[2024-01-24 14:19:18,832] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:18,837] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:18,837] [INFO] DQC Reference Directory: /var/lib/cwl/stg734a967f-5607-4e80-a797-0c8316c06b9f/dqc_reference
[2024-01-24 14:19:20,315] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:20,317] [INFO] Task started: Prodigal
[2024-01-24 14:19:20,317] [INFO] Running command: gunzip -c /var/lib/cwl/stgaf84e78c-00f5-4910-b834-053653ccc747/GCF_002142155.1_ASM214215v1_genomic.fna.gz | prodigal -d GCF_002142155.1_ASM214215v1_genomic.fna/cds.fna -a GCF_002142155.1_ASM214215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:25,065] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:25,066] [INFO] Task started: HMMsearch
[2024-01-24 14:19:25,066] [INFO] Running command: hmmsearch --tblout GCF_002142155.1_ASM214215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg734a967f-5607-4e80-a797-0c8316c06b9f/dqc_reference/reference_markers.hmm GCF_002142155.1_ASM214215v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:25,375] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:25,376] [INFO] Found 6/6 markers.
[2024-01-24 14:19:25,407] [INFO] Query marker FASTA was written to GCF_002142155.1_ASM214215v1_genomic.fna/markers.fasta
[2024-01-24 14:19:25,407] [INFO] Task started: Blastn
[2024-01-24 14:19:25,408] [INFO] Running command: blastn -query GCF_002142155.1_ASM214215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg734a967f-5607-4e80-a797-0c8316c06b9f/dqc_reference/reference_markers.fasta -out GCF_002142155.1_ASM214215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:26,179] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:26,182] [INFO] Selected 13 target genomes.
[2024-01-24 14:19:26,182] [INFO] Target genome list was writen to GCF_002142155.1_ASM214215v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:26,195] [INFO] Task started: fastANI
[2024-01-24 14:19:26,195] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf84e78c-00f5-4910-b834-053653ccc747/GCF_002142155.1_ASM214215v1_genomic.fna.gz --refList GCF_002142155.1_ASM214215v1_genomic.fna/target_genomes.txt --output GCF_002142155.1_ASM214215v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:34,051] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:34,051] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg734a967f-5607-4e80-a797-0c8316c06b9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:34,052] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg734a967f-5607-4e80-a797-0c8316c06b9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:34,060] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:19:34,060] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:34,060] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
Gilliamella apis	strain=NO3	GCA_002142155.1	1970738	1970738	type	True	100.0	812	816	95	conclusive
Gilliamella apicola	strain=DSM 104097	GCA_003201455.1	1196095	1196095	suspected-type	True	81.7016	479	816	95	below_threshold
Gilliamella apicola	strain=wkB1	GCA_000599985.1	1196095	1196095	suspected-type	True	81.6449	492	816	95	below_threshold
Gilliamella bombicola	strain=R-53248	GCA_900094945.1	1798182	1798182	type	True	80.0282	393	816	95	below_threshold
Gilliamella intestini	strain=R-53144	GCA_900094935.1	1798183	1798183	type	True	79.7391	401	816	95	below_threshold
Orbus hercynius	strain=DSM 22228	GCA_003634275.1	593135	593135	type	True	78.3681	148	816	95	below_threshold
Zophobihabitans entericus	strain=IPMB12	GCA_011745665.1	1635327	1635327	type	True	78.201	118	816	95	below_threshold
Frischella japonica	strain=Ac13	GCA_014489845.1	2741544	2741544	type	True	78.1071	192	816	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:34,062] [INFO] DFAST Taxonomy check result was written to GCF_002142155.1_ASM214215v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:34,063] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:34,063] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:34,063] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg734a967f-5607-4e80-a797-0c8316c06b9f/dqc_reference/checkm_data
[2024-01-24 14:19:34,064] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:34,095] [INFO] Task started: CheckM
[2024-01-24 14:19:34,095] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002142155.1_ASM214215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002142155.1_ASM214215v1_genomic.fna/checkm_input GCF_002142155.1_ASM214215v1_genomic.fna/checkm_result
[2024-01-24 14:19:57,122] [INFO] Task succeeded: CheckM
[2024-01-24 14:19:57,123] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:19:57,146] [INFO] ===== Completeness check finished =====
[2024-01-24 14:19:57,146] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:19:57,146] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002142155.1_ASM214215v1_genomic.fna/markers.fasta)
[2024-01-24 14:19:57,147] [INFO] Task started: Blastn
[2024-01-24 14:19:57,147] [INFO] Running command: blastn -query GCF_002142155.1_ASM214215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg734a967f-5607-4e80-a797-0c8316c06b9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002142155.1_ASM214215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:58,400] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:58,403] [INFO] Selected 5 target genomes.
[2024-01-24 14:19:58,403] [INFO] Target genome list was writen to GCF_002142155.1_ASM214215v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:19:58,410] [INFO] Task started: fastANI
[2024-01-24 14:19:58,410] [INFO] Running command: fastANI --query /var/lib/cwl/stgaf84e78c-00f5-4910-b834-053653ccc747/GCF_002142155.1_ASM214215v1_genomic.fna.gz --refList GCF_002142155.1_ASM214215v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002142155.1_ASM214215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:02,194] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:02,201] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:02,201] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCF_002142155.1	s__Gilliamella apis	100.0	812	816	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.52	97.64	0.94	0.89	26	conclusive
GCF_003202775.1	s__Gilliamella apis_A	94.2011	718	816	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	98.23	95.38	0.94	0.89	9	-
GCF_002142215.1	s__Gilliamella sp002142215	92.9435	644	816	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.95	96.09	0.93	0.88	3	-
GCF_003202915.1	s__Gilliamella apicola_Q	86.5074	657	816	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	95.60	95.60	0.89	0.89	2	-
GCF_001693745.1	s__Gilliamella apicola_E	83.4747	594	816	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Enterobacteriaceae;g__Gilliamella	95.0	97.90	97.90	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:02,203] [INFO] GTDB search result was written to GCF_002142155.1_ASM214215v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:02,203] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:02,208] [INFO] DFAST_QC result json was written to GCF_002142155.1_ASM214215v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:02,208] [INFO] DFAST_QC completed!
[2024-01-24 14:20:02,208] [INFO] Total running time: 0h0m43s