Execution halted when writing SBML

[NatashaJorge]

Hello!

I tried running gapseq doall with E. coli genome and I get the following error when writing the xml file.

Wrote file GCA_000005845.2_ASM584v2_genomic.xml Patching file GCA_000005845.2_ASM584v2_genomic.xml ...Error in (grp_block_start + 1):n_lines : argument of length 0 Calls: write_gapseq_sbml -> grep -> is.factor Execution halted

Please, do you know how I can fix it?

This is my command line:

$ time gapseq doall GCA_000005845.2_ASM584v2_genomic.fna

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

gapseq version: 1.2 9b30141 linux-gnu #1 SMP PREEMPT_DYNAMIC Thu Aug 4 02:06:53 UTC 2022

####################### #Checking dependencies# ####################### GNU Awk 5.1.0, API: 3.0 sed (GNU sed) 4.8 grep (GNU grep) 3.4 This is perl 5, version 32, subversion 1 (v5.32.1) built for x86_64-linux-thread-multi tblastn: 2.13.0+ exonerate from exonerate version 2.4.0 bedtools v2.30.0 barrnap 0.9 - rapid ribosomal RNA prediction R version 4.1.3 (2022-03-10) -- "One Push-Up" R scripting front-end version 4.1.3 (2022-03-10) git version 2.37.1 GNU parallel 20220722

Missing dependencies: 0

##################### #Checking R packages# ##################### data.table 1.14.2 stringr 1.4.0 sybil 2.2.0 getopt 1.20.3 doParallel 1.0.17 foreach 1.5.2 R.utils 2.12.0 stringi 1.7.8 glpkAPI 1.3.3 BiocManager 1.30.18 Biostrings 2.62.0 jsonlite 1.8.0 CHNOSZ 1.4.3

Missing R packages: 0

############################## #Checking basic functionality# ############################## Optimization test: OK Building full model: OK Blast test: OK

Passed tests: 3/3

Thanks for your time and attention, Best wishes, Natasha