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harta55 / EnTAP

Eukaryotic Non-Model Transcriptome Annotation Pipeline - Latest Release v1.4.0 - Revamped final graphics coming soon!
https://entap.readthedocs.io/en/latest/
GNU General Public License v3.0
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boost::bad_any_cast: failed conversion using boost::any_cast #18

Closed dy-lin closed 4 years ago

dy-lin commented 4 years ago

Getting this error:

terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::bad_any_cast> >'
  what():  boost::bad_any_cast: failed conversion using boost::any_cast
/projects/amp/peptaid/scripts/run-entap.sh: line 173: 97242 Aborted                 (core dumped) $RUN_ENTAP --runP -i $transcriptome -t $threads --ini $config --out-dir $outdir $databases

Attached the debug file (for this transcriptome, and for the test_data), but it just shows that it only goes up to reading in the transcriptome:

Sun Jul 26 11:36:45 2020: Transcriptome Lines - END
Sun Jul 26 11:36:47 2020: Success!

The main difference between the transcriptome and the test_data, is that the transcriptome uses more of the (originally command-line) options than the test_data, but the debug file isn't super informative either.

Test Data: 

Current EnTAP Version: 0.10.2
Start time: Sun Jul 26 11:21:07 2020

Working directory has been set to: /projects/amp/peptaid/src/EnTAP-0.10.2-beta/entap_outfiles
User Inputs:
out-dir: /projects/amp/peptaid/src/EnTAP-0.10.2-beta/entap_outfiles
config: false
runP: true
runN: false
overwrite: false
ini: /projects/amp/peptaid/src/EnTAP/entap_config.ini
input: /projects/amp/peptaid/src/EnTAP/test_data/trinity.fnn
database: /projects/amp/peptaid/src/EnTAP/test_data/bin/swiss_prot_test.dmnd,
graph: false
no-trim: false
threads: 1
state: +
no-check: false
output-format: 1,3,4,
entap-db-bin: /projects/amp/peptaid/src/EnTAP/extra-db/bin/entap_database.bin
entap-db-sql: /projects/amp/peptaid/src/EnTAP/extra-db/databases/entap_database.db
entap-graph: /projects/amp/peptaid/src/EnTAP/src/entap_graphing.py
data-generate: false
data-type: 0,
fpkm: 0.500000
align: 
single-end: false
rsem-calculate-expression: /libs/RSEM-1.3.0//rsem-calculate-expression
rsem-sam-validator: /libs/RSEM-1.3.0//rsem-sam-validator
rsem-prepare-reference: /libs/RSEM-1.3.0//rsem-prepare-reference
convert-sam-for-rsem: /libs/RSEM-1.3.0//convert-sam-for-rsem
complete: false
frame-selection: 2
genemarkst-exe: gmst.pl
transdecoder-long-exe: /gsc/btl/linuxbrew/bin/TransDecoder.LongOrfs
transdecoder-predict-exe: /gsc/btl/linuxbrew/bin/TransDecoder.Predict
transdecoder-m: 50
diamond-exe: /gsc/btl/linuxbrew/bin/diamond
taxon: 
qcoverage: 50.000000
tcoverage: 50.000000
contam: 
e-value: 0.000010
uninformative: 
ontology: 0,
level: 1,
eggnog-sql: /projects/amp/peptaid/src/EnTAP/extra-db/databases/eggnog.db
eggnog-dmnd: /projects/amp/peptaid/src/EnTAP/extra-db/bin/eggnog_proteins.dmnd
interproscan-exe: /projects/spruceup_scratch/dev/Src/my_interproscan/interproscan-5.30-69.0/interproscan.sh
protein:

Transcriptome data:

