[2024-01-24 11:26:12,619] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:12,622] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:12,622] [INFO] DQC Reference Directory: /var/lib/cwl/stg39fa507a-a9fb-4f6d-a8ee-3a3bd552b0b7/dqc_reference
[2024-01-24 11:26:13,991] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:13,992] [INFO] Task started: Prodigal
[2024-01-24 11:26:13,992] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d9984a1-2313-46e4-8c50-799006f6dd31/GCF_002807015.1_ASM280701v1_genomic.fna.gz | prodigal -d GCF_002807015.1_ASM280701v1_genomic.fna/cds.fna -a GCF_002807015.1_ASM280701v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:24,952] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:24,952] [INFO] Task started: HMMsearch
[2024-01-24 11:26:24,952] [INFO] Running command: hmmsearch --tblout GCF_002807015.1_ASM280701v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39fa507a-a9fb-4f6d-a8ee-3a3bd552b0b7/dqc_reference/reference_markers.hmm GCF_002807015.1_ASM280701v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:25,217] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:25,219] [INFO] Found 6/6 markers.
[2024-01-24 11:26:25,244] [INFO] Query marker FASTA was written to GCF_002807015.1_ASM280701v1_genomic.fna/markers.fasta
[2024-01-24 11:26:25,244] [INFO] Task started: Blastn
[2024-01-24 11:26:25,244] [INFO] Running command: blastn -query GCF_002807015.1_ASM280701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39fa507a-a9fb-4f6d-a8ee-3a3bd552b0b7/dqc_reference/reference_markers.fasta -out GCF_002807015.1_ASM280701v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:25,952] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:25,958] [INFO] Selected 24 target genomes.
[2024-01-24 11:26:25,958] [INFO] Target genome list was writen to GCF_002807015.1_ASM280701v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:25,967] [INFO] Task started: fastANI
[2024-01-24 11:26:25,967] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d9984a1-2313-46e4-8c50-799006f6dd31/GCF_002807015.1_ASM280701v1_genomic.fna.gz --refList GCF_002807015.1_ASM280701v1_genomic.fna/target_genomes.txt --output GCF_002807015.1_ASM280701v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:41,885] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:41,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39fa507a-a9fb-4f6d-a8ee-3a3bd552b0b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:41,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39fa507a-a9fb-4f6d-a8ee-3a3bd552b0b7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:41,899] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:41,899] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:41,900] [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
Avrilella dinanensis	strain=UR159	GCA_002807015.1	2008672	2008672	type	True	100.0	775	775	95	conclusive
Flavobacterium viscosum	strain=YIM 102796	GCA_003858535.1	2488729	2488729	type	True	78.1812	127	775	95	below_threshold
Myroides phaeus	strain=DSM 23313	GCA_900099675.1	702745	702745	type	True	77.9769	50	775	95	below_threshold
Flavobacterium baculatum	strain=SNL9	GCA_008629655.1	2608000	2608000	type	True	77.4476	108	775	95	below_threshold
Myroides odoratus	strain=FDAARGOS_1131	GCA_016726985.1	256	256	type	True	77.1987	57	775	95	below_threshold
Flavobacterium ummariense	strain=DS-12	GCA_900115115.1	913024	913024	type	True	77.1872	144	775	95	below_threshold
Myroides odoratus	strain=NCTC11036	GCA_900453865.1	256	256	type	True	77.1815	58	775	95	below_threshold
Flavobacterium filum	strain=DSM 17961	GCA_000425465.1	370974	370974	type	True	77.1613	67	775	95	below_threshold
Flavobacterium lindanitolerans	strain=DSM 21886	GCA_003663835.1	428988	428988	type	True	77.1303	67	775	95	below_threshold
Flavobacterium cauense	strain=CGMCC 1.7270	GCA_007830385.1	510946	510946	type	True	77.1196	84	775	95	below_threshold
Flavobacterium lindanitolerans	strain=IP-10	GCA_002846575.1	428988	428988	type	True	77.0653	67	775	95	below_threshold
Flavobacterium enshiense	strain=DK69	GCA_000498495.1	1341165	1341165	type	True	77.0266	70	775	95	below_threshold
Flavobacterium microcysteis	strain=MaA-Y11	GCA_006385255.1	2596891	2596891	type	True	76.9082	63	775	95	below_threshold
Flavobacterium swingsii	strain=DSM 21789	GCA_900111965.1	498292	498292	type	True	76.8109	57	775	95	below_threshold
Flavobacterium enshiense	strain=DK69	GCA_000769895.1	1341165	1341165	type	True	76.8095	71	775	95	below_threshold
Flavobacterium luteum	strain=NBRC 112527	GCA_008806775.1	2026654	2026654	type	True	76.4986	50	775	95	below_threshold
