Tue Mar 26 17:01:01 2024: Start - EnTAP
Tue Mar 26 17:01:01 2024: Parsing ini file at: entap_config.ini
Tue Mar 26 17:01:01 2024: Success!
Tue Mar 26 17:01:01 2024: Printing user input...
Tue Mar 26 17:01:01 2024: ------------------------------------------------------
EnTAP Run Information - Execution
------------------------------------------------------
Current EnTAP Version: 1.0.0
Start time: Tue Mar 26 17:01:01 2024

Working directory has been set to: /isg/treegenes/treegenes_store/FTP/.genomes_temp/Jeff/Prav/v1.0/work/2d/a3e730d19d183eeae7163efc2e2df6/entap_outfiles
User Inputs:
out-dir: /isg/treegenes/treegenes_store/FTP/.genomes_temp/Jeff/Prav/v1.0/work/2d/a3e730d19d183eeae7163efc2e2df6/entap_outfiles
config: false
runP: true
runN: false
overwrite: false
ini: entap_config.ini
input: protein.faa
database: /isg/shared/databases/Diamond/RefSeq/complete.protein.faa.216.dmnd,
graph: false
no-trim: false
threads: 12
state: 4x
no-check: false
output-format: 1,3,4,7,
api-taxon: 
entap-db-bin: /core/labs/Wegrzyn/EnTAP/EnTAP_v0.10.8/EnTAP/databases/entap_database.bin
entap-db-sql: entap_database.db
entap-graph: /home/FCAM/jgamer/.nextflow/assets/TreeGenes/New_Genome_Pipeline/bin/entap_graphing.py
data-generate: false
data-type: 0,
fpkm: 0.500000
align: 
single-end: false
rsem-calculate-expression: /usr/local/bin/rsem-calculate-expression
rsem-sam-validator: /usr/local/bin/rsem-sam-validator
rsem-prepare-reference: /usr/local/bin/rsem-prepare-reference
convert-sam-for-rsem: /usr/local/bin/convert-sam-for-rsem
complete: false
frame-selection: 2
genemarkst-exe: gmst.pl
transdecoder-long-exe: /usr/lib/TransDecoder-v5.5.0/TransDecoder.LongOrfs
transdecoder-predict-exe: /usr/lib/TransDecoder-v5.5.0/TransDecoder.Predict
transdecoder-m: 100
transdecoder-no-refine-starts: false
diamond-exe: diamond
taxon: Prunus
qcoverage: 60.000000
tcoverage: 60.000000
contam: bacteria,fungi,
e-value: 0.000010
uninformative: conserved,predicted,unknown,unnamed,hypothetical,putative,unidentified,uncharacterized,uncultured,uninformative,,
ontology: 0,
eggnog-sql: /isg/shared/databases/eggnog/4.1/eggnog.db
eggnog-dmnd: /isg/shared/databases/eggnog/4.1/eggnog4.clustered_proteins.dmnd
interproscan-exe: /usr/local/interproscan/interproscan.sh
protein: 


Tue Mar 26 17:01:01 2024: User has input a database at: /isg/shared/databases/Diamond/RefSeq/complete.protein.faa.216.dmnd
Tue Mar 26 17:01:01 2024: Verifying EnTAP database...
Tue Mar 26 17:01:01 2024: Reading serialized database from: /core/labs/Wegrzyn/EnTAP/EnTAP_v0.10.8/EnTAP/databases/entap_database.bin
 Of type: 2
Tue Mar 26 17:01:19 2024: Success!
Tue Mar 26 17:01:19 2024: Spawn Object - QueryData
Tue Mar 26 17:01:19 2024: Generating transcriptome mappings...
