Unable to load package "Data::IO::Sequence::"

[Qian (Ava) Xu]

Hi,
I am running rf-count on a pair of . bam files (treated and untreated), and here are my scripts:
rf-count -r -m -ow -f trans.fa *.bam

The output is :
[+] Making output directory...
[+] Guessing file types:
Sample Type 5'-end trimming SS5_namechange BAM Ignored SSP_namechange BAM Ignored [+] Getting transcripts from reference, and building count table base structure... [!] Exception [Data::IO::Sequence->new()]: Unable to load package "Data::IO::Sequence::" Reason: Can't locate Data/IO/Sequence/.pm in @inc (@inc contains: /data/qianxu0517/DMS_MaPseq/RNAFramework/lib /data/qianxu0517/DMS_MaPseq/RNAFramework/lib/Data/IO/Sequence/Vienna.pm /usr/local/lib64/perl5 /usr/local/share/perl5 /usr/lib64/perl5/vendor_perl /usr/share/perl5/vendor_perl /usr/lib64/perl5 /usr/share/perl5 .) at /data/qianxu0517/DMS_MaPseq/RNAFramework/lib/Core/Base.pm line 66. -> Caught at /data/qianxu0517/DMS_MaPseq/RNAFramework/lib/Core/Base.pm line 126.

I am using the system Perl, the version of Perl is v5.16.3 built for x86_64-linux-thread-multi.

Many thanks for any help!

[Qian (Ava) Xu]

by the way, I have tried:
export PER5LIB=/data/qianxu0517/DMS_MaPseq/RNAFramework/lib/Data/IO/Sequence/

but it doesn't help....

[Danny Incarnato]

Dear Qian,

This usually happens when RNAFramework tries to guess the file format and it fails.
Can you please share your "trans.fa" file?

Thanks,

Danny

[Qian (Ava) Xu]

The link of the trans.fa is:
https://drive.google.com/file/d/16g5yTOg6ast8OeotfkhISgY7pC65Cmjt/view?usp=sharing
The original file is downloaded from genecode:ftp://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_mouse/release_M25/gencode.vM25.transcripts.fa.gz, we only kept the 1st and 6th part of the long name of each transcript.

[Danny Incarnato]

Hi Qian,

the problem is that when you edited the file, you introduced mixed line endings (\r\n), typical of Windows systems.
Your file should contain only UNIX line endings (\n).
To do so, you can use the "dos2unix" tool (available from apt).

For the future, I recommend you to only edit your sequence files on Linux.

Hope this helps,

Danny

[Qian (Ava) Xu]

Hi Dr. Incarnato, thanks for your help! Now the problem is solved!