ok thanks again.
I will let you know any news and I will upgrade to the 0.6.4b.
All the best
I will let you know any news and I will upgrade to the 0.6.4b.
All the best
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WORK_DIR=/data/ngs/solid/PROJETS/Comp_bowtie_bfast/BFAST REF_GENOME=/data/ngs/annotations/bfast_indexes/hg19.fa BFAST_BIN_DIR=/bioinfo/local/build/bfast_0.6.4d/bin NB_THREADS=8 nohup $BFAST_BIN_DIR/bfast match -f $REF_GENOME -n $NB_THREADS -A 1 -r $WORK_DIR/FastQ/reads100000.200.fastq > $WORK_DIR/Bmf/bmfbfast.matches.file.hg19.200.bmf
************************************************************ Checking input parameters supplied by the user ... Validating fastaFileName /data/ngs/annotations/bfast_indexes/hg19.fa. Validating readsFileName /data/ngs/solid/PROJETS/Comp_bowtie_bfast/BFAST/FastQ/reads100000.200.fastq. Validating tmpDir path ./. **** Input arguments look good! ************************************************************ ************************************************************ Printing Program Parameters: programMode: [ExecuteProgram] fastaFileName: /data/ngs/annotations/bfast_indexes/hg19.fa mainIndexes [Auto-recognizing] secondaryIndexes [Not Using] readsFileName: /data/ngs/solid/PROJETS/Comp_bowtie_bfast/BFAST/FastQ/reads100000.200.fastq offsets: [Using All] loadAllIndexes: [Not Using] compression: [Not Using] space: [Color Space] startReadNum: 1 endReadNum: 2147483647 keySize: [Not Using] maxKeyMatches: 8 maxNumMatches: 384 whichStrand: [Both Strands] numThreads: 8 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 /data/ngs/annotations/bfast_indexes/hg19.fa.cs.brg. In total read 25 contigs for a total of 3095693983 bases ************************************************************ Reading /data/ngs/solid/PROJETS/Comp_bowtie_bfast/BFAST/FastQ/reads100000.200.fastq into a temp file. Will process 100000 reads. ************************************************************ Searching index file 1/10 (index #1, bin #1)... Reading index from /data/ngs/annotations/bfast_indexes/hg19.fa.cs.1.1.bif. Read index from /data/ngs/annotations/bfast_indexes/hg19.fa.cs.1.1.bif. Reads processed: 100000 Cleaning up index. Searching index file 1/10 (index #1, bin #1) complete... Found 60065 matches. ************************************************************ Searching index file 2/10 (index #2, bin #1)... Reading index from /data/ngs/annotations/bfast_indexes/hg19.fa.cs.2.1.bif.
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