Using samtools version 0.1.18, the following bowtie alignment pipeline works well to create a sorted BAM file:

bowtie -v 0 -S genome.fasta test.fastq | samtools view -S -b -u - | samtools sort - test0.1.18
[samopen] SAM header is present: 2108 sequences.
# reads processed: 80094
# reads with at least one reported alignment: 70028 (87.43%)
# reads that failed to align: 10066 (12.57%)
Reported 70028 alignments to 1 output stream(s)

However, if I install and use samtools version 0.1.19, I get an error message claiming the input is truncated (2nd line below):

bowtie -v 0 -S genome.fasta test.fastq | samtools view -S -b -u - | samtools sort - test0.1.19
[bam_header_read] EOF marker is absent. The input is probably truncated.
[samopen] SAM header is present: 2108 sequences.
# reads processed: 80094
# reads with at least one reported alignment: 70028 (87.43%)
# reads that failed to align: 10066 (12.57%)
Reported 70028 alignments to 1 output stream(s)

I assume the error message is coming from samtools sort. But it is confusing, since both versions create identical results, including fully intact headers and properly formatted BAM alignments. Removing the -u switch in the samtools view call has no effect.

I'd like to fix the reporting of this error because a similar pipeline is used in some scripts of mine -- users who have samtools 0.1.19 are worried about the error message. I know I could just send the STDERR of the samtools sort to /dev/null, but I'd rather try and understand what is happening first ...