[2024-01-25 20:14:20,869] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:14:20,870] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:14:20,870] [INFO] DQC Reference Directory: /var/lib/cwl/stg0b8c1b01-8181-493e-8b2a-effcfb91376f/dqc_reference
[2024-01-25 20:14:21,984] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:14:21,984] [INFO] Task started: Prodigal
[2024-01-25 20:14:21,985] [INFO] Running command: gunzip -c /var/lib/cwl/stg7eb7dec7-120f-4d5e-961b-53b533e211e5/GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/cds.fna -a GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:14:31,984] [INFO] Task succeeded: Prodigal
[2024-01-25 20:14:31,984] [INFO] Task started: HMMsearch
[2024-01-25 20:14:31,984] [INFO] Running command: hmmsearch --tblout GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0b8c1b01-8181-493e-8b2a-effcfb91376f/dqc_reference/reference_markers.hmm GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:14:32,216] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:14:32,217] [INFO] Found 6/6 markers.
[2024-01-25 20:14:32,249] [INFO] Query marker FASTA was written to GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:14:32,250] [INFO] Task started: Blastn
[2024-01-25 20:14:32,250] [INFO] Running command: blastn -query GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b8c1b01-8181-493e-8b2a-effcfb91376f/dqc_reference/reference_markers.fasta -out GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:33,162] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:33,164] [INFO] Selected 19 target genomes.
[2024-01-25 20:14:33,165] [INFO] Target genome list was writen to GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:14:33,174] [INFO] Task started: fastANI
[2024-01-25 20:14:33,174] [INFO] Running command: fastANI --query /var/lib/cwl/stg7eb7dec7-120f-4d5e-961b-53b533e211e5/GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna.gz --refList GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:47,841] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:47,842] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0b8c1b01-8181-493e-8b2a-effcfb91376f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:47,842] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0b8c1b01-8181-493e-8b2a-effcfb91376f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:47,854] [INFO] Found 19 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:14:47,854] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:14:47,854] [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
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	100.0	1295	1298	95	conclusive
Palleronia marisminoris	strain=CECT 7066	GCA_900172315.1	315423	315423	type	True	99.9976	1218	1298	95	conclusive
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	79.7665	525	1298	95	below_threshold
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	79.7046	533	1298	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	79.5078	510	1298	95	below_threshold
Limimaricola pyoseonensis	strain=DSM 21424	GCA_900102015.1	521013	521013	type	True	79.1998	485	1298	95	below_threshold
Roseivivax isoporae	strain=LMG 25204	GCA_000521865.1	591206	591206	type	True	78.9505	494	1298	95	below_threshold
Roseivivax marinus	strain=DSM 27511	GCA_900109705.1	1379903	1379903	type	True	78.7787	471	1298	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	78.5885	438	1298	95	below_threshold
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	78.4832	442	1298	95	below_threshold
Limimaricola cinnabarinus	strain=LL-001	GCA_000466965.1	1125964	1125964	type	True	78.4732	372	1298	95	below_threshold
Pseudooceanicola endophyticus	strain=CBS1P-1	GCA_018760365.1	2841273	2841273	type	True	78.2819	411	1298	95	below_threshold
Halovulum marinum	strain=2CG4	GCA_009697225.1	2662447	2662447	type	True	78.2419	422	1298	95	below_threshold
Hasllibacter halocynthiae	strain=DSM 29318	GCA_003003095.1	595589	595589	type	True	78.0628	345	1298	95	below_threshold
Paracoccus mutanolyticus	strain=RSP-02	GCA_003285265.1	1499308	1499308	type	True	78.0314	304	1298	95	below_threshold
Paracoccus aminovorans		GCA_900005615.1	34004	34004	type	True	77.9291	332	1298	95	below_threshold
Paenimaribius caenipelagi	strain=JBTF-M29	GCA_007004065.1	2489174	2489174	type	True	77.926	302	1298	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.9215	410	1298	95	below_threshold
Paracoccus aminovorans	strain=DSM 8537	GCA_900113565.1	34004	34004	type	True	77.8945	324	1298	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:47,856] [INFO] DFAST Taxonomy check result was written to GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:14:47,856] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:47,856] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:47,857] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0b8c1b01-8181-493e-8b2a-effcfb91376f/dqc_reference/checkm_data
[2024-01-25 20:14:47,857] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:47,897] [INFO] Task started: CheckM
[2024-01-25 20:14:47,898] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/checkm_input GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:15:20,627] [INFO] Task succeeded: CheckM
[2024-01-25 20:15:20,628] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:15:20,647] [INFO] ===== Completeness check finished =====
[2024-01-25 20:15:20,647] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:15:20,647] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:15:20,647] [INFO] Task started: Blastn
[2024-01-25 20:15:20,648] [INFO] Running command: blastn -query GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0b8c1b01-8181-493e-8b2a-effcfb91376f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:15:22,460] [INFO] Task succeeded: Blastn
[2024-01-25 20:15:22,464] [INFO] Selected 18 target genomes.
[2024-01-25 20:15:22,465] [INFO] Target genome list was writen to GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:15:22,475] [INFO] Task started: fastANI
[2024-01-25 20:15:22,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg7eb7dec7-120f-4d5e-961b-53b533e211e5/GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna.gz --refList GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:15:38,780] [INFO] Task succeeded: fastANI
[2024-01-25 20:15:38,792] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:15:38,792] [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_900172315.1	s__Palleronia marisminoris	99.9976	1218	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_900302445.1	s__Palleronia abyssalis	81.1056	651	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141995.1	s__Palleronia salina	79.8684	537	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_000743715.1	s__Palleronia rufa	79.7566	526	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110115.1	s__Palleronia pelagia	79.7084	533	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_016412875.1	s__Palleronia pontilimi	79.6231	503	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115595.1	s__Tranquillimonas alkanivorans	79.4153	527	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Tranquillimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363795.1	s__Palleronia sp900609015	79.2619	520	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900102015.1	s__Limimaricola pyoseonensis	79.1588	488	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Limimaricola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002869745.1	s__Oceaniglobus roseus	79.083	504	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceaniglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000153305.1	s__Oceanicola granulosus	78.9912	450	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Oceanicola	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004005435.1	s__CCMM004 sp004005435	78.9023	428	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CCMM004	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109705.1	s__Roseivivax marinus	78.7824	470	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseivivax	95.0	97.84	97.84	0.91	0.91	2	-
GCF_003340555.1	s__Jannaschia formosa	78.6033	436	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253995.1	s__Palleronia aestuarii	78.5188	438	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002166865.1	s__Roseovarius sp002166865	77.9667	342	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Roseovarius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004065.1	s__Palleronia caenipelagi	77.9426	303	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003217735.2	s__Marinibacterium sp003217735	77.886	444	1298	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Marinibacterium	95.0	98.81	98.75	0.89	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:15:38,794] [INFO] GTDB search result was written to GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:15:38,794] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:15:38,798] [INFO] DFAST_QC result json was written to GCF_900113405.1_IMG-taxon_2615840708_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:15:38,799] [INFO] DFAST_QC completed!
[2024-01-25 20:15:38,799] [INFO] Total running time: 0h1m18s