[2024-01-24 14:04:31,859] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:04:31,861] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:04:31,861] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f6618d1-2722-4ea2-8896-27519d9d882c/dqc_reference
[2024-01-24 14:04:33,256] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:04:33,258] [INFO] Task started: Prodigal
[2024-01-24 14:04:33,258] [INFO] Running command: gunzip -c /var/lib/cwl/stg67a820ad-55f1-49ba-9715-139fa91967bb/GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/cds.fna -a GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:01,298] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:01,299] [INFO] Task started: HMMsearch
[2024-01-24 14:05:01,299] [INFO] Running command: hmmsearch --tblout GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f6618d1-2722-4ea2-8896-27519d9d882c/dqc_reference/reference_markers.hmm GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:01,654] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:01,656] [INFO] Found 6/6 markers.
[2024-01-24 14:05:01,701] [INFO] Query marker FASTA was written to GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:05:01,701] [INFO] Task started: Blastn
[2024-01-24 14:05:01,701] [INFO] Running command: blastn -query GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f6618d1-2722-4ea2-8896-27519d9d882c/dqc_reference/reference_markers.fasta -out GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:02,383] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:02,386] [INFO] Selected 27 target genomes.
[2024-01-24 14:05:02,387] [INFO] Target genome list was writen to GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:05:02,436] [INFO] Task started: fastANI
[2024-01-24 14:05:02,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg67a820ad-55f1-49ba-9715-139fa91967bb/GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna.gz --refList GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:20,577] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:20,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f6618d1-2722-4ea2-8896-27519d9d882c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:20,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f6618d1-2722-4ea2-8896-27519d9d882c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:20,601] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:05:20,601] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:05:20,601] [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
Maribacter thermophilus	strain=HT7-2	GCA_001020565.1	1197874	1197874	type	True	83.1223	260	1661	95	below_threshold
Zobellia uliginosa	strain=DSM 2061	GCA_900156625.1	143224	143224	type	True	80.1683	477	1661	95	below_threshold
Zobellia galactanivorans	strain=DsiJT	GCA_000973105.1	63186	63186	type	True	79.8963	468	1661	95	below_threshold
Euzebyella marina	strain=CY01	GCA_014855515.1	1761453	1761453	type	True	77.8003	318	1661	95	below_threshold
Euzebyella saccharophila	strain=7SM30	GCA_014855495.1	679664	679664	type	True	77.7814	283	1661	95	below_threshold
Zobellia russellii	strain=KMM 3677	GCA_018728565.1	248907	248907	type	True	77.7432	261	1661	95	below_threshold
Zobellia amurskyensis	strain=KMM 3526	GCA_009725985.1	248905	248905	type	True	77.3214	235	1661	95	below_threshold
Aggregatimonas sangjinii	strain=F202Z8	GCA_005943945.1	2583587	2583587	type	True	76.9082	153	1661	95	below_threshold
Maribacter polysiphoniae	strain=DSM 23514	GCA_003148665.1	429344	429344	type	True	76.9015	169	1661	95	below_threshold
Pricia antarctica	strain=DSM 23421	GCA_900101815.1	641691	641691	type	True	76.8471	216	1661	95	below_threshold
Muricauda antarctica	strain=CGMCC 1.12174	GCA_900142405.1	1055723	1055723	type	True	76.6899	148	1661	95	below_threshold
Ulvibacterium marinum	strain=CCMM003	GCA_003626755.1	2419782	2419782	type	True	76.657	147	1661	95	below_threshold
Muricauda lutaonensis	strain=CC-HSB-11	GCA_000963865.1	516051	516051	type	True	76.6339	132	1661	95	below_threshold
Muricauda hadalis	strain=MT-229	GCA_007785775.2	2597517	2597517	type	True	76.596	141	1661	95	below_threshold
Muricauda beolgyonensis	strain=KCTC 23501	GCA_003992615.1	864064	864064	type	True	76.5684	143	1661	95	below_threshold
Muricauda taeanensis	strain=JCM 17757	GCA_003584105.1	1005926	1005926	type	True	76.5451	145	1661	95	below_threshold
Muricauda antarctica	strain=DSM 26351	GCA_900112295.1	1055723	1055723	type	True	76.5355	146	1661	95	below_threshold
Muriicola marianensis	strain=CGMCC 1.12606	GCA_014638095.1	1324801	1324801	type	True	76.5138	76	1661	95	below_threshold
Maribacter flavus	strain=KCTC 42508	GCA_008386635.1	1658664	1658664	type	True	76.4983	154	1661	95	below_threshold
Sinomicrobium kalidii	strain=HD2P242	GCA_021183825.1	2900738	2900738	type	True	76.2306	55	1661	95	below_threshold
