Cannot read BAM file created by samtools 0.1.19

[dap...@gmail.com]

Hello all,

Disclaimer: I'm not a bioinformatician, just a local sysadmin who is trying to compile bedtools on our compute cluster for a local university group.

I'm trying to use bedtools on an IBM POWER5 machine. In case it's necessary, here is my compilation log: http://sprunge.us/TKXZ

My installed version of bedtools 2.20.1 doesn't seem to be able to read BAM files created by samtools 0.1.19, as evident from the output of "make test": http://sprunge.us/iCMi

Basically, any call to "bedtools bamtobed -i <bamfile.bam>" results in "Failed to open BAM file <bamfile.bam>".

I've found hardly anything on the issue. Samtools is in my path and seems to work fine.

Thanks in advance for any pointer!

Regards,
Patrice

[Charles Plessy]

Le Mon, Jun 30, 2014 at 06:12:57AM -0700, dap...@gmail.com a écrit :
>
> I'm trying to use bedtools on an IBM POWER5 machine. In case it's
> necessary, here is my compilation log: http://sprunge.us/TKXZ
>
> My installed version of bedtools 2.20.1 doesn't seem to be able to read BAM
> files created by samtools 0.1.19, as evident from the output of "make
> test": http://sprunge.us/iCMi
>
> Basically, any call to "bedtools bamtobed -i <bamfile.bam>" results in
> "Failed to open BAM file <bamfile.bam>".

Dear Patrice and everybody,

for the record, the same error seems to occur when runnign BEDTools' regression
tests at build time on powerpc in Debian. You can see build logs at the
following URL.

https://buildd.debian.org/status/fetch.php?pkg=bedtools&arch=powerpc&ver=2.20.1-1&stamp=1402091719

Have a nice day,

--
Charles Plessy
http://charles.plessy.org
Tsurumi, Kanagawa, Japan

[dap...@gmail.com]

Am Montag, 30. Juni 2014 21:12:34 UTC+2 schrieb Charles Plessy:

Le Mon, Jun 30, 2014 at 06:12:57AM -0700, dap...@gmail.com a écrit :
>
> I'm trying to use bedtools on an IBM POWER5 machine. In case it's
> necessary, here is my compilation log: http://sprunge.us/TKXZ
>
> My installed version of bedtools 2.20.1 doesn't seem to be able to read BAM
> files created by samtools 0.1.19, as evident from the output of "make
> test": http://sprunge.us/iCMi
>
> Basically, any call to "bedtools bamtobed -i <bamfile.bam>" results in
> "Failed to open BAM file <bamfile.bam>".

Dear Patrice and everybody,

for the record, the same error seems to occur when runnign BEDTools' regression
tests at build time on powerpc in Debian.  You can see build logs at the
following URL.

https://buildd.debian.org/status/fetch.php?pkg=bedtools&arch=powerpc&ver=2.20.1-1&stamp=1402091719

Could this have anything to do with the Power architecture being big endian instead of little endian?