Version1.1.1: interproscan database error
AlexGaithuma opened this issue · 4 comments
I cant ran Interproscan on Entap.
my debug file is as below:
interproscan-exe: /data2/Alex_MulengaLab/tools/interproscan-5.67-99.0/interproscan.sh
protein: pfam
hgt-donor:
hgt-recipient:
hgt-gff:
Fri May 31 10:19:21 2024: User has input a database at: /data2/Alex_MulengaLab/db/uniprot_trembl.dmnd
Fri May 31 10:19:21 2024: User has input a database at: /data2/Alex_MulengaLab/db/Refseq.protein.dmnd
Fri May 31 10:19:21 2024: User has input a database at: /data2/Alex_MulengaLab/db/uniprot_trembl.dmnd
Fri May 31 10:19:21 2024: Verifying EnTAP database...
Fri May 31 10:19:21 2024: Reading serialized database from: /data2/Alex_MulengaLab/db/bin/entap_database.bin Of type: 2
Fri May 31 10:19:40 2024: Success!
Fri May 31 10:19:40 2024: Spawn Object - QueryData
Fri May 31 10:19:40 2024: Generating transcriptome mappings...
Fri May 31 10:19:40 2024: Transcriptome Lines - START
Fri May 31 10:19:40 2024: >JF1A_TRINITY_DN10022_c0_g1_i1.p1 JF1A_TRINITY_DN10022_c0_g1~~JF1A_TRINITY_DN10022_c0_g1_i1.p1 ORF type:internal len:108 (+),score=23.54,Defensin_4|PF07936.12|6.1e+03,Defensin_4|PF07936.12|0.15,Defensin_4|PF07936.12|6.8e+03 JF1A_TRINITY_DN10022_c0_g1_i1:2-322(+)
Fri May 31 10:19:40 2024: AGGAAAAAGGGTTCTCGAGATTCGGTGGGCCTTACAGTGTCAGCTAATGGAATTCATTGG
Fri May 31 10:19:40 2024: CGAAGAGGAACTGGACACATTCAGACTGATGATGATGTTGGTATTGTCATGGAATGCAGT
Fri May 31 10:19:40 2024: GATGATTGGTGGGCCTTTGATACTGAGATTGTTCGACCATCTGATATTCTTATACTGTCT
Fri May 31 10:19:40 2024: AGTGAGAAGCTGAAAGCCTCAAGTGGGGTTTATTGGATGTTTTATTCGGGATGCAACTCG
Fri May 31 10:19:40 2024: GATGAGATAAATGTTCCCCAAGTGTTGCTTGGGAACCCTTGGAAGTTTGAGGAGACTTGC
Fri May 31 10:19:40 2024: CTTGAATCTACTCTTTTTAGG
Fri May 31 10:19:40 2024: >JF1A_TRINITY_DN10032_c0_g1_i1.p1 JF1A_TRINITY_DN10032_c0_g1~~JF1A_TRINITY_DN10032_c0_g1_i1.p1 ORF type:5prime_partial len:102 (+),score=5.52 JF1A_TRINITY_DN10032_c0_g1_i1:1-306(+)
Fri May 31 10:19:40 2024: AATGTGCCCTTGTTAATGTTTCCGTTCATGATAACGAACTGGCTTCTTACAGTTTTGTCA
Fri May 31 10:19:40 2024: Transcriptome Lines - END
Fri May 31 10:19:40 2024: Success!
Fri May 31 10:19:40 2024: Verifying input flag fpkm
Fri May 31 10:19:40 2024: Verifying input flag qcoverage
Fri May 31 10:19:40 2024: Verifying input flag tcoverage
Fri May 31 10:19:40 2024: Verifying input flag ontology
Fri May 31 10:19:40 2024: Verifying input flag level
Fri May 31 10:19:40 2024: Killing Object - EntapDatabase
Fri May 31 10:19:45 2024: Killing Object - QueryData
Fri May 31 10:19:45 2024: QuerySequence data freed
Fri May 31 10:19:45 2024: Error code (10) not recognized
Fri May 31 10:19:45 2024: Error code: 10
InterProScan selected, but invalid databases input!
Fri May 31 10:19:45 2024: End - EnTAP
fixed issue by installing python 2.7 in my conda environment which had python 3.7 already installed
conda env update -n my_env --file python27.yml
my .yml file contains
name: python27
dependencies:
- python=2.7
- virtualenv
- ipython
- numpy
- scipy
Hey! Did you modify the config file interproscan-db or protein (if using older version) commands in between runs? By default, there aren't databases listed for those commands which would give you an error.
Hi! I already use EnTap Version1.2.1 in docker, and I guess the problem is at the database flag "morbidblite" in the file "entap_run.params". When I put all database:
interproscan-db=tigrfam
interproscan-db=sfld
interproscan-db=prodom
interproscan-db=hamap
interproscan-db=pfam
interproscan-db=smart
interproscan-db=cdd
interproscan-db=prositeprofiles
interproscan-db=prositepatterns
interproscan-db=superfamily
interproscan-db=prints
interproscan-db=panther
interproscan-db=gene3d
interproscan-db=pirsf
interproscan-db=coils
interproscan-db=morbidblite
in "entap_run.params", the error message "Error code: 10 InterProScan selected, but invalid databases input!" was shown.
However, when I removed the final one "interproscan-db=morbidblite", the EnTap worked.
But another problem happens that the output file "interpro_results.gff3" only shows the result of "Coils" database when I used all interproscan database.
Corrected EnTAP not recognizing all InterProScan databases in latest version 1.4.0