[2024-01-25 20:13:20,413] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:20,415] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:20,416] [INFO] DQC Reference Directory: /var/lib/cwl/stgcfc7ffeb-5633-4416-b57d-dc7a434380d9/dqc_reference
[2024-01-25 20:13:21,557] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:21,558] [INFO] Task started: Prodigal
[2024-01-25 20:13:21,558] [INFO] Running command: gunzip -c /var/lib/cwl/stgad35c746-d2e7-469c-b2df-fa327d31bb92/GCF_000772535.1_ASM77253v1_genomic.fna.gz | prodigal -d GCF_000772535.1_ASM77253v1_genomic.fna/cds.fna -a GCF_000772535.1_ASM77253v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:27,906] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:27,906] [INFO] Task started: HMMsearch
[2024-01-25 20:13:27,906] [INFO] Running command: hmmsearch --tblout GCF_000772535.1_ASM77253v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcfc7ffeb-5633-4416-b57d-dc7a434380d9/dqc_reference/reference_markers.hmm GCF_000772535.1_ASM77253v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:28,112] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:28,113] [INFO] Found 6/6 markers.
[2024-01-25 20:13:28,136] [INFO] Query marker FASTA was written to GCF_000772535.1_ASM77253v1_genomic.fna/markers.fasta
[2024-01-25 20:13:28,136] [INFO] Task started: Blastn
[2024-01-25 20:13:28,136] [INFO] Running command: blastn -query GCF_000772535.1_ASM77253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfc7ffeb-5633-4416-b57d-dc7a434380d9/dqc_reference/reference_markers.fasta -out GCF_000772535.1_ASM77253v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:28,784] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:28,787] [INFO] Selected 20 target genomes.
[2024-01-25 20:13:28,787] [INFO] Target genome list was writen to GCF_000772535.1_ASM77253v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:28,809] [INFO] Task started: fastANI
[2024-01-25 20:13:28,809] [INFO] Running command: fastANI --query /var/lib/cwl/stgad35c746-d2e7-469c-b2df-fa327d31bb92/GCF_000772535.1_ASM77253v1_genomic.fna.gz --refList GCF_000772535.1_ASM77253v1_genomic.fna/target_genomes.txt --output GCF_000772535.1_ASM77253v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:39,866] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:39,866] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcfc7ffeb-5633-4416-b57d-dc7a434380d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:39,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcfc7ffeb-5633-4416-b57d-dc7a434380d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:39,874] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:13:39,874] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:13:39,874] [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
Pasteurella testudinis	strain=DSM 23072	GCA_900176075.1	761	761	type	True	80.5805	555	853	95	below_threshold
Pasteurella testudinis	strain=DSM 23072	GCA_019633665.1	761	761	type	True	80.5805	555	853	95	below_threshold
Pasteurella testudinis	strain=NCTC12150	GCA_900454705.1	761	761	type	True	80.5492	568	853	95	below_threshold
Testudinibacter aquarius	strain=ELNT2x	GCA_006227605.1	1524974	1524974	type	True	79.5835	425	853	95	below_threshold
Testudinibacter aquarius	strain=ELNT2X	GCA_009761355.1	1524974	1524974	type	True	79.4582	465	853	95	below_threshold
Testudinibacter aquarius	strain=DSM 28140	GCA_004342725.1	1524974	1524974	type	True	79.4493	472	853	95	below_threshold
Spirabiliibacterium falconis	strain=NCTC 11878	GCA_014885015.1	572023	572023	type	True	77.4293	117	853	95	below_threshold
Mesocricetibacter intestinalis	strain=DSM 28403	GCA_004363295.1	1521930	1521930	type	True	77.0752	118	853	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=DSM 8324	GCA_000372365.1	714	714	type	True	76.8055	135	853	95	below_threshold
Salmonella enterica subsp. enterica	strain=PartC-Senterica-RM8376	GCA_022869965.1	59201	28901	suspected-type	True	76.0899	57	853	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:39,876] [INFO] DFAST Taxonomy check result was written to GCF_000772535.1_ASM77253v1_genomic.fna/tc_result.tsv
[2024-01-25 20:13:39,876] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:39,876] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:39,876] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcfc7ffeb-5633-4416-b57d-dc7a434380d9/dqc_reference/checkm_data
[2024-01-25 20:13:39,877] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:39,904] [INFO] Task started: CheckM
[2024-01-25 20:13:39,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000772535.1_ASM77253v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000772535.1_ASM77253v1_genomic.fna/checkm_input GCF_000772535.1_ASM77253v1_genomic.fna/checkm_result
[2024-01-25 20:14:03,291] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:03,292] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:03,329] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:03,330] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:03,330] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000772535.1_ASM77253v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:03,330] [INFO] Task started: Blastn
[2024-01-25 20:14:03,331] [INFO] Running command: blastn -query GCF_000772535.1_ASM77253v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcfc7ffeb-5633-4416-b57d-dc7a434380d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000772535.1_ASM77253v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:04,432] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:04,435] [INFO] Selected 15 target genomes.
[2024-01-25 20:14:04,435] [INFO] Target genome list was writen to GCF_000772535.1_ASM77253v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:04,451] [INFO] Task started: fastANI
[2024-01-25 20:14:04,451] [INFO] Running command: fastANI --query /var/lib/cwl/stgad35c746-d2e7-469c-b2df-fa327d31bb92/GCF_000772535.1_ASM77253v1_genomic.fna.gz --refList GCF_000772535.1_ASM77253v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000772535.1_ASM77253v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:11,586] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:11,595] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:11,595] [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_000772535.1	s__Chelonobacter oris	100.0	850	853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900176075.1	s__Chelonobacter testudinis	80.5912	554	853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCA_006228005.1	s__Chelonobacter sp006228005	79.5033	432	853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	99.89	99.87	0.94	0.93	5	-
GCF_004342725.1	s__Chelonobacter aquarius	79.4492	472	853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	97.20	95.17	0.92	0.86	10	-
GCF_014884995.1	s__Spirabiliibacterium pneumoniae	77.5884	128	853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014885015.1	s__Spirabiliibacterium falconis	77.4293	117	853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000827595.2	s__Necropsobacter massiliensis	77.3345	161	853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017160915.1	s__Aggregatibacter actinomycetemcomitans_B	77.3244	147	853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003130075.1	s__Aggregatibacter segnis_A	77.2025	96	853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	95.43	95.32	0.90	0.88	6	-
GCA_000751835.1	s__Necropsobacter rosorum	77.181	197	853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014884965.1	s__Spirabiliibacterium mucosae	77.1551	150	853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium	95.0	96.18	96.18	0.92	0.92	2	-
GCF_004363295.1	s__Mesocricetibacter intestinalis	77.0946	117	853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Mesocricetibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014843355.1	s__Basfia_A sp014843355	76.9693	135	853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Basfia_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260095.1	s__Glaesserella australis	76.7163	66	853	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Glaesserella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:11,597] [INFO] GTDB search result was written to GCF_000772535.1_ASM77253v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:11,597] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:11,600] [INFO] DFAST_QC result json was written to GCF_000772535.1_ASM77253v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:11,600] [INFO] DFAST_QC completed!
[2024-01-25 20:14:11,600] [INFO] Total running time: 0h0m51s