[2024-01-25 19:46:35,618] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:46:35,619] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:46:35,619] [INFO] DQC Reference Directory: /var/lib/cwl/stg65d959d4-2228-42e1-aedf-91ad28c7f749/dqc_reference
[2024-01-25 19:46:36,748] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:46:36,749] [INFO] Task started: Prodigal
[2024-01-25 19:46:36,749] [INFO] Running command: gunzip -c /var/lib/cwl/stgab9b9516-d555-4eb1-a0d1-f219b25362f6/GCF_003096035.1_ASM309603v1_genomic.fna.gz | prodigal -d GCF_003096035.1_ASM309603v1_genomic.fna/cds.fna -a GCF_003096035.1_ASM309603v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:46:52,444] [INFO] Task succeeded: Prodigal
[2024-01-25 19:46:52,444] [INFO] Task started: HMMsearch
[2024-01-25 19:46:52,444] [INFO] Running command: hmmsearch --tblout GCF_003096035.1_ASM309603v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg65d959d4-2228-42e1-aedf-91ad28c7f749/dqc_reference/reference_markers.hmm GCF_003096035.1_ASM309603v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:46:52,731] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:46:52,732] [INFO] Found 6/6 markers.
[2024-01-25 19:46:52,764] [INFO] Query marker FASTA was written to GCF_003096035.1_ASM309603v1_genomic.fna/markers.fasta
[2024-01-25 19:46:52,764] [INFO] Task started: Blastn
[2024-01-25 19:46:52,765] [INFO] Running command: blastn -query GCF_003096035.1_ASM309603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65d959d4-2228-42e1-aedf-91ad28c7f749/dqc_reference/reference_markers.fasta -out GCF_003096035.1_ASM309603v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:46:53,396] [INFO] Task succeeded: Blastn
[2024-01-25 19:46:53,399] [INFO] Selected 17 target genomes.
[2024-01-25 19:46:53,399] [INFO] Target genome list was writen to GCF_003096035.1_ASM309603v1_genomic.fna/target_genomes.txt
[2024-01-25 19:46:53,415] [INFO] Task started: fastANI
[2024-01-25 19:46:53,415] [INFO] Running command: fastANI --query /var/lib/cwl/stgab9b9516-d555-4eb1-a0d1-f219b25362f6/GCF_003096035.1_ASM309603v1_genomic.fna.gz --refList GCF_003096035.1_ASM309603v1_genomic.fna/target_genomes.txt --output GCF_003096035.1_ASM309603v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:47:05,057] [INFO] Task succeeded: fastANI
[2024-01-25 19:47:05,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg65d959d4-2228-42e1-aedf-91ad28c7f749/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:47:05,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg65d959d4-2228-42e1-aedf-91ad28c7f749/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:47:05,066] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:47:05,067] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:47:05,067] [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
Flavobacterium album	strain=HYN0059	GCA_003096035.1	2175091	2175091	type	True	100.0	1327	1327	95	conclusive
Flavobacterium sediminilitoris	strain=YSM-43	GCA_023008245.1	2024526	2024526	type	True	78.8495	51	1327	95	below_threshold
Flavobacterium akiainvivens	strain=IK-1	GCA_001278115.1	1202724	1202724	type	True	77.782	294	1327	95	below_threshold
Flavobacterium zepuense	strain=ZT4R6	GCA_007097145.1	2593302	2593302	type	True	77.7677	349	1327	95	below_threshold
Flavobacterium subsaxonicum	strain=DSM 21790	GCA_000422725.1	426226	426226	type	True	77.744	350	1327	95	below_threshold
Flavobacterium akiainvivens	strain=DSM 25510	GCA_900115875.1	1202724	1202724	type	True	77.7002	293	1327	95	below_threshold
Flavobacterium rivuli	strain=WB 3.3-2	GCA_000769825.1	498301	498301	type	True	77.695	309	1327	95	below_threshold
Flavobacterium subsaxonicum	strain=WB 4.1-42	GCA_000769935.1	426226	426226	type	True	77.6911	354	1327	95	below_threshold
Flavobacterium rivuli	strain=DSM 21788	GCA_000378485.1	498301	498301	type	True	77.6646	305	1327	95	below_threshold
Flavobacterium cyanobacteriorum	strain=TH021	GCA_002251835.1	2022802	2022802	type	True	77.6404	267	1327	95	below_threshold
Flavobacterium coralii	strain=D11R37	GCA_019891545.1	2838017	2838017	type	True	77.5744	272	1327	95	below_threshold
Flavobacterium salilacus subsp. salilacus	strain=SaA2.12	GCA_004634195.1	2545633	2898423	type	True	77.2913	237	1327	95	below_threshold
Flavobacterium rakeshii	strain=JCM 17928	GCA_009741375.1	1038845	1038845	type	True	77.2395	213	1327	95	below_threshold
