'align_to_contig.sam.sai' : No such file or directory

[dh10]

Producing this error with our own bams using v0.79 built on Mountain Lion. However, using the demo bam and bed file included with abra runs perfectly.

Command: java -Xmx16G -jar $JAR --in $inputBam --out ${inputBam/bam/realigned.bam} --ref /seq/data/GATK_Bundles/hg19/ucsc.hg19.fasta --targets $targets --threads 8 --working /Volumes/fastdata/tmp/abraTest > abra_test.log

Error message: Exception in thread "main" java.lang.RuntimeException: BWA exited with non-zero return code : [1] for command: [bwa samse /Volumes/fastdata/tmp/abraTest/clean_contigs.fasta /Volumes/fastdata/tmp/abraTest/temp1/align_to_contig.sam.sai /Volumes/fastdata/tmp/abraTest/temp1/original_reads.fastq.gz -n 1000 > /Volumes/fastdata/tmp/abraTest/temp1/align_to_contig.sam] at abra.Aligner.runCommand(Aligner.java:66) at abra.Aligner.shortAlign(Aligner.java:86) at abra.ReAligner.alignToContigs(ReAligner.java:1006) at abra.ReAligner.alignReads(ReAligner.java:525) at abra.ReAligner.alignReads(ReAligner.java:385) at abra.ReAligner.reAlign(ReAligner.java:193) at abra.ReAligner.run(ReAligner.java:1282) at abra.Abra.main(Abra.java:12)

bwa error message: [bwa_sai2sam_se_core] fail to open file '/Volumes/fastdata/tmp/abraTest/temp1/align_to_contig.sam.sai' : No such file or directory

bwa version used for with Abra: 0.7.9a-r786 bwa version used for original alignment: 0.7.6a-r433 javac: 1.7.0_67

[mozack]

I know the log files are ridiculously big right now, but could you zip and send to me?

lmose at unc dot edu

[mozack]

bwa appears to be ignoring the -f flag and is writing SAI output directly to stdout. Possibly specific to Mountain Lion. Attempting to gain access to a Mountain Lion environment to confirm.

[ckandoth]

I'd also recommend switching to the latest version of BWA. This thread mentions a critical bug in BWA 0.7.9a-r786.