Tue Mar 26 17:01:19 2024: Transcriptome Lines - START
Tue Mar 26 17:01:19 2024: >XP_021799890.1 pentatricopeptide repeat-containing protein At1g51965, mitochondrial [Prunus avium]
Tue Mar 26 17:01:19 2024: MTPRRHLRLLGLTKPTRSTTAVPTMRRHYATKYTAKITSTSPTGLSVSAEVTPPPPLPTDIRGYALPRRDLICKATQILL
Tue Mar 26 17:01:19 2024: RQSPSATSADPFSDLSDYLSSLSLHLTPSEASEILKSLNCPDLAIRFFRFCPSLSPNFHHDPYTCNRLLLILSKSTSPAR
Tue Mar 26 17:01:19 2024: FDLARSILRDMDRSNIRGNISTVNILIGLFGDTEDLQTCIGLVKKWCLNMNCYTYKCLLQAFLRSYDSTKAFDTYLEMRR
Tue Mar 26 17:01:19 2024: RGYKLDIFGYNMLLDALAKDEKVEHAYKVFDDMKKKHCEPDEFTYTIMIRMSGKLGKGDESLGLFQEMITKGCSPNMIVY
Tue Mar 26 17:01:19 2024: NTMIQALARSKMVEKAIIVFSKMVENNCRPNEFTYSVILNLLVAEGQLGRFDKVVEMSKKYMTKSIYAYLVRTLSKLGHA
Tue Mar 26 17:01:19 2024: GEAHRLFCNMWSFHDRGDRDAYVSMLESLCSAGKTAEAIDMLSNIHEKGVTTDTMMYNTVLSALGRLKQISHLSELYEKM
Tue Mar 26 17:01:19 2024: KLDGPEPDIFTYNILISSYGRAGKVDEAVTIFEQLENSDCKPDIISYNSLINCLGKNGDVDEAHMRFKEMQEKGFSPDVV
Tue Mar 26 17:01:19 2024: TYSTLIECFGKTDRVEMACRLFEDMLAQGCYPNIVTYNILLDCLERCGRTAEAVDLYAKLKQQGLTPDSITYAVLERLQS
Tue Mar 26 17:01:19 2024: Transcriptome Lines - END
Tue Mar 26 17:01:19 2024: Success!
Tue Mar 26 17:01:19 2024: Verifying input flag taxon
Tue Mar 26 17:01:19 2024: Verified species: prunus
Tue Mar 26 17:01:19 2024: Verifying input flag contam
Tue Mar 26 17:01:19 2024: Verified species: bacteria
Tue Mar 26 17:01:19 2024: Verified species: fungi
Tue Mar 26 17:01:19 2024: Verifying input flag fpkm
Tue Mar 26 17:01:19 2024: Verifying input flag qcoverage
Tue Mar 26 17:01:19 2024: Verifying input flag tcoverage
Tue Mar 26 17:01:19 2024: Verifying input flag ontology
Tue Mar 26 17:01:19 2024: Verifying input flag level
Tue Mar 26 17:01:19 2024: Verifying input flag frame-selection
Tue Mar 26 17:01:19 2024: Verifying input flag transdecoder-m
Tue Mar 26 17:01:19 2024: Success! Input verified
Tue Mar 26 17:01:19 2024: Killing Object - EntapDatabase
Tue Mar 26 17:01:22 2024: Killing Object - QueryData
Tue Mar 26 17:01:22 2024: QuerySequence data freed
Tue Mar 26 17:01:22 2024: EnTAP Executing...
Tue Mar 26 17:01:22 2024: verifying state...
Tue Mar 26 17:01:22 2024: Spawn Object - QueryData
Tue Mar 26 17:01:22 2024: Generating transcriptome mappings...
Tue Mar 26 17:01:22 2024: Transcriptome Lines - START
Tue Mar 26 17:01:22 2024: >XP_021799890.1 pentatricopeptide repeat-containing protein At1g51965, mitochondrial [Prunus avium]
Tue Mar 26 17:01:22 2024: MTPRRHLRLLGLTKPTRSTTAVPTMRRHYATKYTAKITSTSPTGLSVSAEVTPPPPLPTDIRGYALPRRDLICKATQILL
Tue Mar 26 17:01:22 2024: RQSPSATSADPFSDLSDYLSSLSLHLTPSEASEILKSLNCPDLAIRFFRFCPSLSPNFHHDPYTCNRLLLILSKSTSPAR
Tue Mar 26 17:01:22 2024: FDLARSILRDMDRSNIRGNISTVNILIGLFGDTEDLQTCIGLVKKWCLNMNCYTYKCLLQAFLRSYDSTKAFDTYLEMRR
Tue Mar 26 17:01:22 2024: RGYKLDIFGYNMLLDALAKDEKVEHAYKVFDDMKKKHCEPDEFTYTIMIRMSGKLGKGDESLGLFQEMITKGCSPNMIVY
Tue Mar 26 17:01:22 2024: NTMIQALARSKMVEKAIIVFSKMVENNCRPNEFTYSVILNLLVAEGQLGRFDKVVEMSKKYMTKSIYAYLVRTLSKLGHA
Tue Mar 26 17:01:22 2024: GEAHRLFCNMWSFHDRGDRDAYVSMLESLCSAGKTAEAIDMLSNIHEKGVTTDTMMYNTVLSALGRLKQISHLSELYEKM
Tue Mar 26 17:01:22 2024: KLDGPEPDIFTYNILISSYGRAGKVDEAVTIFEQLENSDCKPDIISYNSLINCLGKNGDVDEAHMRFKEMQEKGFSPDVV
Tue Mar 26 17:01:22 2024: TYSTLIECFGKTDRVEMACRLFEDMLAQGCYPNIVTYNILLDCLERCGRTAEAVDLYAKLKQQGLTPDSITYAVLERLQS
Tue Mar 26 17:01:22 2024: Transcriptome Lines - END
Tue Mar 26 17:01:23 2024: Success!