Flavobacterium sharifuzzamanii	strain=A7.6	GCA_003254585.1	2211133	2211133	type	True	76.3725	57	775	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:41,901] [INFO] DFAST Taxonomy check result was written to GCF_002807015.1_ASM280701v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:41,902] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:41,902] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:41,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39fa507a-a9fb-4f6d-a8ee-3a3bd552b0b7/dqc_reference/checkm_data
[2024-01-24 11:26:41,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:41,936] [INFO] Task started: CheckM
[2024-01-24 11:26:41,936] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002807015.1_ASM280701v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002807015.1_ASM280701v1_genomic.fna/checkm_input GCF_002807015.1_ASM280701v1_genomic.fna/checkm_result
[2024-01-24 11:27:17,524] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:17,525] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.75%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:17,548] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:17,549] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:17,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002807015.1_ASM280701v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:17,550] [INFO] Task started: Blastn
[2024-01-24 11:27:17,550] [INFO] Running command: blastn -query GCF_002807015.1_ASM280701v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg39fa507a-a9fb-4f6d-a8ee-3a3bd552b0b7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002807015.1_ASM280701v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:18,446] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:18,450] [INFO] Selected 24 target genomes.
[2024-01-24 11:27:18,450] [INFO] Target genome list was writen to GCF_002807015.1_ASM280701v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:18,468] [INFO] Task started: fastANI
[2024-01-24 11:27:18,468] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d9984a1-2313-46e4-8c50-799006f6dd31/GCF_002807015.1_ASM280701v1_genomic.fna.gz --refList GCF_002807015.1_ASM280701v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002807015.1_ASM280701v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:31,744] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:31,764] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:31,765] [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_002807015.1	s__Flavobacterium dinanensis	100.0	775	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900108395.1	s__Flavobacterium marinum	79.0251	161	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151275.1	s__Flavobacterium sp004151275	78.7146	163	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003858535.1	s__Flavobacterium viscosum	78.1753	126	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013874595.1	s__Flavobacterium sp013874595	78.0989	91	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	0.97	0.97	3	-
GCF_900099675.1	s__Flavobacterium phaeum	77.9769	50	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008629655.1	s__Flavobacterium baculatum	77.4476	108	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009799805.1	s__Flavobacterium phaeum_A	77.4225	57	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000243275.1	s__Flavobacterium odoratum	77.208	56	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	98.25	95.68	0.94	0.87	6	-
GCF_001549985.1	s__Flavobacterium odoratum_A	77.1939	53	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115115.1	s__Flavobacterium ummariense	77.1766	143	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425465.1	s__Flavobacterium filum	77.1613	67	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846575.1	s__Flavobacterium lindanitolerans	77.0926	68	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	97.86	97.14	0.91	0.85	11	-
GCF_000498495.1	s__Flavobacterium enshiense	77.0266	70	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_006385255.1	s__Flavobacterium microcysteis	76.9082	63	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111965.1	s__Flavobacterium swingsii	76.8109	57	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014145635.1	s__Flavobacterium sp014145635	76.5274	64	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008806775.1	s__Flavobacterium luteum	76.4986	50	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254585.1	s__Flavobacterium sharifuzzamanii	76.3725	57	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017833855.1	s__Flavobacterium sp017833855	76.3142	63	775	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:31,767] [INFO] GTDB search result was written to GCF_002807015.1_ASM280701v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:31,767] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:31,771] [INFO] DFAST_QC result json was written to GCF_002807015.1_ASM280701v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:31,772] [INFO] DFAST_QC completed!
[2024-01-24 11:27:31,772] [INFO] Total running time: 0h1m19s