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tderrien / FEELnc

FEELnc : FlExible Extraction of LncRNA
GNU General Public License v3.0
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Can't call method "close" on an undefined value at.... Running FEELnc_classifier.pl #18

Closed Tichaboni closed 6 years ago

Tichaboni commented 6 years ago

Hi, I have the following when running the 'classifier' module (in cleanup) Can't call method "close" on an undefined value at /home/new/perl5/lib/perl5/Bio/DB/SeqFeature/Store/berkeleydb.pm line 1455.

It shows the line twice on the terminal and doesn't print the output. How do I get it to run all the way to the end and print the .txt?

Your help will be appreciated.

tderrien commented 6 years ago

Hi Tichaboni, This message is not an error but a warning which depends on how the berkeleydb.pm has been installed on your system: https://github.com/tderrien/FEELnc#warnings

Thus, FEELnc_filter.pl should run normally and print in STDOUT if you wait a bit for the program to be finished.

Best,

Thomas

Tichaboni commented 6 years ago

@tderrien @vwucher

Hi The module is running with the above warning. It is printing the output text but it has the heading only.

FEELnc_classifier.pl -i 253candidate_lncRNA.gtf.lncRNA.gtf -a Gallus_gallusannotation.gtf > 253lncRNA_classes.txt

cat 253lncRNA_classes.txt isBest lncRNA_gene lncRNA_transcript partnerRNA_gene partnerRNA_transcript direction type distance subtype location

What options should i use?

tderrien commented 6 years ago

Hello,

It seems that none of you lncRNAs are in a window of 100kb around transcripts from the gallus annotation. You could increase the size of the window to search for new interactions further away e.g ( here 1Mb with the option --maxwindow): FEELnc_classifier.pl --lncrna=253candidate_lncRNA.gtf.lncRNA.gtf --mrna= Gallus_gallusannotation.gtf --window=100000 --maxwindow=1000000 > 253lncRNA_classes.txt HTH