Problem running BSmooth

[shocker8786]

I'm trying to use BSmooth to align RRBS reads. I keep getting an error after the program processes 70000 reads:

Processed 65000 reads (19.171 knt/s, 28.502% align in 1 orientation, 48.277% in >1, 23.222% in 0)..
.
Processed 70000 reads (19.058 knt/s, 28.486% align in 1 orientation, 48.230% in >1, 23.284% in 0)..
.
Can't locate Scalar/Util.pm: Too many open files at /usr/share/perl/5.14/overload.pm line 97, <$al_cri_fh> line 78708.
bowtie2-align died with signal 13 (PIPE)
bowtie2-align died with signal 13 (PIPE)

Line 97 states:

require Scalar::Util;

I looked up Scalar::Util and found the path:

Scalar/Util.pm => /usr/lib/perl/5.14/Scalar/Util.pm

But I can't seem to get the program to locate Scalar/Util.pm. This is my first time trying to use BSmooth, does anyone know how to fix this issue? Thanks!

[GenoMax]

If the module is indeed installed at the path you are referring to above (and that path is not in @INC variable) then you can extend the perl library path to include that location as indicated here: http://www.perlhowto.com/extending_the_library_path. Use one of the three options indicated on that page.

[shocker8786]

Thanks for your reply. I tried extending the library using those options in the link, but I still have the same error. I checked the @INC paths and the path to the Scalar/Util.pm (/usr/lib/perl/5.14/Scalar/Util.pm) is there.

/usr/local/lib/perl/5.14.2
/usr/local/share/perl/5.14.2
/usr/lib/perl5
/usr/share/perl5
/usr/lib/perl/5.14
/usr/share/perl/5.14
/usr/local/lib/site_perl

Is there anything else I can check?

[GenoMax]

What OS are you running this on? I am wondering if the "Too many open files at /usr/share/perl/5.14/" error is coming from OS.

[brentp]

Yes, that's a message from the OS. On linux you can increase that like so: http://www.cyberciti.biz/faq/linux-i...of-open-files/

you could also try reducing the number of threads that BSmooth => bowtie is using.

[shocker8786]

Thanks. I do not have administrative privilages, so I'm unable to increase the maximum number of open files (16384).

How would I go about reducing the number of threads used?

[genefan]

Hi Shocker, does the command perl bswc_bowtie2_align.pl work in your case?
Thanks!

#############################
I was aligning short reads obtained from Illumina but always got an error as following:
perl bswc_bowtie2_align.pl --out=./outReadslevel/ --sam=./outputSAM/chr ./h.sapiens.bsIndex/chr ./h.sapiens.ref/chr*.fa ./SRA/sra_data.fastq
Error: <mate1s/reads> not specified