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jiwoongbio / FMAP

Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies
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Error in FMAP_plot.pl #4

Open lwebercoralgirl opened 7 years ago

lwebercoralgirl commented 7 years ago

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?

jiwoongbio commented 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

lwebercoralgirl commented 7 years ago

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.

jiwoongbio commented 7 years ago

I think that the input file, "FMAP_bulksw.vs.ecosphere/bulk_vs_coralcubaonly.comparison.pathways.txt ", can be empty. Can you please check that?

lwebercoralgirl commented 7 years ago

I just checked the file and it looks like it's all there.

jiwoongbio commented 7 years ago

If you are okay, can you please share the input file with me? My mail address is "jiwoong.kim@utsouthwestern.edu".

lwebercoralgirl commented 7 years ago

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!

Sofie8 commented 5 years ago

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

jiwoongbio commented 5 years ago

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

Sofie8 commented 5 years ago

Hi Jiwoon,

Yes, here is the FMAP_plot.pl script I am using: FMAP_plot.zip

Thanks, Sofie

ehj000 commented 5 years ago

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

jiwoongbio commented 5 years ago

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

ehj000 commented 5 years ago

Hi Jiwoon, Thank you for your quick response and for fixing the bug. I got the plots:) Best regards Erik

adixit213 commented 2 years ago

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