path ./.
**** Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: MgIM62u.fasta
mainIndexes [Auto-recognizing]
secondaryIndexes [Not Using]
readsFileName: A1.fastq
offsets: [Using All]
loadAllIndexes: [Not Using]
compression: [Not Using]
space: [NT Space]
startReadNum: 1
endReadNum: 2147483647
keySize: [Not Using]
maxKeyMatches: 8
maxNumMatches: 384
whichStrand: [Both Strands]
numThreads: 1
queueLength: 250000
tmpDir: ./
timing: [Not Using]
************************************************************
Searching for main indexes...
Found 1 index (1 file).
Not using secondary indexes.
************************************************************
Reading in reference genome from MgIM62u.fasta.nt.brg.
In total read 1546 contigs for a total of 313500235 bases
************************************************************
Reading A1.fastq into a temp file.
Will process 30325510 reads.
************************************************************
Searching index file 1/1 (index #1, bin #1)...
Reading index from MgIM62u.fasta.nt.1.1.bif.
Read index from MgIM62u.fasta.nt.1.1.bif.
Reads processed: 0************************************************************
In function "FindMatches": Fatal Error[ThreadError]. Variable/Value: pthread_create: errCode.
Message: Could not start thread.
***** Exiting due to errors *****
************************************************************
Any ideas what this is related to? Since I have no idea what the problem is related to, I don't really know what additional information I should provide to help you help me.
Thanks in advance for your help!
-BoryanaLast edited by bsk8635; 06-15-2011, 09:18 AM.
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