Aborted BWA run - what is wrong?

[yaximik]

I hit a strange error when attempting alignment of my Illumina readset to individual genes. I extracted from hg19 the entire genes of FOXP2 (chr7) and COL1A1 (chr17) as fasta files, then did indexing:

bwa index -a is -p hFOXP2gene /media/Ext2TB-A/RefSeq/Human/hg19/hFOXP2gene.fa
bwa index -a is -p hCOL1A1gene /media/Ext2TB-A/RefSeq/Huma/hg1/hCOL1A1gene.fa

which completed without problems. Then I tried to do alignment:

bwa mem -p -t15 /media/Ext2TB-A/RefSeq/Human/hg19/bwadb/hFOXP2gene /home/yaximik/Desktop/Ext2TB-A/Data/MiSeq/SC/AdQ30/SC_050813peOrd.fastq > SC_050813peOrd_hFOXP2gene-pe.sam && samtools view -bS -@15 SC_050813peOrd_hFOXP2gene-pe.sam -o SC_050813peOrd_hFOXP2gene-pe.bam && samtools sort -@15 -m 20G SC_050813peOrd_hFOXP2gene-pe.bam SC_050813peOrd_hFOXP2gene-pe_sorted && samtools index SC_050813peOrd_hFOXP2gene-pe_sorted.bam &&  samtools idxstats SC_050813peOrd_hFOXP2gene-pe_sorted.bam > SC_050813peOrd_hFOXP2gene-peStats.txt

However I got the following to stout:

[main] Version: 0.7.3a-r367
[main] CMD: bwa mem -p -t15 /media/Ext2TB-A/RefSeq/Human/hg19/bwadb/hFOXP2gene /home/yaximik/Desktop/Ext2TB-A/Data/MiSeq/SC/AdQ30/SC_050813peOrd.fastq
[main] Real time: 0.001 sec; CPU: 0.001 sec
[samopen] SAM header is present: 1 sequences.
[sam_read1] reference 'SN:hFOXP2        LN:280776
' is recognized as '*'.
[main_samview] truncated file.

Exactly the same happened for COL1A1gene.
The same set of commands completes just fine when the entire chr7 is used as reference and there were quite a lot of matches to some regions of the FOXP2 gene.
What could be the problem?

[mastal]

Aborted BWA run - what is wrong?

Have you tried running your commands one at a time to see at which stage the problem arises?