Current EnTAP Version: 0.10.2
Start time: Sun Jul 26 11:35:38 2020

Working directory has been set to: /projects/amp/peptaid/hymenoptera/omonticola/venom/annotation_20200726_113527
User Inputs:
out-dir: /projects/amp/peptaid/hymenoptera/omonticola/venom/annotation_20200726_113527
config: false
runP: true
runN: false
overwrite: false
ini: /projects/amp/peptaid/hymenoptera/omonticola/venom/annotation_20200726_113527/entap_config_custom.ini
input: /projects/amp/peptaid/hymenoptera/omonticola/venom/expression_20200724_165228/rnabloom.transcripts.filtered.fa
database: /projects/amp/peptaid/src/EnTAP/extra-db/bin/uniprot_sprot.dmnd,/projects/amp/peptaid/src/EnTAP/extra-db/bin/uniprot_trembl.dmnd,/projects/amp/peptaid/src/EnTAP/extra-db/bin/nr.dmnd,/projects/amp/peptaid/src/EnTAP/extra-db/bin/refseq.dmnd,
graph: false
no-trim: false
threads: 1
state: +
no-check: false
output-format: 1,3,4,
entap-db-bin: /projects/amp/peptaid/src/EnTAP/extra-db/bin/entap_database.bin
entap-db-sql: /projects/amp/peptaid/src/EnTAP/extra-db/databases/entap_database.db
entap-graph: /projects/amp/peptaid/src/EnTAP/src/entap_graphing.py
data-generate: false
data-type: 0,
fpkm: 0.500000
align: 
single-end: false
rsem-calculate-expression: /libs/RSEM-1.3.0//rsem-calculate-expression
rsem-sam-validator: /libs/RSEM-1.3.0//rsem-sam-validator
rsem-prepare-reference: /libs/RSEM-1.3.0//rsem-prepare-reference
convert-sam-for-rsem: /libs/RSEM-1.3.0//convert-sam-for-rsem
complete: false
frame-selection: 2
genemarkst-exe: gmst.pl
transdecoder-long-exe: /gsc/btl/linuxbrew/bin/TransDecoder.LongOrfs
transdecoder-predict-exe: /gsc/btl/linuxbrew/bin/TransDecoder.Predict
transdecoder-m: 50
diamond-exe: /gsc/btl/linuxbrew/bin/diamond
taxon: insecta,
qcoverage: 50.000000
tcoverage: 50.000000
contam: bacteria,fungi,
e-value: 0.000010
uninformative: 
ontology: 0,1,
level: 1,
eggnog-sql: /projects/amp/peptaid/src/EnTAP/extra-db/databases/eggnog.db
eggnog-dmnd: /projects/amp/peptaid/src/EnTAP/extra-db/bin/eggnog_proteins.dmnd
interproscan-exe: /projects/spruceup_scratch/dev/Src/my_interproscan/interproscan-5.30-69.0/interproscan.sh
protein: pfam,panther,
dy-lin commented 4 years ago

Update:

If I run the test_data using the same .ini file as the transcriptome, the same error is encountered:

terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::bad_any_cast> >'
  what():  boost::bad_any_cast: failed conversion using boost::any_cast
./test.sh: line 5: 101772 Aborted                 (core dumped) ./EnTAP --runP -i $(pwd)/test_data/trinity.fnn -d $(pwd)/test_data/bin/swiss_prot_test.dmnd --ini $(pwd)/entap_config_custom.ini -t 1

Debug file here.

zhangrengang commented 4 years ago

I also get the same error:

$ ../v0.10.2/EnTAP/build/EnTAP  --runP -i trinity.faa -d /io/bin/EnTAP/test_data/test_data/bin/swiss_prot_test.dmnd --ini ../entap_config.ini
terminate called after throwing an instance of 'boost::exception_detail::clone_impl<boost::exception_detail::error_info_injector<boost::bad_any_cast> >'
  what():  boost::bad_any_cast: failed conversion using boost::any_cast
Aborted
harta55 commented 4 years ago

This is due to a parsing error of the "taxon"/"species" input. The software was treating is as a multi-string (as implied in the ini file) rather than just a single string. This is corrected and tagged as v0.10.3.

Thanks!

dy-lin commented 4 years ago

Ahh, speaking of which-- are we supposed to end all the options accepted multiple times with a , (e.g. protein=pfam,panther, and ontology=0,1,)? For example, if I had put taxon=insecta,, would this error have been avoided?

harta55 commented 4 years ago

No need to put a comma at the end. You can just do protein=pfam,panther