jiwoongbio / fmap Goto Github PK

Hi,
I find the tool promising, but I was wondering if it is possible to run the analysis without comparing two groups? For example if I have samples from unique environments, and I want to explore what pathways that are present in a single sample.
Thanks in advanced
Erik

Hi,
As I'm trying to run FMP_download.pl, I added usearch path. (Because I use a Mac, I can't use diamond).

I was wondering is it better to build usearch db for blast at this step or I can simply skip? Because when I use the 32 bit usearch (free of charge), I got the following error:

`2020-01-03 13:30:17 URL:https://qbrc.swmed.edu/FMAP/FMAP_data/database [46/46] -> "/Users/daia1/MSK/work/projects/FMAP/software/FMAP/FMAP_data/database" [1]
2020-01-03 13:41:10 URL:https://qbrc.swmed.edu/FMAP/FMAP_data/orthology_uniref90_2_2157_4751.20190806012959.fasta.gz [992986879/992986879] -> "/Users/daia1/MSK/work/projects/FMAP/software/FMAP/FMAP_data/orthology_uniref90_2_2157_4751.20190806012959.fasta.gz" [1]
usearch v11.0.667_i86osx32, 4.0Gb RAM (34.4Gb total), 16 cores
(C) Copyright 2013-18 Robert C. Edgar, all rights reserved.
https://drive5.com/usearch

License: [email protected]

00:10 2.3Gb 100.0% Reading /Users/daia1/MSK/work/projects/FMAP/software/FMAP/FMAP_data/orthology_uniref90_2_2157_4751.20190806012959.fasta
00:27 2.2Gb 100.0% Masking (fastamino)
01:02 2.2Gb 100.0% Word stats
usearch11.0.667_i86osx32(33884,0x420080) malloc: can't allocate region
*** mach_vm_map(size=268337152) failed (error code=3)
usearch11.0.667_i86osx32(33884,0x420080) malloc: *** set a breakpoint in malloc_error_break to debug

/Users/daia1/projects/FMAP/software/usearch11.0.667_i86osx32 -makeudb_ublast /Users/daia1/MSK/work/projects/FMAP/software/FMAP/FMAP_data/orthology_uniref90_2_2157_4751.20190806012959.fasta -output /Users/daia1/MSK/work/projects/FMAP/software/FMAP/FMAP_data/orthology_uniref90_2_2157_4751.20190806012959.udb

---Fatal error---
Memory limit of 32-bit process exceeded, 64-bit build required`

Thank you and happy new year.

Angel

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/FMAP_plot.pl: Use of uninitialized value $_ in pattern match (m//) at /usr/local/FMAP/FMAP_plot.pl line 38.

Any suggestions?

Hello!

I would like to make a heatmap of the abundances of KOs that are linked to the significantly enriched pathways across all of my samples. Is there a way to do this using FMAP? For example, if the photosynthesis pathway is enriched across a sample group, would it be possible to link the pathway back to the KO's used to construct that pathway and then construct a data matrix of those abundances?

Thanks for your time!

Greetings

I have been trying to use your tool, and a problem arose in the FMAP_assembly.pl part of the workflow.

diamond: error: no such option: --query
ERROR in FMAP_assembly.pl: readline() on closed filehandle $reader at FMAP_assembly.pl line 283.

I compiled FMAP as it is suggested, and DIAMOND was installed as follows:

wget http://github.com/bbuchfink/diamond/releases/download/v0.9.9/diamond-linux64.tar.gz
tar xzf diamond-linux64.tar.gz
sudo apt-get install python-configobj

Since I have used DIAMOND before without such errors, I have no idea what is going on here. I did associated FMAP with the DIAMOND binary that so far gave me no errors.

Thank you for your attention

Hello,
Thank you for the excellent pipeline tool.

I have a question about the FMAP_comparison.pl. I have 4 samples in duplicate, how i can run the comparison step (sample group information) ?

Thanks.

Hi any idea why it´s not creating the multithreads ??

echo "perl /home/da/work/FMAP/FMAP_mapping.pl allgenes.fa -p 10 -t tmp > outfile" | qsub -pe parallel_smp 10 -e err -o out

==> err <==
[3.08769s]
Building query histograms... [0.144188s]
Error: Failed to create thread.

