[2024-01-25 19:06:50,746] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:06:50,748] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:06:50,748] [INFO] DQC Reference Directory: /var/lib/cwl/stg0a7da33f-2989-4224-8dcc-84a4f0fc6dbe/dqc_reference
[2024-01-25 19:06:51,893] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:06:51,895] [INFO] Task started: Prodigal
[2024-01-25 19:06:51,895] [INFO] Running command: gunzip -c /var/lib/cwl/stgead8d391-58c0-4d54-9484-7f35e5607862/GCF_002921145.1_ASM292114v1_genomic.fna.gz | prodigal -d GCF_002921145.1_ASM292114v1_genomic.fna/cds.fna -a GCF_002921145.1_ASM292114v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:06:56,187] [INFO] Task succeeded: Prodigal
[2024-01-25 19:06:56,187] [INFO] Task started: HMMsearch
[2024-01-25 19:06:56,187] [INFO] Running command: hmmsearch --tblout GCF_002921145.1_ASM292114v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0a7da33f-2989-4224-8dcc-84a4f0fc6dbe/dqc_reference/reference_markers.hmm GCF_002921145.1_ASM292114v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:06:56,400] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:06:56,401] [INFO] Found 6/6 markers.
[2024-01-25 19:06:56,422] [INFO] Query marker FASTA was written to GCF_002921145.1_ASM292114v1_genomic.fna/markers.fasta
[2024-01-25 19:06:56,422] [INFO] Task started: Blastn
[2024-01-25 19:06:56,423] [INFO] Running command: blastn -query GCF_002921145.1_ASM292114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a7da33f-2989-4224-8dcc-84a4f0fc6dbe/dqc_reference/reference_markers.fasta -out GCF_002921145.1_ASM292114v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:06:57,026] [INFO] Task succeeded: Blastn
[2024-01-25 19:06:57,028] [INFO] Selected 11 target genomes.
[2024-01-25 19:06:57,029] [INFO] Target genome list was writen to GCF_002921145.1_ASM292114v1_genomic.fna/target_genomes.txt
[2024-01-25 19:06:57,034] [INFO] Task started: fastANI
[2024-01-25 19:06:57,034] [INFO] Running command: fastANI --query /var/lib/cwl/stgead8d391-58c0-4d54-9484-7f35e5607862/GCF_002921145.1_ASM292114v1_genomic.fna.gz --refList GCF_002921145.1_ASM292114v1_genomic.fna/target_genomes.txt --output GCF_002921145.1_ASM292114v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:07:02,830] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:02,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0a7da33f-2989-4224-8dcc-84a4f0fc6dbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:07:02,831] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0a7da33f-2989-4224-8dcc-84a4f0fc6dbe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:07:02,837] [INFO] Found 8 fastANI hits (5 hits with ANI > threshold)
[2024-01-25 19:07:02,837] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 19:07:02,837] [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
Avibacterium endocarditidis	strain=20186H4H1	GCA_002921145.1	380674	380674	type	True	99.9999	666	677	95	inconclusive
Avibacterium gallinarum	strain=NCTC11188	GCA_900454485.1	755	755	type	True	95.5851	612	677	95	inconclusive
Avibacterium gallinarum	strain=DSM 17481	GCA_004362535.1	755	755	type	True	95.5406	623	677	95	inconclusive
Avibacterium gallinarum	strain=NCTC 11188	GCA_002921135.1	755	755	type	True	95.5151	619	677	95	inconclusive
Avibacterium volantium	strain=NCTC3438	GCA_900635775.1	762	762	type	True	95.3312	569	677	95	inconclusive
Avibacterium avium	strain=NCTC 11297	GCA_900454535.1	751	751	type	True	93.5959	522	677	95	below_threshold
Avibacterium paragallinarum	strain=CCUG 12835	GCA_002921155.1	728	728	type	True	86.556	419	677	95	below_threshold
Avibacterium paragallinarum	strain=NCTC11296	GCA_900450705.1	728	728	type	True	86.4338	475	677	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:07:02,841] [INFO] DFAST Taxonomy check result was written to GCF_002921145.1_ASM292114v1_genomic.fna/tc_result.tsv
[2024-01-25 19:07:02,842] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:07:02,842] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:07:02,842] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0a7da33f-2989-4224-8dcc-84a4f0fc6dbe/dqc_reference/checkm_data
[2024-01-25 19:07:02,844] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:07:02,871] [INFO] Task started: CheckM
[2024-01-25 19:07:02,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002921145.1_ASM292114v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002921145.1_ASM292114v1_genomic.fna/checkm_input GCF_002921145.1_ASM292114v1_genomic.fna/checkm_result
[2024-01-25 19:07:21,576] [INFO] Task succeeded: CheckM
[2024-01-25 19:07:21,577] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:07:21,596] [INFO] ===== Completeness check finished =====
[2024-01-25 19:07:21,597] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:07:21,597] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002921145.1_ASM292114v1_genomic.fna/markers.fasta)
[2024-01-25 19:07:21,597] [INFO] Task started: Blastn
[2024-01-25 19:07:21,598] [INFO] Running command: blastn -query GCF_002921145.1_ASM292114v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0a7da33f-2989-4224-8dcc-84a4f0fc6dbe/dqc_reference/reference_markers_gtdb.fasta -out GCF_002921145.1_ASM292114v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:07:22,414] [INFO] Task succeeded: Blastn
[2024-01-25 19:07:22,418] [INFO] Selected 9 target genomes.
[2024-01-25 19:07:22,418] [INFO] Target genome list was writen to GCF_002921145.1_ASM292114v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:07:22,425] [INFO] Task started: fastANI
[2024-01-25 19:07:22,425] [INFO] Running command: fastANI --query /var/lib/cwl/stgead8d391-58c0-4d54-9484-7f35e5607862/GCF_002921145.1_ASM292114v1_genomic.fna.gz --refList GCF_002921145.1_ASM292114v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002921145.1_ASM292114v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:07:26,852] [INFO] Task succeeded: fastANI
[2024-01-25 19:07:26,857] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:07:26,857] [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_002921145.1	s__Avibacterium endocarditidis	99.9999	666	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.5151	N/A	N/A	N/A	N/A	1	conclusive
GCF_002921135.1	s__Avibacterium gallinarum	95.5151	619	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	100.00	100.00	1.00	1.00	3	-
GCF_900635775.1	s__Avibacterium volantium	95.3463	568	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.623	96.13	96.13	0.89	0.89	2	-
GCF_900454535.1	s__Avibacterium avium	93.621	521	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.0	95.69	95.67	0.83	0.83	3	-
GCF_900450705.1	s__Avibacterium paragallinarum	86.4174	476	677	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Avibacterium	95.0	97.58	96.82	0.90	0.82	41	-
--------------------------------------------------------------------------------
[2024-01-25 19:07:26,858] [INFO] GTDB search result was written to GCF_002921145.1_ASM292114v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:07:26,859] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:07:26,861] [INFO] DFAST_QC result json was written to GCF_002921145.1_ASM292114v1_genomic.fna/dqc_result.json
[2024-01-25 19:07:26,862] [INFO] DFAST_QC completed!
[2024-01-25 19:07:26,862] [INFO] Total running time: 0h0m36s