must provide a file or filehandle for this Bio::FeatureIO

[ConstantinV]

Hi,
thank you a lot for lyve-SET!

I have the following issue

set_findCliffs.pl: main: Finding cliffs whose slopes are at least 5 with an rSquared value of at least 0.7 in a sliding window size of 10.
set_findCliffs.pl: findCliffsBySlope(TID2): Calculating depth of /export/home/pipelines/lk/Shigella_lk/bams/Sh2.fastq.gz-ss046.sorted.bam:ch6
set_findCliffs.pl: findCliffsBySlope(TID4): Calculating depth of /export/home/pipelines/lk/Shigella_lk/bams/Sh2.fastq.gz-ss046.sorted.bam:ch4
set_findCliffs.pl: findCliffsBySlope(TID1): Calculating depth of /export/home/pipelines/lk/Shigella_lk/bams/Sh2.fastq.gz-ss046.sorted.bam:ch3
set_findCliffs.pl: findCliffsBySlope(TID5): Calculating depth of /export/home/pipelines/lk/Shigella_lk/bams/Sh2.fastq.gz-ss046.sorted.bam:ch1
set_findCliffs.pl: findCliffsBySlope(TID3): Calculating depth of /export/home/pipelines/lk/Shigella_lk/bams/Sh2.fastq.gz-ss046.sorted.bam:ch2
set_findCliffs.pl: findCliffsBySlope(TID6): Calculating depth of /export/home/pipelines/lk/Shigella_lk/bams/Sh2.fastq.gz-ss046.sorted.bam:ch5
set_findCliffs.pl: main: Joining contiguous cliff regions
set_findCliffs.pl: Bio::Root::Root::throw:
------------- EXCEPTION -------------
MSG: must provide a file or filehandle for this Bio::FeatureIO
STACK Bio::FeatureIO::_init_stream /export/home/kkuleshov/pipelines/lk/lyve-SET-2.0.1/lib/lib/perl5/Bio/FeatureIO.pm:486
STACK Bio::FeatureIO::_initialize /export/home/kkuleshov/pipelines/lk/lyve-SET-2.0.1/lib/lib/perl5/Bio/FeatureIO.pm:300
STACK Bio::FeatureIO::bed::_initialize /export/home/kkuleshov/pipelines/lk/lyve-SET-2.0.1/scripts/../lib/lib/perl5/Bio/FeatureIO/bed.pm:41
STACK Bio::FeatureIO::new /export/home/kkuleshov/pipelines/lk/lyve-SET-2.0.1/lib/lib/perl5/Bio/FeatureIO.pm:250
STACK Bio::FeatureIO::new /export/home/kkuleshov/pipelines/lk/lyve-SET-2.0.1/lib/lib/perl5/Bio/FeatureIO.pm:272
STACK main::main /export/home/kkuleshov/pipelines/lk/lyve-SET-2.0.1/scripts/set_findCliffs.pl:81
STACK toplevel /export/home/kkuleshov/pipelines/lk/lyve-SET-2.0.1/scripts/set_findCliffs.pl:22
-------------------------------------

I'm not Perl programmer. Any ideas???

Thank you

[lskatz]

Hi Konstantin! Good to hear from you, and, thank you for using Lyve-SET! Sorry for that weird error!

It looks like you have Bio::FeatureIO installed, and so that's good.

I noticed that you might be running version 2.0.1 and I cannot vouch for it yet--we haven't gone through rigorous testing like we did for v1.1.4f. Could you tell me if it works in that version instead?

[ConstantinV]

Hi Lee! It is the great tool with many useful options. Yes, I installed the last version. I let you know how v1.1.4f work in my hands.

[lskatz]

Any update?

[ConstantinV]

Hi,
I've installed the v1.1.4f version and received the same error while searching cliff regions. I think I have problems with the installation of Bio::FeatureIO module. Could you explain in detail how to install FeatureIO ?
I also found that the latest version has a problem with the exclude region bed file, meanwhile, the older 1.1.4f doesn't.

[lskatz]

Hi @ConstantinV , you can install FeatureIO with cpan:

cpanm Bio::FeatureIO