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bsk8635 06-15-2011 08:08 AM

BFAST error during match: Could not start thread

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!


nilshomer 06-15-2011 03:47 PM

Report what the error code is. To do so, add the following to the code and re-compile:

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

bsk8635 06-16-2011 07:27 AM

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

nilshomer 06-16-2011 10:18 PM

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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