Comments (9)
Hi Arianna, hm this looks strange indeed! It seems that something in the subunit detection is not running correctly. Do you have exonerate installed? gapseq needs fastaindex and fastafetch from this package.
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Hi,
I followed your suggestion and I checked exonerate, but it is properly installed. I have performed additional checks on the other dependencies needed and they seem ok.
I was wondering if the problem could be due to lack of space in the "/tmp/" directory where gapseq is trying to save these files (there are a couple of Gb available). Alternatively, is it possible to set the working directory where gapseq is writing these files?
Thanks again for your assistance.
Arianna
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Hi,
After a series of trials, I managed to fix all the installation problems, they were mainly related to the sybilSBML that was not properly installed at the beginning. We would like to know if you are planning in the next future to complete the section related to Archaea pathways prediction and implementation in the models.
Thanks in advance.
Sincerely
Arianna
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Dear Arianna,
We are currently testing and implementing first features for the reconstruction of archaeal metabolic networks. We aim to add the possibility to reconstruct Archaea models in the next 3-4 weeks and provide an example workflow for Archaea in the gapseq documentation.
In the meanwhile, the first step of gapseq, the pathway prediction, works already for Archaea. For instance:
$gapseq find -p all -t Archaea ../genomes/genome.fna.gz
I hope this helps and we will let you know, when more features for Archaea are implemented.
Best wishes
Silvio
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Dear Silvio,
thank you a lot for your help and the useful information.
Looking forward to the Archaea universe then :)
Best regards,
Arianna
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Dear Silvio,
any news about the Archaea universe? 🥇
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Dear Arianna,
yes, we are still performing some tests for Archaea-specific pathways, but with the latest gapseq development version you can do the following example workflow to reconstruct a metabolic model for an Archaeal genome (in this example xyz.fna.gz
):
#!/bin/bash
model="xyz"
# Reaction & pathway prediction
./gapseq find -p all -t Archaea $model.fna.gz
# Transporter prediction
./gapseq find-transport $model.fna.gz
# Draft network reconstruction
./gapseq draft -r $model-all-Reactions.tbl -t $model-Transporter.tbl -p $model-all-Pathways.tbl -l 100 -b archaea
# Gapfilling
./gapseq fill -m $model-draft.RDS -n [media.csv] -c $model-rxnWeights.RDS -g $model-rxnXgenes.RDS -b 100
For [media.csv]
please provide the path to the gapfilling media. In the gapseq directory dat/media/
there are two minimal growth media, that we used in our test cases for Methanogens:
dat/media/MM_anaerobic_Acetate_H2.csv
dat/media/MM_anaerobic_CO2_H2.csv
We hope this helps and please let us know if you experience issues.
Best regards
Silvio
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there is also a tutorial on archaea reconstruction out:
https://gapseq.readthedocs.io/en/latest/tutorials/archaea.html
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please reopen if still an issue
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Related Issues (20)
- Reaction inferred from pseudogene regions when using gapseq on genome fasta file.
- CHNOSZ NOT FOUND HOT 1
- [Request Update] [Tutorial] For anyone who intend to use CPLEX in gapseq HOT 3
- Diamond not used for the transport-find command HOT 2
- Could not use find-transport function using '-m' option for specific metabolite. HOT 8
- subex.tbl issue HOT 1
- Any plans on updating MetaCyc database? HOT 2
- Using seed reaction database in Adapt function HOT 8
- adding pathways| Error: No model reactions found and Error: Error in !opt$sbml.no.output : invalid argument type HOT 6
- Inquiry on instllation HOT 2
- Inquiry on error HOT 5
- Missing exchange reactions are not being added in the "adapt" module HOT 3
- Seawater and related media HOT 1
- Possible inconsistencies in pathway completeness percentages. HOT 2
- windows installation problems HOT 6
- Exploit gapfilled model for metabolic comparison HOT 5
- Comparison of amino acid auxotrophy prediction with GapMind HOT 3
- transporter prediction leads to a zerobytes Transporter.tbl result HOT 2
- gapseq with Gurobi HOT 2
- Gapseq returns models based on SEED reactions even when database is specified as vmh
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