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jotech / gapseq

Informed prediction and analysis of bacterial metabolic pathways and genome-scale networks
GNU General Public License v3.0
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Inquiry on error #213

Open songmj86 opened 7 months ago

songmj86 commented 7 months ago

for bug reports and errors please report the output of: ./gapseq test

Hi

I am now test-running a gapseq with the following command

conda activate Gapseq ; Tool="/home/sandia/softwares/gapseq/gapseq" ; $Tool doall -h ; $Tool doall -K 70 Bin10.fa ;

And I got several error "Error in checkForRemoteErrors(val)"

But the process is keep running.

Can I ask the meaning of the error ? Does it affect the outcomes? If so, how can I resolve the issue?

Thank you !

Bin10.fa /tmp/tmp.bTF58C5zAg Nucleotide fasta detected. Warning: [blastn] Query is Empty! Warning message: package ‘data.table’ was built under R version 4.3.3 Predicted taxonomy: Bacteria Checking updates for Bacteria /home/softwares/gapseq/src/../dat/seq/Bacteria Reference sequences are up-to-date. 3540 Warning: [tblastn] lcl|Query_3 UniRef50_A0A6J4S0Y1 Aspartyl-tRNA(Asn) amidotransferase subunit C @ Glutamyl-tRNA(Gln) amidotransferase subunit C (Fragment) n=1 Tax=uncultured Solirubrobacteraceae bacterium TaxID=1162706 RepID=A0A6J4S0Y1_9ACTN Subunit 3: Warning: Could not calculate ungapped Karlin-Altschul parameters due to an invalid query sequence or its translation. Please verify the query sequence(s) and/or filtering options Warning: [tblastn] lcl|Query_1 UniRef50_O30642 Monomethylamine methyltransferase MtmB1 n=108 Tax=cellular organisms TaxID=131567 RepID=MTMB1_METBA: Warning: One or more U or O characters replaced by X for alignment score calculations at positions 201 Warning: [tblastn] lcl|Query_1 UniRef90_Q18TV3 Trimethylamine methyltransferase MttB n=7 RepID=MTTB_DESHD: Warning: One or more U or O characters replaced by X for alignment score calculations at positions 330 Error in checkForRemoteErrors(val) : one node produced an error: URL rejected: Malformed input to a URL function Calls: parLapply ... clusterApply -> staticClusterApply -> checkForRemoteErrors Execution halted md5sum: 8373c6b3d06f1c3d61e20fe6e553b41e.fasta: No such file or directory cat: 8373c6b3d06f1c3d61e20fe6e553b41e.fasta: No such file or directory Error in checkForRemoteErrors(val) : one node produced an error: URL rejected: Malformed input to a URL function Calls: parLapply ... clusterApply -> staticClusterApply -> checkForRemoteErrors Execution halted md5sum: 8373c6b3d06f1c3d61e20fe6e553b41e.fasta: No such file or directory cat: 8373c6b3d06f1c3d61e20fe6e553b41e.fasta: No such file or directory %CPU %MEM COMMAND

The following is the "test outcome"

gapseq version: 1.2 9e85ab17 linux-gnu

111-Ubuntu SMP Tue Mar 5 20:16:58 UTC 2024

#######################

Checking dependencies

####################### ldconfig (Ubuntu GLIBC 2.35-0ubuntu3.6) 2.35 libsbml.so.5 -> libsbml.so.5.18.0 libsbml.so.5 -> libsbml.so.5.19.0 libglpk.so.40 -> libglpk.so.40.3.1 libglpk.so.40 -> libglpk.so.40.3.1 GNU Awk 5.3.0, API 4.0, PMA Avon 8-g1, (GNU MPFR 4.2.1, GNU MP 6.3.0) sed (GNU sed) 4.8 grep (GNU grep) 3.11 This is perl 5, version 34, subversion 0 (v5.34.0) built for x86_64-linux-thread-multi tblastn: 2.5.0+ exonerate from exonerate version 2.4.0 bedtools v2.31.1 barrnap 0.9 - rapid ribosomal RNA prediction R version 4.3.2 (2023-10-31) -- "Eye Holes" git version 2.42.0 GNU parallel 20240322 HMMER 3.4 (Aug 2023); http://hmmer.org/ bc 1.07.1

