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jiwoongbio / FMAP

Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies
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FMAP_comparison.pl error - what is right abundance.txt format? #15

Closed jzrapp closed 4 years ago

jzrapp commented 4 years ago

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:

Screen Shot 2019-11-27 at 5 00 45 PM

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!

jzrapp commented 4 years ago

When I run the command on the example table SRP044400.table.txt everything runs fine. When I remove one or two columns/samples (and also remove them the comparison.pl command) the script gives the same error.. always the last column that is "not on the table"..

jzrapp commented 4 years ago

ok, sorry, this was a line ending issue. Apparently, my editor changed them when resaving. Had to transform all line endings to unix and then it worked fine.