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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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Pipeline error BlastHSPMapperParamsNew #10

Closed maringos closed 5 years ago

maringos commented 5 years ago

Dear All,

I am working with the GapSeq version fe42620 and I am facing the following issue. My input is ~/gapseq/./gapseq_quickstart.sh NZ_CP015698_1.fasta ~/gapseq/dat/media/MM_glu.csv The output is:

....
No transporter found for compounds (existing transporter/exchanges should be removed?):
acetoin
butyrate
cholesterol
cysteine
d-lactate
fucose
gluconate
glycogen
hydrogen
hydrogen sulfide
inosine
melibiose
n-acetyl-d-glucosamine
n-acetylgalactosamine
propionate
pyruvate
raffinose
raffinose
rhamnose
ribitol
salicin
sucrose
tryptophan
tyrosine
uridine
index file NZ_CP015698_1.fasta.tmp.fai not found, generating...
blastn: symbol lookup error: /usr/lib/ncbi-blast+/libxblast.so: undefined symbol: BlastHSPMapperParamsNew

Predicted gram staining:  ambiguous 
Error in build_draft_model_from_blast_results(blast.res = blast.res, transporter.res = transporter.res,  : 
  ERROR: Gram-staining prediction failed or ambiguous result. Please check whether genome sequence contains 16S rRNA gene(s).
No traceback available 
Error in saveRDS(mod$mod, file = paste0(model.name, ".RDS")) : 
  object 'mod' not found
2: stop("ERROR: Gram-staining prediction failed or ambiguous result. Please check whether genome sequence contains 16S rRNA gene(s).")
1: build_draft_model_from_blast_results(blast.res = blast.res, transporter.res = transporter.res, 
       gram = gram, model.name = model.name, genome.seq = genome.seq, 
       high.evi.rxn.BS = high.evi.rxn.BS, script.dir = script.dir)
Error in saveRDS(mod$cand.rxns, file = paste0(model.name, "-rxnWeights.RDS")) : 
  object 'mod' not found
1: saveRDS(mod$mod, file = paste0(model.name, ".RDS"))
Error in gzfile(file, "rb") : cannot open the connection
Calls: readRDS -> gzfile
In addition: Warning message:
In gzfile(file, "rb") :
  cannot open compressed file 'NZ_CP015698_1-rxnWeights.RDS', probable reason 'No such file or directory'
Execution halted

I would be grateful if you had a look on that. Just to inform you that the fasta file worked with a previous commit.

Kind Regards, @maringos

Waschina commented 5 years ago

@jotech do you have an idea, why George has this issue? I did not figure it out so far.

maringos commented 5 years ago

Dear All,

I would like to inform you that after trying the commit https://github.com/jotech/gapseq/commit/f3093cc3e896dcee2495a81090584be2935bf472 in a brand new debian, GapSeq can finish its operation successfully.

Kind Regards, Georgios