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jiwoongbio / FMAP

Functional Mapping and Analysis Pipeline for metagenomics and metatranscriptomics studies
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Getting error at FMAP_quantification.pl #5

Closed JosephAdelskov closed 6 years ago

JosephAdelskov commented 6 years ago

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

jiwoongbio commented 6 years ago

Hi Joseph,

The input and output table files of FMAP have values separated by "tab". Can you please check if the delimiter of "blastx_hits.txt" is tab or space? Thanks.

Best Regards, Jiwoong

JosephAdelskov commented 6 years ago

Hi Jiwoong,

The file does appear to be tab delimited. I also tried running the file through awk to replace with tabs but I still get the same error.

jiwoongbio commented 6 years ago

The quantification function works well with first 10 lines of your "blastx_hits.txt". Can you please share the whole file? Do you have a way to share?

JosephAdelskov commented 6 years ago

Sorry for the late reply.

I don't have a simple way to send the whole file but I tried running just the sample I had posted which returned the same error. Could there be perl libraries specific dependency to this script that I am missing?

JosephAdelskov commented 6 years ago

I was able to work around the problem by cloning the repository instead of using the release. Making sure it was directed to the correct version of diamond and run the mapping analysis again.