[2024-01-24 12:15:18,800] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:18,802] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:18,803] [INFO] DQC Reference Directory: /var/lib/cwl/stg220c5a1d-a1b8-4031-b87f-12515faf009b/dqc_reference
[2024-01-24 12:15:20,108] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:20,109] [INFO] Task started: Prodigal
[2024-01-24 12:15:20,109] [INFO] Running command: gunzip -c /var/lib/cwl/stgd11cb281-f3f3-4bc0-beda-d82736d13be7/GCF_014884965.1_ASM1488496v1_genomic.fna.gz | prodigal -d GCF_014884965.1_ASM1488496v1_genomic.fna/cds.fna -a GCF_014884965.1_ASM1488496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:27,538] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:27,539] [INFO] Task started: HMMsearch
[2024-01-24 12:15:27,539] [INFO] Running command: hmmsearch --tblout GCF_014884965.1_ASM1488496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg220c5a1d-a1b8-4031-b87f-12515faf009b/dqc_reference/reference_markers.hmm GCF_014884965.1_ASM1488496v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:27,782] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:27,783] [INFO] Found 6/6 markers.
[2024-01-24 12:15:27,810] [INFO] Query marker FASTA was written to GCF_014884965.1_ASM1488496v1_genomic.fna/markers.fasta
[2024-01-24 12:15:27,811] [INFO] Task started: Blastn
[2024-01-24 12:15:27,811] [INFO] Running command: blastn -query GCF_014884965.1_ASM1488496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg220c5a1d-a1b8-4031-b87f-12515faf009b/dqc_reference/reference_markers.fasta -out GCF_014884965.1_ASM1488496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:28,466] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:28,469] [INFO] Selected 21 target genomes.
[2024-01-24 12:15:28,470] [INFO] Target genome list was writen to GCF_014884965.1_ASM1488496v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:28,478] [INFO] Task started: fastANI
[2024-01-24 12:15:28,478] [INFO] Running command: fastANI --query /var/lib/cwl/stgd11cb281-f3f3-4bc0-beda-d82736d13be7/GCF_014884965.1_ASM1488496v1_genomic.fna.gz --refList GCF_014884965.1_ASM1488496v1_genomic.fna/target_genomes.txt --output GCF_014884965.1_ASM1488496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:40,115] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:40,116] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg220c5a1d-a1b8-4031-b87f-12515faf009b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:40,117] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg220c5a1d-a1b8-4031-b87f-12515faf009b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:40,133] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:40,134] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:40,134] [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
Spirabiliibacterium mucosae	strain=20609_3	GCA_014884965.1	28156	28156	type	True	100.0	684	684	95	conclusive
Spirabiliibacterium pneumoniae	strain=HPA106	GCA_014884995.1	221400	221400	type	True	84.9363	538	684	95	below_threshold
Spirabiliibacterium falconis	strain=NCTC 11878	GCA_014885015.1	572023	572023	type	True	80.0233	365	684	95	below_threshold
Pasteurella testudinis	strain=DSM 23072	GCA_900176075.1	761	761	type	True	77.7196	183	684	95	below_threshold
Pasteurella testudinis	strain=DSM 23072	GCA_019633665.1	761	761	type	True	77.7183	183	684	95	below_threshold
Pasteurella testudinis	strain=NCTC12150	GCA_900454705.1	761	761	type	True	77.6133	189	684	95	below_threshold
Testudinibacter aquarius	strain=DSM 28140	GCA_004342725.1	1524974	1524974	type	True	77.4858	166	684	95	below_threshold
Testudinibacter aquarius	strain=ELNT2X	GCA_009761355.1	1524974	1524974	type	True	77.4554	161	684	95	below_threshold
Haemophilus paraphrohaemolyticus	strain=CCUG 3718	GCA_002015045.1	736	736	type	True	77.2147	55	684	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=DSM 8324	GCA_000372365.1	714	714	type	True	76.9975	83	684	95	below_threshold
Aggregatibacter actinomycetemcomitans	strain=NCTC_9710	GCA_008085305.1	714	714	type	True	76.8701	79	684	95	below_threshold
Serratia bockelmannii	strain=S3	GCA_008011855.1	2703793	2703793	type	True	75.6428	57	684	95	below_threshold
Pantoea latae	strain=AS1	GCA_002077695.1	1964541	1964541	type	True	75.6086	51	684	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:40,135] [INFO] DFAST Taxonomy check result was written to GCF_014884965.1_ASM1488496v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:40,136] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:40,136] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:40,136] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg220c5a1d-a1b8-4031-b87f-12515faf009b/dqc_reference/checkm_data
[2024-01-24 12:15:40,138] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:40,161] [INFO] Task started: CheckM
[2024-01-24 12:15:40,162] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014884965.1_ASM1488496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014884965.1_ASM1488496v1_genomic.fna/checkm_input GCF_014884965.1_ASM1488496v1_genomic.fna/checkm_result
[2024-01-24 12:16:07,251] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:07,253] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 98.96%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:07,286] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:07,286] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:07,287] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014884965.1_ASM1488496v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:07,287] [INFO] Task started: Blastn
[2024-01-24 12:16:07,288] [INFO] Running command: blastn -query GCF_014884965.1_ASM1488496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg220c5a1d-a1b8-4031-b87f-12515faf009b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014884965.1_ASM1488496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:08,163] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:08,168] [INFO] Selected 15 target genomes.
[2024-01-24 12:16:08,168] [INFO] Target genome list was writen to GCF_014884965.1_ASM1488496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:08,178] [INFO] Task started: fastANI
[2024-01-24 12:16:08,179] [INFO] Running command: fastANI --query /var/lib/cwl/stgd11cb281-f3f3-4bc0-beda-d82736d13be7/GCF_014884965.1_ASM1488496v1_genomic.fna.gz --refList GCF_014884965.1_ASM1488496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014884965.1_ASM1488496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:15,227] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:15,237] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:15,237] [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_014884965.1	s__Spirabiliibacterium mucosae	100.0	684	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium	95.0	96.18	96.18	0.92	0.92	2	conclusive
GCF_014884995.1	s__Spirabiliibacterium pneumoniae	84.9363	538	684	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	80.0233	365	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Spirabiliibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176075.1	s__Chelonobacter testudinis	77.7282	181	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004342725.1	s__Chelonobacter aquarius	77.5025	165	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	97.20	95.17	0.92	0.86	10	-
GCA_006228005.1	s__Chelonobacter sp006228005	77.4518	153	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Chelonobacter	95.0	99.89	99.87	0.94	0.93	5	-
GCF_002015045.1	s__Haemophilus_A paraphrohaemolyticus	77.1689	56	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Haemophilus_A	95.0	97.72	95.26	0.95	0.91	7	-
GCF_000372365.1	s__Aggregatibacter actinomycetemcomitans	76.9978	83	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	98.51	97.12	0.94	0.88	80	-
GCF_003130205.1	s__Aggregatibacter actinomycetemcomitans_A	76.9245	88	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	97.99	96.75	0.93	0.87	15	-
GCF_017160915.1	s__Aggregatibacter actinomycetemcomitans_B	76.7929	105	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Aggregatibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000751835.1	s__Necropsobacter rosorum	76.5955	107	684	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Pasteurellaceae;g__Necropsobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:15,239] [INFO] GTDB search result was written to GCF_014884965.1_ASM1488496v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:15,240] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:15,245] [INFO] DFAST_QC result json was written to GCF_014884965.1_ASM1488496v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:15,246] [INFO] DFAST_QC completed!
[2024-01-24 12:16:15,246] [INFO] Total running time: 0h0m56s