Missing dependencies: 0

#####################

Checking R packages

##################### data.table 1.15.2 stringr 1.5.1 sybil 2.2.0 getopt 1.20.4 doParallel 1.0.17 foreach 1.5.2 R.utils 2.12.3 stringi 1.8.3 glpkAPI 1.3.4 BiocManager 1.30.22 Biostrings 2.70.1 jsonlite 1.8.8 CHNOSZ 2.1.0 httr 1.4.7

Missing R packages: 0

##############################

Checking basic functionality

############################## Warning message: package ‘lattice’ was built under R version 4.3.3 Optimization test: OK Warning messages: 1: package ‘data.table’ was built under R version 4.3.3 2: package ‘lattice’ was built under R version 4.3.3 Building full model: OK Blast test: OK

Passed tests: 3/3

jotech commented 7 months ago

hi @songmj86

Thank you for reporting the issue! It seems related to parallelization. Could you try running

$Tool doall -K 1 Bin10.fa

and check whether the error occurs again?

songmj86 commented 6 months ago

Thanks for reply

I have another issue on xml file

Opening xml file shows "gapseq version:1.2 ...." as I want to examine "Top 10 produced metabolites"

But no result is shown

How can I resolve this issue?

The attachment is the output I got

Thank you !

Bin44.zip

Waschina commented 6 months ago

Hi @songmj86

the xml file is the genome-scale metabolic model in SBML-format. To predict metabolite production you can read the xml file and use flux-balance-analysis using software packages such as cobrapy or cobra toolbox.

jotech commented 6 months ago

top 10 produced compounds is indeed just a list of compounds with the highest outflux obtained from pFBA https://github.com/jotech/gapseq/blob/86f1896664998596ca0786d3fb14d23d0d6351bc/src/gf.suite.R#L668-L686

you should be able to reproduce with any cobra framework that can read sbml files.

SY0712 commented 5 months ago

Hi

I am not sure if this issue has been completely resolved, but I am experiencing the same problem.

Error in checkForRemoteErrors(val) : one node produced an error: URL rejected: Malformed input to a URL function Calls: parLapply ... clusterApply -> staticClusterApply -> checkForRemoteErrors Execution halted md5sum: 8373c6b3d06f1c3d61e20fe6e553b41e.fasta: No such file or directory cat: 8373c6b3d06f1c3d61e20fe6e553b41e.fasta: No such file or directory

And the process keeps running. End of run, I got outcomes.

"-K 1" is not working for me.

I saw the same issue on a closed page(link).

I understand you are busy, but could you please check?

Thank you.

"$ ./gapseq test" outcomes:

gapseq version: 1.2 2d739a5 linux-gnu

1 SMP Tue Nov 30 15:51:32 UTC 2021

#######################

Checking dependencies

####################### ldconfig (GNU libc) 2.17 libsbml.so.5 -> libsbml.so.5.18.0 libglpk.so.40 -> libglpk.so.40.3.1 libglpk.so.36 -> libglpk.so.36.0.1 GNU Awk 5.3.0, API 4.0, PMA Avon 8-g1, (GNU MPFR 4.2.1, GNU MP 6.3.0) sed (GNU sed) 4.8 grep (GNU grep) 3.11 This is perl 5, version 32, subversion 1 (v5.32.1) built for x86_64-linux-thread-multi tblastn: 2.15.0+ exonerate from exonerate version 2.4.0 bedtools v2.31.1 barrnap 0.9 - rapid ribosomal RNA prediction R version 4.3.3 (2024-02-29) -- "Angel Food Cake" git version 2.45.1 GNU parallel 20240322 HMMER 3.4 (Aug 2023); http://hmmer.org/ bc 1.07.1

Missing dependencies: 0

#####################

Checking R packages

##################### data.table 1.15.2 stringr 1.5.1 sybil 2.2.0 getopt 1.20.4 doParallel 1.0.17 foreach 1.5.2 R.utils 2.12.3 stringi 1.8.4 glpkAPI 1.3.4 BiocManager 1.30.23 Biostrings 2.70.1 jsonlite 1.8.8 CHNOSZ 2.1.0 httr 1.4.7

Missing R packages: 0

##############################

Checking basic functionality

############################## Optimization test: OK Building full model: OK Blast test: OK

Passed tests: 3/3