Tue Mar 26 17:01:23 2024: Spawn Object - GraphingManager
Tue Mar 26 17:01:23 2024: Executing command: 
python /home/FCAM/jgamer/.nextflow/assets/TreeGenes/New_Genome_Pipeline/bin/entap_graphing.py -g -1
Tue Mar 26 17:01:25 2024: 
Std Err:
Matplotlib created a temporary config/cache directory at /tmp/matplotlib-5tl26uxs because the default path (/home/FCAM/jgamer/.config/matplotlib) is not a writable directory; it is highly recommended to set the MPLCONFIGDIR environment variable to a writable directory, in particular to speed up the import of Matplotlib and to better support multiprocessing.
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories
Fontconfig error: No writable cache directories

Tue Mar 26 17:01:25 2024: Graphing is supported
Tue Mar 26 17:01:25 2024: Reading serialized database from: /core/labs/Wegrzyn/EnTAP/EnTAP_v0.10.8/EnTAP/databases/entap_database.bin
 Of type: 2
Tue Mar 26 17:01:40 2024: STATE - SIMILARITY SEARCH
Tue Mar 26 17:01:40 2024: Spawn Object - SimilaritySearch
Tue Mar 26 17:01:40 2024: opendir: Path could not be read: /isg/treegenes/treegenes_store/FTP/.genomes_temp/Jeff/Prav/v1.0/work/2d/a3e730d19d183eeae7163efc2e2df6/entap_outfiles/similarity_search/DIAMOND/figures/
Tue Mar 26 17:01:40 2024: opendir: Path could not be read: /isg/treegenes/treegenes_store/FTP/.genomes_temp/Jeff/Prav/v1.0/work/2d/a3e730d19d183eeae7163efc2e2df6/entap_outfiles/similarity_search/DIAMOND/processed/
Tue Mar 26 17:01:40 2024: Setting working directory to: /isg/treegenes/treegenes_store/FTP/.genomes_temp/Jeff/Prav/v1.0/work/2d/a3e730d19d183eeae7163efc2e2df6/entap_outfiles/similarity_search/DIAMOND
Tue Mar 26 17:01:40 2024: Success! Working directory set
Tue Mar 26 17:01:40 2024: opendir: Path could not be read: /isg/treegenes/treegenes_store/FTP/.genomes_temp/Jeff/Prav/v1.0/work/2d/a3e730d19d183eeae7163efc2e2df6/entap_outfiles/similarity_search/DIAMOND/overall_results
Tue Mar 26 17:01:40 2024: Spawn Object - ModDiamond
Tue Mar 26 17:01:40 2024: Verifying previous execution of database: /isg/shared/databases/Diamond/RefSeq/complete.protein.faa.216.dmnd...
Tue Mar 26 17:01:40 2024: File for database complete does not exist.
/isg/treegenes/treegenes_store/FTP/.genomes_temp/Jeff/Prav/v1.0/work/2d/a3e730d19d183eeae7163efc2e2df6/entap_outfiles/similarity_search/DIAMOND/blastp_protein_complete.out
Tue Mar 26 17:01:40 2024: Success! Verified files for DIAMOND, continuing...
Tue Mar 26 17:01:40 2024: Executing DIAMOND for necessary files....
Tue Mar 26 17:01:40 2024: File not found, executing against database at: /isg/shared/databases/Diamond/RefSeq/complete.protein.faa.216.dmnd
Tue Mar 26 17:01:40 2024: Executing command: 
diamond blastp -p 12 -o /isg/treegenes/treegenes_store/FTP/.genomes_temp/Jeff/Prav/v1.0/work/2d/a3e730d19d183eeae7163efc2e2df6/entap_outfiles/similarity_search/DIAMOND/blastp_protein_complete.out --very-sensitive  --max-target-seqs 3 --evalue 0.000010 -f 6 qseqid sseqid pident length mismatch gapopen qstart qend sstart send evalue bitscore qcovhsp stitle --subject-cover 60.000000 --query-cover 60.000000 -q /isg/treegenes/treegenes_store/FTP/.genomes_temp/Jeff/Prav/v1.0/work/2d/a3e730d19d183eeae7163efc2e2df6/entap_outfiles/transcriptomes//protein.faa -d /isg/shared/databases/Diamond/RefSeq/complete.protein.faa.216.dmnd