Inquiry on error

[songmj86]

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 9e85ab1
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]

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]

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]

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]

top 10 produced compounds is indeed just a list of compounds with the highest outflux obtained from pFBA

gapseq/src/gf.suite.R

Lines 668 to 686 in 86f1896

	mod.fill4.sol <- optimizeProb(mod.fill4, retOptSol=F, algorithm = "mtf")
	dt.sol <- data.table(rxn = mod.fill4@react_id,
	flux = mod.fill4.sol$fluxes[1:mod.fill4@react_num],
	lb = mod.fill4@lowbnd,
	met.name = gsub("-e0 Exchange","",mod.fill4@react_name))
	dt.sol[, met.name := gsub(" Exchange","", met.name)]
	dt.sol.u <- copy(dt.sol[flux < 0 & grepl("^EX_", rxn) & flux <= lb*0.999])
	dt.sol.p <- copy(dt.sol[flux > 0 & grepl("^EX_", rxn)][order(-flux)][1:min(c(10,.N))])
	cat("\rGapfill summary:\n")
	cat("Filled components: ",mod.fill4.counter, "(",paste(mod.fill4.names, collapse = ","),")\n")
	cat("Added reactions: ",length(mod.fill4@react_id)-length(mod.fill3@react_id),"\n")
	cat("Final growth rate: ",mod.fill4.sol$fluxes[which(mod.fill4@obj_coef==1)],"\n\n")
	cat("Uptake at limit:\n")
	cat(paste0(paste(dt.sol.u$met.name, round(-dt.sol.u$flux, digits = 3), sep = ":"), collapse = ", "),"\n\n")
	cat("Top 10 produced metabolites [mmol / (gDW * hr)]:\n")
	cat(paste0(paste(dt.sol.p$met.name, round(dt.sol.p$flux, digits = 3), sep = ":"), collapse = ", "),"\n")

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