Open lwebercoralgirl opened 7 years ago
Can you try the command without ">" (standard output) like below?
perl /usr/local/FMAP/FMAP_plot.pl FMAP_bulksw.vs.ecosphere/bulk_vs_coralcubaonly.comparison.pathways.txt bulk_vs_coralcubaonly.comparison.pathways.pdf
Thanks, Jiwoong
Hi Jiwoong, I tried this suggestion and now I am seeing this error:
Use of uninitialized value $line in chomp at /usr/local/FMAP/FMAP_plot.pl line 45.
I think that the input file, "FMAP_bulksw.vs.ecosphere/bulk_vs_coralcubaonly.comparison.pathways.txt ", can be empty. Can you please check that?
I just checked the file and it looks like it's all there.
If you are okay, can you please share the input file with me? My mail address is "jiwoong.kim@utsouthwestern.edu".
Hi! I'm sorry I haven't followed up. I got it to work! I must have been doing something wrong on my end. Sorry about that!
Hi Jiwoong,
I am having the same issue as above when running FMAP_plot.pl on the operon.txt, not on the pathway and module.txt: ERROR in /ddn1/vol1/site_scratch/leuven/314/vsc31426/db/FMAP_master/FMAP_plot.pl: Use of uninitialized value $tokenHash{"orthology.count"} in pattern match (m//) at /ddn1/vol1/site_scratch/leuven/314/vsc31426/db/FMAP_master/FMAP_plot.pl line 66, <$reader> line 2.
I don't see what's wrong..
My input file: BiBo.operon.txt
Thanks, Sofie
Hi Sofie,
Can you please share the file "FMAP_plot.pl" you used? I would like to know if it is the latest version or not. Thanks.
Best Regards, Jiwoong
Hi Jiwoon, Thank you for a nice tool.
I am experiencing similar errors as reported by others: ERROR in FMAP_plot.pl: Use of uninitialized value $tokenHash{"orthology.count"} in pattern match (m//) at FMAP_plot.pl line 69, <$reader> line 6. Best regards Erik
Hi all,
I am sorry for the late response. The error bug was fixed. Please try with the latest version of FMAP_plot.pl Thanks.
Best Regards, Jiwoong
Hi Jiwoon, Thank you for your quick response and for fixing the bug. I got the plots:) Best regards Erik
Hi Jiwoon, Thanks a lot for a nice tool. Everytime I run the FMAP_plot.pl with the recommended usage "perl FMAP_plot.pl [options] pathway.txt|module.txt|operon.txt plot.pdf" is get the error "ERROR in FMAPplot.pl: Use of uninitialized value $ in pattern match (m//) at FMAP_plot.pl line 38.".
The perl script works just fine if I am using the pathways as input but nothing for either operon or module. I did look into the module and operon output file and there are entries that satisfy the "-p FLOAT p-value cutoff [0.05]" criteria.
I am by no means an expert but does the FMAP_plot.pl call for any R scripts? If it does, then do you recommend a specific version of the R?
Also, I couldn't tell which version of the perl script I am using but I am attaching it here. Any help to resolve this will be great. Thank you. FMAP_plot.zip
Hello,
I am running into issues when using the FMAP_plot.pl script.
When I run: perl /usr/local/FMAP/FMAP_plot.pl FMAP_bulksw.vs.ecosphere/bulk_vs_coralcubaonly.comparison.pathways.txt > bulk_vs_coralcubaonly.comparison.pathways.pdf
I get the error warning: ERROR in /usr/local/FMAP/FMAPplot.pl: Use of uninitialized value $ in pattern match (m//) at /usr/local/FMAP/FMAP_plot.pl line 38.
Any suggestions?