parsing problem with Ab3P

[mandiayba]

Le module Ab3P ne passe pas sur plusieurs textes avec la version alvisnlp 0.10.0 avec le plan suivant. Un batch pour reproduire est disponible ici https://forgemia.inra.fr/omnicrobe/text-mining-workflow/-/blob/dev/corpora/pubmed/batches-test/2765/2765.xml

[2023-03-28 09:47:29.290][entities.abbrev] Failed to find sentence: Based on our observations, we speculate that the presence of alternative SMCs such as MksB or other SMC homologues might have rescued the scpb mutant phenotype in M. smegmatis .
[2023-03-28 09:47:29.290][entities.abbrev] in text: Multi-subunit SMC complexes are required to perform essential functions, such as chromosome compaction, segregation and DNA repair, from bacteria to humans. Prokaryotic SMC proteins form complexes with two non-SMC subunits, ScpA and ScpB, to condense the chromosome. The mutants of both                      scpa                      and                      scpb                      genes in                      Bacillus subtilis                      have been shown to display characteristic phenotypes such as growth defects and increased frequency of anucleate cells. Here, we studied the function of the Smc-ScpAB complex from                      Mycobacterium smegmatis                     . We observed no significant growth difference between the                      scpb                      null mutant and wild-type                      M. smegmatis                      under both standard and stress conditions. Furthermore, we characterized the Smc-ScpAB holocomplex from                      M. smegmatis                     . The MsSMC consists of the dimerization hinge and ATPase head domains connected by long coiled-coils. The MsSMC interacts with two non-SMC proteins, ScpA and ScpB, and the resulting holocomplex binds to different DNA substrates independent of ATP. The Smc-ScpAB complex showed DNA-stimulated ATPase activity in the presence of ssDNA. A cytological profiling assay revealed that upon overexpression the Smc-ScpAB ternary complex compacts the decondensed nucleoid of rifampicin-treated wild-type and null                      mukb                      mutant of                      Escherichia coli in vivo                     . Together, our study suggests that                      M. smegmatis                      has a functional Smc-ScpAB complex capable of DNA binding and condensation. Based on our observations, we speculate that the presence of alternative SMCs such as MksB or other SMC homologues might have rescued the                      scpb                      mutant phenotype in                      M. smegmatis                     .
[2023-03-28 09:47:29.307][entities.abbrev] ab3p-to-alvisnlp
[2023-03-28 09:47:29.310][alvisnlp] �[31;1mSEVERE unrecoverable error

### error type:
###     fr.inra.maiage.bibliome.alvisnlp.core.module.ProcessingException
###
### error message:
###     failed check line : 'Lactobacillus rhamnosus                  GG Reduces                  ?-conglycinin-                 Allergy-Induced Apoptotic Cells by Regulating                  Bacteroides                  and Bile Secretion Pathway in Intestinal Contents of BALB/c Mice.' / 'Lactobacillus rhamnosus                  GG Reduces                  ?-conglycinin-                 Allergy-Induced Apoptotic Cells by Regulating                  Bacteroides                  and Bile Secretion Pathway in Intestinal Contents of BALB/c Mice.'
###
### stack trace:
###     fr.inra.maiage.bibliome.alvisnlp.bibliomefactory.modules.ab3p.Ab3PExternalHandler.collect(Ab3PExternalHandler.java:69)
###     fr.inra.maiage.bibliome.alvisnlp.core.module.lib.ExternalHandler.doCollect(ExternalHandler.java:139)
###     fr.inra.maiage.bibliome.alvisnlp.core.module.lib.ExternalHandler.start(ExternalHandler.java:101)
###     fr.inra.maiage.bibliome.alvisnlp.core.module.lib.ExternalHandler.start(ExternalHandler.java:106)
###     fr.inra.maiage.bibliome.alvisnlp.bibliomefactory.modules.ab3p.Ab3P.process(Ab3P.java:49)
###     fr.inra.maiage.bibliome.alvisnlp.bibliomefactory.modules.ab3p.Ab3P.process(Ab3P.java:36)
###     fr.inra.maiage.bibliome.alvisnlp.core.app.cli.CommandLineProcessingContext.processCorpus(CommandLineProcessingContext.java:121)
###     fr.inra.maiage.bibliome.alvisnlp.bibliomefactory.modules.Sequence_Impl.process(Sequence_Impl.java:112)
###     fr.inra.maiage.bibliome.alvisnlp.bibliomefactory.modules.Sequence_Impl.process(Sequence_Impl.java:45)
###     fr.inra.maiage.bibliome.alvisnlp.core.app.cli.CommandLineProcessingContext.processCorpus(CommandLineProcessingContext.java:121)
###     fr.inra.maiage.bibliome.alvisnlp.core.app.cli.AbstractAlvisNLP.process(AbstractAlvisNLP.java:1060)
###     fr.inra.maiage.bibliome.alvisnlp.core.app.cli.AbstractAlvisNLP.run(AbstractAlvisNLP.java:1178)
###     fr.inra.maiage.bibliome.alvisnlp.core.app.cli.AlvisNLP.main(AlvisNLP.java:87)

�[0m[Tue Mar 28 11:47:29 2023]
Error in rule run_pubmed_entities:
    jobid: 0
    output: corpora/pubmed/batches/2765/relations.txt, corpora/pubmed/batches/2765/phenotype-relations.txt, corpora/pubmed/batches/2765/uses-relations.txt, corpora/pubmed/batches/2765/microorganisms.txt, corpora/pubmed/batches/2765/habitats.txt, corpora/pubmed/batches/2765/phenotypes.txt, corpora/pubmed/batches/2765/uses.txt, corpora/pubmed/batches/2765/index
    shell:
        
		mkdir -p corpora/pubmed/batches/2765/bionlp-st && alvisnlp -J-XX:+UseSerialGC -J-Xmx30g -cleanTmp -tmp /work_projet/omnicrobe_data/tm_workflow/text-mining-workflow/tmp -verbose 		-log alvisnlp.log 		-alias format pubmed 		-alias input corpora/pubmed/batches/2765/batch.xml 		-alias input-xslt corpora/pubmed/microbes-2019-pubmed2alvisnlp.xslt 		-alias batch batch=2765 		-outputDir corpora/pubmed/batches/2765/ 		-feat inhibit-syntax inhibit-syntax 		-alias ontobiotope-habitat ancillaries/BioNLP-OST+EnovFood-Habitat.obo 		-xalias '<ontobiotope-tomap-habitat empty-words="ancillaries/stopwords_EN.ttg" graylist="ancillaries/graylist_extended.heads" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Habitat.tomap</ontobiotope-tomap-habitat>' 		-alias ontobiotope-phenotypes ancillaries/BioNLP-OST+EnovFood-Phenotype.obo 		-xalias '<ontobiotope-tomap-phenotypes empty-words="ancillaries/stopwords_EN.ttg" whole-proxy-distance="false">ancillaries/BioNLP-OST+EnovFood-Phenotype.tomap</ontobiotope-tomap-phenotypes>' 		-alias ontobiotope-use ancillaries/BioNLP-OST+EnovFood-Use.obo 		-alias taxid_microorganisms ancillaries/extended-microorganisms-taxonomy/taxid_microorganisms.txt 		-alias taxa+id_full ancillaries/extended-microorganisms-taxonomy/taxa+id_full.txt 		plans/entities.plan
		
        (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message