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Nesvilab / philosopher

PeptideProphet, PTMProphet, ProteinProphet, iProphet, Abacus, and FDR filtering
https://philosopher.nesvilab.org
GNU General Public License v3.0
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wrong output using `${PHILOSOPHER} database` v4.3 #365

Closed cpanse closed 2 years ago

cpanse commented 2 years ago

Describe the bug

${PHILOSOPHER} database--id ... with different UP IDs always returns human

To Reproduce

Steps to reproduce the behavior:

PHILOSOPHER=/usr/local/nesvilab/philosopher_v4.3.0/philosopher 

${PHILOSOPHER} workspace --clean

${PHILOSOPHER} workspace --init 

${PHILOSOPHER} database --id UP000000625 --contam --reviewed  
${PHILOSOPHER} database --id UP000001940 --contam --reviewed  
${PHILOSOPHER} database --id UP000005640,UP000000558,UP000002311 --contam --reviewed

output:

cpanse@fgcz-c-073:/scratch/FRAGPIPE.databases > md5sum  *.fas
161ce45546a70b4b00d75b9445cdc712  2022-07-04-decoys-UP000000625.fas
a5d8dcdc1b90608804ba00cb8a8820f7  2022-07-04-decoys-reviewed-contam-UP000000625.fas
a5d8dcdc1b90608804ba00cb8a8820f7  2022-07-04-decoys-reviewed-contam-UP000001940.fas
a5d8dcdc1b90608804ba00cb8a8820f7  2022-07-04-decoys-reviewed-contam-UP000005640-UP000000558-UP000002311.fas
cpanse@fgcz-c-073:/scratch/FRAGPIPE.databases > head -n 1 *.fas
==> 2022-07-04-decoys-UP000000625.fas <==
>rev_tr|A0A024QZ33|A0A024QZ33_HUMAN Nuclear speckle splicing regulatory protein 1 OS=Homo sapiens OX=9606 GN=NSRP1 PE=1 SV=1

==> 2022-07-04-decoys-reviewed-contam-UP000000625.fas <==
>rev_sp|A0A024RBG1|NUD4B_HUMAN Diphosphoinositol polyphosphate phosphohydrolase NUDT4B OS=Homo sapiens OX=9606 GN=NUDT4B PE=3 SV=1

==> 2022-07-04-decoys-reviewed-contam-UP000001940.fas <==
>rev_sp|A0A024RBG1|NUD4B_HUMAN Diphosphoinositol polyphosphate phosphohydrolase NUDT4B OS=Homo sapiens OX=9606 GN=NUDT4B PE=3 SV=1

==> 2022-07-04-decoys-reviewed-contam-UP000005640-UP000000558-UP000002311.fas <==
>rev_sp|A0A024RBG1|NUD4B_HUMAN Diphosphoinositol polyphosphate phosphohydrolase NUDT4B OS=Homo sapiens OX=9606 GN=NUDT4B PE=3 SV=1
cpanse@fgcz-c-073:/scratch/FRAGPIPE.databases >

Please complete the following information:

cpanse@fgcz-c-073:/scratch/FRAGPIPE.databases > uname -a
Linux fgcz-c-073 5.4.121-0504121-generic #202105220633 SMP Sat May 22 10:38:55 UTC 2021 x86_64 GNU/Linux

cpanse@fgcz-c-073:/scratch/FRAGPIPE.databases > ${PHILOSOPHER}  version
INFO[16:18:43] Current Philosopher build and version         build=1656533314 version=v4.3.0

Additional context

I double checked with @tobiasko and @wolski . What am I doing wrong?

guoci commented 2 years ago

The UP ID was hardcoded to human by accident, please use the fix below. philosopher-v4.3.0-RC.zip

cpanse commented 2 years ago 
cpanse@fgcz-c-073:/scratch/FRAGPIPE.databases > ${PHILOSOPHER} version
INFO[20:04:37] Current Philosopher build and version         build=202207041335 version=v4.3.0
cpanse@fgcz-c-073:/scratch/FRAGPIPE.databases > head -n 1 *.fas
==> 2022-07-04-decoys-UP000000625.fas <==
>rev_tr|A0A385XJN2|A0A385XJN2_ECOLI Uncharacterized protein OS=Escherichia coli (strain K12) OX=83333 GN=ygiA PE=4 SV=1

==> 2022-07-04-decoys-reviewed-contam-UP000000625.fas <==
>rev_sp|A0A385XJ53|INSA9_ECOLI Insertion element IS1 9 protein InsA OS=Escherichia coli (strain K12) OX=83333 GN=insA9 PE=3 SV=1

==> 2022-07-04-decoys-reviewed-contam-UP000001940.fas <==
>rev_sp|A0A061ACU2|PIEZ1_CAEEL Piezo-type mechanosensitive ion channel component 1 OS=Caenorhabditis elegans OX=6239 GN=pezo-1 PE=1 SV=1

==> 2022-07-04-decoys-reviewed-contam-UP000005640-UP000000558-UP000002311.fas <==
>rev_sp|A0A023PYF4|YE145_YEAST Uncharacterized protein YER145C-A OS=Saccharomyces cerevisiae (strain ATCC 204508 / S288c) OX=559292 GN=YER145C-A PE=3 SV=1
cpanse@fgcz-c-073:/scratch/FRAGPIPE.databases >

thanks; C