Bfast match .bmf? file - anybody seen .bmf? before

[jfk]

Hi everyone

I've used BFAST (0.7.0a) before on our institute computing cluster successfully before, however, after running 'bfast match' last night I have a '.bmf?' file instead of the normal '.bmf' file.

Has anybody else observed this?

bfast match seems to have executed correctly, my .fastq file is 2.3GB and the .bmf? file is 1.3GB.

I am analysing SOLiD whole genome resequencing data of yeast strain.

bfast match output below (I've #'d out some of the path details on purpose):

************************************************************
Checking input parameters supplied by the user ...
Validating fastaFileName ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.
Validating readsFileName PYR4b.fastq.
Validating tmpDir path ./.
**** Input arguments look good!
************************************************************
************************************************************
Printing Program Parameters:
programMode: [ExecuteProgram]
fastaFileName: ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa
mainIndexes [Auto-recognizing]
secondaryIndexes [Not Using]
readsFileName: PYR4b.fastq
offsets: [Using All]
loadAllIndexes: [Not Using]
compression: [Not Using]
space: [Color Space]
startReadNum: 1
endReadNum: 2147483647
keySize: [Not Using]
maxKeyMatches: 8
keyMissFraction: 1.000000
maxNumMatches: 384
whichStrand: [Both Strands]
numThreads: 1
queueLength: 250000
tmpDir: ./
timing: [Not Using]
************************************************************
Searching for main indexes...
Found 10 index (10 total files).
Not using secondary indexes.
************************************************************
Reading in reference genome from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.brg.
In total read 18 contigs for a total of 12163423 bases
************************************************************
Reading PYR4b.fastq into a temp file.
Will process 19816967 reads.
************************************************************
Searching index file 1/10 (index #1, bin #1)...
Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.1.1.bif.
Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.1.1.bif.
Reads processed: 19816967
Cleaning up index.
Searching index file 1/10 (index #1, bin #1) complete...
Found 14240487 matches.
************************************************************
Searching index file 2/10 (index #2, bin #1)...
Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.2.1.bif.
Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.2.1.bif.
Reads processed: 19816967
Cleaning up index.
Searching index file 2/10 (index #2, bin #1) complete...
Found 14554594 matches.
************************************************************
Searching index file 3/10 (index #3, bin #1)...
Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.3.1.bif.
Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.3.1.bif.
Reads processed: 19816967
Cleaning up index.
Searching index file 3/10 (index #3, bin #1) complete...
Found 14101690 matches.
************************************************************
Searching index file 4/10 (index #4, bin #1)...
Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.4.1.bif.
Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.4.1.bif.
Reads processed: 19816967
Cleaning up index.
Searching index file 4/10 (index #4, bin #1) complete...
Found 13814082 matches.
************************************************************
Searching index file 5/10 (index #5, bin #1)...
Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.5.1.bif.
Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.5.1.bif.
Reads processed: 19816967
Cleaning up index.
Searching index file 5/10 (index #5, bin #1) complete...
Found 14599217 matches.
************************************************************
Searching index file 6/10 (index #6, bin #1)...
Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.6.1.bif.
Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.6.1.bif.
Reads processed: 19816967
Cleaning up index.
Searching index file 6/10 (index #6, bin #1) complete...
Found 13805101 matches.
************************************************************
Searching index file 7/10 (index #7, bin #1)...
Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.7.1.bif.
Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.7.1.bif.
Reads processed: 19816967
Cleaning up index.
Searching index file 7/10 (index #7, bin #1) complete...
Found 14758412 matches.
************************************************************
Searching index file 8/10 (index #8, bin #1)...
Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.8.1.bif.
Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.8.1.bif.
Reads processed: 19816967
Cleaning up index.
Searching index file 8/10 (index #8, bin #1) complete...
Found 14517528 matches.
************************************************************
Searching index file 9/10 (index #9, bin #1)...
Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.9.1.bif.
Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.9.1.bif.
Reads processed: 19816967
Cleaning up index.
Searching index file 9/10 (index #9, bin #1) complete...
Found 13907379 matches.
************************************************************
Searching index file 10/10 (index #10, bin #1)...
Reading index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.10.1.bif.
Read index from ###/scratch/genomeIndexes/sacCer3/fasta/sacCer3.fa.cs.10.1.bif.
Reads processed: 19816967
Cleaning up index.
Searching index file 10/10 (index #10, bin #1) complete...
Found 13016565 matches.
************************************************************
Merging the output from each index...
[19816967]... completed.
Found matches for 16501187 reads.
Searching main indexes complete.
************************************************************
************************************************************
In total, found matches for 16501187 out of 19816967 reads.
************************************************************
Terminating successfully!

[jfk]

Problem solved.

The windows carriage return creeping into my script... was using notepad++ on my linux desktop.

.. lesson: use vim/gedit!