Flavobacterium taihuense	strain=NAS39	GCA_019351435.1	2857508	2857508	type	True	76.7333	60	1327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:47:05,069] [INFO] DFAST Taxonomy check result was written to GCF_003096035.1_ASM309603v1_genomic.fna/tc_result.tsv
[2024-01-25 19:47:05,070] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:47:05,070] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:47:05,070] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg65d959d4-2228-42e1-aedf-91ad28c7f749/dqc_reference/checkm_data
[2024-01-25 19:47:05,071] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:47:05,110] [INFO] Task started: CheckM
[2024-01-25 19:47:05,110] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003096035.1_ASM309603v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003096035.1_ASM309603v1_genomic.fna/checkm_input GCF_003096035.1_ASM309603v1_genomic.fna/checkm_result
[2024-01-25 19:47:49,276] [INFO] Task succeeded: CheckM
[2024-01-25 19:47:49,277] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:47:49,291] [INFO] ===== Completeness check finished =====
[2024-01-25 19:47:49,291] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:47:49,291] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003096035.1_ASM309603v1_genomic.fna/markers.fasta)
[2024-01-25 19:47:49,292] [INFO] Task started: Blastn
[2024-01-25 19:47:49,292] [INFO] Running command: blastn -query GCF_003096035.1_ASM309603v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg65d959d4-2228-42e1-aedf-91ad28c7f749/dqc_reference/reference_markers_gtdb.fasta -out GCF_003096035.1_ASM309603v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:47:50,169] [INFO] Task succeeded: Blastn
[2024-01-25 19:47:50,173] [INFO] Selected 14 target genomes.
[2024-01-25 19:47:50,173] [INFO] Target genome list was writen to GCF_003096035.1_ASM309603v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:47:50,187] [INFO] Task started: fastANI
[2024-01-25 19:47:50,188] [INFO] Running command: fastANI --query /var/lib/cwl/stgab9b9516-d555-4eb1-a0d1-f219b25362f6/GCF_003096035.1_ASM309603v1_genomic.fna.gz --refList GCF_003096035.1_ASM309603v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003096035.1_ASM309603v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:00,657] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:00,666] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:00,666] [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_003096035.1	s__Flavobacterium album	100.0	1326	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_001708385.1	s__Flavobacterium psychrophilum_A	78.033	319	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003243255.1	s__Flavobacterium psychrophilum_B	77.9421	320	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003350375.1	s__Flavobacterium sp003350375	77.9172	297	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012932585.1	s__Flavobacterium sp012932585	77.8747	306	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003403075.1	s__Flavobacterium sp003403075	77.7655	293	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007097145.1	s__Flavobacterium sp007097145	77.7593	349	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422725.1	s__Flavobacterium subsaxonicum	77.7348	351	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009826935.1	s__Flavobacterium sp009826935	77.6957	259	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002714575.1	s__Flavobacterium sp002714575	77.6914	263	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004151245.1	s__Flavobacterium beibuense_A	77.6748	241	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000378485.1	s__Flavobacterium rivuli	77.6724	305	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002251835.1	s__Flavobacterium cyanobacteriorum	77.6543	265	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009848495.1	s__Flavobacterium sp009848495	77.3825	242	1327	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Flavobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:00,668] [INFO] GTDB search result was written to GCF_003096035.1_ASM309603v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:00,669] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:00,672] [INFO] DFAST_QC result json was written to GCF_003096035.1_ASM309603v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:00,672] [INFO] DFAST_QC completed!
[2024-01-25 19:48:00,672] [INFO] Total running time: 0h1m25s