Hi there,
I am testing out your program with a single sample. The FMAP_assembly work flow worked. However I am trying the FMAP_mapping work flow and get an error when parsing the output of FMAP_mapping.pl to FMAP_quantification.pl

$ FMAP_quantification.pl blastx_hits.txt > CS1BS_mapping_abundance.txt

ERROR in /home/joseph/biotools/programs/FMAP-0.10/FMAP_quantification.pl: Use of uninitialized value $percentIdentity in numeric lt (<) at /home/joseph/biotools/programs/FMAP-0.10/FMAP_quantification.pl line 86, <$reader> line 1.

perl version is v5.22.1 on ubuntu server.

First 10 lines of my blastx_hits.txt

M00566:77:000000000-ATBW8:1:2106:7118:2648 K06911_UniRef90_E8YRU9 50.0 70 35 0 211 2 28 97 5.5e-11 70.9
M00566:77:000000000-ATBW8:1:2106:14488:2648 K08641_UniRef90_A0A1D7QDD3 50.7 71 35 0 1 213 158 228 1.1e-17 93.6
M00566:77:000000000-ATBW8:1:2106:9279:2649 K02037_UniRef90_A0A0D5NE94 75.3 97 24 0 291 1 186 282 1.4e-33 146.4
M00566:77:000000000-ATBW8:1:2106:8751:2649 K13688_UniRef90_D3P6W0 51.8 112 40 1 1 294 296 407 5.6e-19 97.8
M00566:77:000000000-ATBW8:1:2106:9476:2650 K00784_UniRef90_D2BNS6 43.5 62 35 0 188 3 8 69 3.8e-07 58.5
M00566:77:000000000-ATBW8:1:2106:16489:2650 K01961_UniRef90_F8I902 76.9 52 12 0 24 179 1 52 2.9e-15 84.7
M00566:77:000000000-ATBW8:1:2106:14734:2650 K02660_UniRef90_K9THH3 41.8 98 55 2 300 10 665 761 1.0e-07 60.5
M00566:77:000000000-ATBW8:1:2106:14734:2650 K02660_UniRef90_K9THH3 37.9 58 33 1 198 25 576 630 5.4e-01 38.1
M00566:77:000000000-ATBW8:1:2106:7969:2650 K03088_UniRef90_C1AB78 57.3 89 38 0 6 272 14 102 5.9e-23 110.9

Dear sir:
I am doing a functional comparison for two group of samples. I used ngless to do the KEGG based profiling.
And I tried to use FMAP for my function comparison.
I am having a problem for my FMAP_module.pl comand.
It complained that my fisher test failed because of such error.

Problem while running this R command:
p.value <- fisher.test(matrix(c(18,13,4776,-2406), 2), alternative = "greater")$p.value

Error:
fisher.test(matrix(c(18, 13, 4776, -2406), 2), alternative = "greater") :
all entries of 'x' must be nonnegative and finite
Execution halted

However, the same script FMAP_module.pl works fine for the example dataset.
I tried to modify the script to print something.
my $test= $orthologyCount - $moduleOrthologyCount - $targetOrthologyCount + $moduleTargetOrthologyCount;
print $orthologyCount,",",$moduleOrthologyCount,",",$targetOrthologyCount,",",$moduleTargetOrthologyCount,",",$test,"\n";

the result looks like this.
2401,31,4794,18,-2406
2401,12,4794,7,-2398
2401,20,4794,13,-2400
2401,15,4794,10,-2398
2401,1,4794,1,-2393
2401,6,4794,4,-2395
2401,6,4794,4,-2395
2401,5,4794,5,-2393
2401,40,4794,27,-2406
2401,6,4794,5,-2394
2401,34,4794,22,-2405
2401,9,4794,7,-2395
2401,9,4794,6,-2396
2401,12,4794,6,-2399
2401,4,4794,3,-2394
2401,14,4794,9,-2398

This made me to think about the kegg orthology I used. They came from the result of gene profiling by eggnog.
I noticed that many Ks were not in your KEGG database. (You seem to use KEGG_orthology.txt for profiling?? )
I think the variable represent the meanings. Please kindly explain what are their meaning and how you calculated them
They are all based on orthology in KEGG_orthology2module.txt ???
$orthologyCount ---- total orthology count ???
$moduleOrthologyCount ---- total orthologyCount in this module ???
$targetOrthologyCount ---- orthologyCount passed ???
$moduleTargetOrthologyCount ---- orthologyCount of passed in this module ???