Robertkochia sediminum	strain=1368	GCA_016786255.1	2785326	2785326	type	True	76.2283	52	1661	95	below_threshold
Robiginitalea sediminis	strain=O458	GCA_002198115.1	1982593	1982593	type	True	76.0698	77	1661	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:20,603] [INFO] DFAST Taxonomy check result was written to GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:05:20,604] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:20,604] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:20,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f6618d1-2722-4ea2-8896-27519d9d882c/dqc_reference/checkm_data
[2024-01-24 14:05:20,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:20,655] [INFO] Task started: CheckM
[2024-01-24 14:05:20,655] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/checkm_input GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:06:35,437] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:35,438] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:35,455] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:35,455] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:35,455] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:06:35,456] [INFO] Task started: Blastn
[2024-01-24 14:06:35,456] [INFO] Running command: blastn -query GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f6618d1-2722-4ea2-8896-27519d9d882c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:36,501] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:36,506] [INFO] Selected 21 target genomes.
[2024-01-24 14:06:36,506] [INFO] Target genome list was writen to GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:36,534] [INFO] Task started: fastANI
[2024-01-24 14:06:36,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg67a820ad-55f1-49ba-9715-139fa91967bb/GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna.gz --refList GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:52,959] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:52,979] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:52,979] [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_900141855.1	s__Pseudozobellia thermophila	100.0	1657	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900156625.1	s__Zobellia uliginosa	80.1802	476	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000973105.1	s__Zobellia galactanivorans	79.9235	469	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	99.09	99.05	0.92	0.91	3	-
GCF_017810075.1	s__Pseudozobellia sp017810075	78.6892	431	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002813285.1	s__Pseudozobellia sp002813285	78.6441	426	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Pseudozobellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014855515.1	s__Euzebyella marina	77.7964	318	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	97.49	97.10	0.92	0.88	10	-
GCF_014855495.1	s__Euzebyella saccharophila	77.7814	283	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Euzebyella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018728565.1	s__Zobellia russellii	77.7383	261	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Zobellia	95.0	97.51	97.51	0.91	0.91	2	-
GCF_003148665.1	s__Maribacter_A polysiphoniae	77.0239	169	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	99.27	98.55	0.95	0.91	3	-
GCA_002749285.1	s__Maribacter_A sp002749285	76.6953	95	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003992615.1	s__Muricauda beolgyonensis	76.6668	144	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626755.1	s__Ulvibacterium marinum	76.661	146	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Ulvibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007785775.2	s__Muricauda sp003973595	76.596	141	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	98.36	98.36	0.87	0.87	2	-
GCF_003584105.1	s__Muricauda taeanensis	76.5603	144	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muricauda	95.0	97.68	97.68	0.85	0.85	3	-
GCF_008386635.1	s__Maribacter flavus	76.5247	152	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Maribacter	95.0	96.59	96.59	0.88	0.88	2	-
GCF_014638095.1	s__Muriicola marianensis	76.5023	75	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Muriicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141935.1	s__Arenibacter nanhaiticus	76.1164	82	1661	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Arenibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:52,981] [INFO] GTDB search result was written to GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:52,982] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:52,986] [INFO] DFAST_QC result json was written to GCF_900141855.1_IMG-taxon_2622736519_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:06:52,986] [INFO] DFAST_QC completed!
[2024-01-24 14:06:52,986] [INFO] Total running time: 0h2m21s