EOF error in BAM file using canfam3

[mboursnell]

I have made BAM files using canfam3 as a reference.
Then I am getting this error when using picard/BuildBamIndex

Exception in thread "main" net.sf.samtools.util.RuntimeEOFException: Premature EOF; BinaryCodec in readmode;

and using samtools I get:

[bam_header_read] EOF marker is absent. The input is probably truncated.

The weird thing is this doesn't happen when I create the BAM file using the canfam2 dog sequence as reference, but it does happen when using the canfam3 sequence as reference.

[maubp]

It does sound like you are getting a truncated BAM file. Are there any error messages or warnings when creating the BAM file? What tool are you using for this?

[mboursnell]

EOF error - production of BAM files

These are the commands (with a few of the long paths taken out)

bwa64 aln canfam3.fasta WT22_1.fastq > WT22_1_aln_sa1.sai

bwa64 aln canfam3.fasta WT22_2.fastq > WT22_1_aln_sa2.sai

bwa64 sampe canfam3.fasta WT22_1_aln_sa1.sai WT22_1_aln_sa2.sai WT22_1.fastq WT22_2.fastq > WT22_1_aligned.sam

java -Xmx4g -jar SortSam.jar I=WT22_1_aligned.sam O=WT22_1_aligned_sorted.sam SO=coordinate VALIDATION_STRINGENCY=LENIENT

java -Xmx4g -jar SamFormatConverter.jar I=WT22_1_aligned_sorted.sam O=WT22_1_aligned_sorted.bam VALIDATION_STRINGENCY=LENIENT

java -Xmx4g -jar AddOrReplaceReadGroups.jar I=WT22_1_aligned_sorted.bam O=WT22_1_aligned_sorted_rg.bam rgID=WT LB='Lib1' PL='ILLUMINA' PU=WT22_1 SM=WT22_1