Please kindly suggest,

my1.comparison.txt

Hi,
I am working on a dataset consisting of normal and crohn's disease patients sample. After mapping KO genes to pathways I am getting a plot of pathways, but how to determine those differentially abundant pathways are from which sample?

Hi,
When computing abundances i see a strange behaviour (see exemple below)
Each file processed individually and then grouped.

I would expect the sum of the two files should be 11+7=18 genes and it returns 17 genes ??
Not sure if there is an extra filter added beyond the 80% ident.

perl FMAP_quantification.pl 36.uniprot.blast.txt  | grep K00001
K00001  E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]       7     997.386527521675

perl FMAP_quantification.pl 35.uniprot.blast.txt  | grep K00001
K00001  E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]       11      416.346777952545

perl FMAP_quantification.pl 35.uniprot.blast.txt  36.uniprot.blast.txt | grep K00001
K00001  E1.1.1.1, adh; alcohol dehydrogenase [EC:1.1.1.1]       17      537.487924074303

Hi,
Really like FMAP, starting to learn how to use it. Just wondered how you calculated RPK - I saw your code says readRpk = 1 / ($proteinLength * 3 / 1000). Wondered why you multiplied proteinlength by 3. Shouldnt it just be readRpk = 1 / ($proteinLength / 1000)?

Also would there be a update that builds a database on the entire Uniref90 for mapping and quantification rather than just the IDs that have KO. I would like to use it for gene enrichment analysis using GO.

Thanks,
Nabil

Running perl $FMAP_DIR/FMAP_prepare.pl -k results in: ERROR in FMAP_prepare.pl: Use of uninitialized value $line in chomp at FMAP_prepare.pl line 186.

I completed the first step and got the output file (file1).
But, when I run perl FMAP_quantification.pl [file1] > [file2], it shows ERROR in FMAP_quantification.pl: Use of uninitialized value $orthology in hash element at FMAP_quantification.pl line 71, <$reader> line 1773. What should do to fix it.

I tried to run the FMAP_all.pl script on multiple datasets (the example dataset among them) and got the following error message every time at the mapping step:

Error: Error calling stat on file [filepath]
" is not available.a/FMAP/FMAP_mapping.pl: The input "[file]

After checking the .sh file created by the program, the problem seems to be that there is an "^M" ending after each filename.
Converting the .config and .sh files with the dos2unix tool solved the problem for me.

Hi @jiwoongbio

I'm trying to use FMAP only for the final steps of comparison and statistical testing, so I need to create the right input format for FMAP_comparison.pl

My table head looks like this:

But when I try to run the command:
perl FMAP_comparison.pl abundance.txt SI3U_2017,SI3L_2017,SB_12_2017,SB_02_2017,SB_02_2018 CB4_2018,CBIA_2018,CB1_2018,CBIW_2018,CBIW_02_2017,CBIW_12_2017 > orthology_test_stat.txt

It returns:
ERROR in FMAP_comparison.pl: The sample "CBIW_12_2017" is not on the table.

I'm guessing there is something wrong with my format, but it looks exactly like the example files.. Thanks for the help!

Tried to run 'perl FMAP_download.pl' and got the following error:

ERROR: cannot verify qbrc.swmed.edu's certificate, issued by '/C=US/ST=MI/L=Ann Arbor/O=Internet2/OU=InCommon/CN=InCommon RSA Server CA':
Issued certificate has expired.
To connect to qbrc.swmed.edu insecurely, use `--no-check-certificate'.
ERROR in FMAP_download.pl: Use of uninitialized value $line in chomp at FMAP_download.pl line 127.

Seems like a certificate needs to be updated.

Thanks

Any chance of making a conda install for FMAP. So many of us use this installation approach it would be a real help.

Hello!

I was wondering if there was a way to obtain the direction (log2foldchange value) of the significantly different enriched pathways that are revealed from the FMAP_pathway.pl command. Is there a way to do this using the FMAP_module.pl command to?

Thanks!

Is there any method in place to do the FMAP_mapping.pl step for paired end fastq files? Is giving both the files as parameters for the perl script sufficient or is there any other way to go about this?