[2024-01-24 14:20:00,908] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:20:00,921] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:20:00,921] [INFO] DQC Reference Directory: /var/lib/cwl/stgc8c6e1d8-ce8b-4e7c-8158-16e426d5a516/dqc_reference
[2024-01-24 14:20:02,096] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:20:02,097] [INFO] Task started: Prodigal
[2024-01-24 14:20:02,098] [INFO] Running command: gunzip -c /var/lib/cwl/stg4158d64c-95fa-45ed-971e-be25600bffb5/GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna.gz | prodigal -d GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/cds.fna -a GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:20:14,950] [INFO] Task succeeded: Prodigal
[2024-01-24 14:20:14,950] [INFO] Task started: HMMsearch
[2024-01-24 14:20:14,951] [INFO] Running command: hmmsearch --tblout GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc8c6e1d8-ce8b-4e7c-8158-16e426d5a516/dqc_reference/reference_markers.hmm GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:20:15,219] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:20:15,221] [INFO] Found 6/6 markers.
[2024-01-24 14:20:15,262] [INFO] Query marker FASTA was written to GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/markers.fasta
[2024-01-24 14:20:15,262] [INFO] Task started: Blastn
[2024-01-24 14:20:15,262] [INFO] Running command: blastn -query GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8c6e1d8-ce8b-4e7c-8158-16e426d5a516/dqc_reference/reference_markers.fasta -out GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:16,213] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:16,216] [INFO] Selected 18 target genomes.
[2024-01-24 14:20:16,217] [INFO] Target genome list was writen to GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/target_genomes.txt
[2024-01-24 14:20:16,223] [INFO] Task started: fastANI
[2024-01-24 14:20:16,224] [INFO] Running command: fastANI --query /var/lib/cwl/stg4158d64c-95fa-45ed-971e-be25600bffb5/GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna.gz --refList GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/target_genomes.txt --output GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:20:28,852] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:28,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc8c6e1d8-ce8b-4e7c-8158-16e426d5a516/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:20:28,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc8c6e1d8-ce8b-4e7c-8158-16e426d5a516/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:20:28,879] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:20:28,879] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:20:28,879] [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=CECT 7066	GCA_900172315.1	315423	315423	type	True	81.2093	625	1445	95	below_threshold
Palleronia marisminoris	strain=DSM 26347	GCA_900113405.1	315423	315423	type	True	81.1018	644	1445	95	below_threshold
Maribius pelagius	strain=DSM 26893	GCA_900110115.1	387096	387096	type	True	80.0953	578	1445	95	below_threshold
Maribius salinus	strain=DSM 26892	GCA_900141995.1	313368	313368	type	True	79.5679	558	1445	95	below_threshold
Palleronia rufa	strain=MOLA 401	GCA_000743715.1	1530186	1530186	type	True	79.1549	546	1445	95	below_threshold
Palleronia sediminis	strain=SS33	GCA_004358695.1	2547833	2547833	type	True	79.0412	481	1445	95	below_threshold
Pseudooceanicola aestuarii	strain=E2-1	GCA_010614805.1	2697319	2697319	type	True	78.4174	329	1445	95	below_threshold
Jannaschia formosa	strain=12N15	GCA_003340555.1	2259592	2259592	type	True	78.2873	372	1445	95	below_threshold
Hwanghaeicola aestuarii	strain=DSM 22009	GCA_003253995.1	568105	568105	type	True	78.1069	374	1445	95	below_threshold
Antarcticimicrobium luteum	strain=318-1	GCA_004358185.1	2547397	2547397	type	True	77.946	354	1445	95	below_threshold
Roseibacterium elongatum	strain=DFL-43	GCA_000590925.1	159346	159346	type	True	77.8248	335	1445	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	77.8082	333	1445	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	77.7871	330	1445	95	below_threshold
Paenimaribius caenipelagi	strain=JBTF-M29	GCA_007004065.1	2489174	2489174	type	True	77.7309	295	1445	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_010435925.1	2705421	2705421	type	True	77.6527	289	1445	95	below_threshold
Pseudoroseicyclus tamaricis	strain=CLL3-39	GCA_012070395.1	2705421	2705421	type	True	77.6501	290	1445	95	below_threshold
Maritimibacter alexandrii	strain=LZ-17	GCA_005871115.1	2570355	2570355	type	True	77.6099	345	1445	95	below_threshold
Salipiger marinus	strain=DSM 26424	GCA_900100085.1	555512	555512	type	True	77.5967	374	1445	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:20:28,881] [INFO] DFAST Taxonomy check result was written to GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/tc_result.tsv
[2024-01-24 14:20:28,882] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:20:28,882] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:20:28,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc8c6e1d8-ce8b-4e7c-8158-16e426d5a516/dqc_reference/checkm_data
[2024-01-24 14:20:28,884] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:20:28,923] [INFO] Task started: CheckM
[2024-01-24 14:20:28,924] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/checkm_input GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/checkm_result
[2024-01-24 14:21:08,798] [INFO] Task succeeded: CheckM
[2024-01-24 14:21:08,800] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:21:08,818] [INFO] ===== Completeness check finished =====
[2024-01-24 14:21:08,818] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:21:08,819] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/markers.fasta)
[2024-01-24 14:21:08,819] [INFO] Task started: Blastn
[2024-01-24 14:21:08,819] [INFO] Running command: blastn -query GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/markers.fasta -db /var/lib/cwl/stgc8c6e1d8-ce8b-4e7c-8158-16e426d5a516/dqc_reference/reference_markers_gtdb.fasta -out GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:21:10,551] [INFO] Task succeeded: Blastn
[2024-01-24 14:21:10,555] [INFO] Selected 15 target genomes.
[2024-01-24 14:21:10,555] [INFO] Target genome list was writen to GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:21:10,578] [INFO] Task started: fastANI
[2024-01-24 14:21:10,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg4158d64c-95fa-45ed-971e-be25600bffb5/GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna.gz --refList GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/target_genomes_gtdb.txt --output GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:21:21,504] [INFO] Task succeeded: fastANI
[2024-01-24 14:21:21,529] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:21:21,529] [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_900302445.1	s__Palleronia abyssalis	100.0	1443	1445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900172315.1	s__Palleronia marisminoris	81.1966	627	1445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_900110115.1	s__Palleronia pelagia	80.091	579	1445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	96.3515	N/A	N/A	N/A	N/A	1	-
GCF_001975705.1	s__Salipiger abyssi	79.5724	364	1445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Salipiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900141995.1	s__Palleronia salina	79.5615	556	1445	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	79.1828	517	1445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363795.1	s__Palleronia sp900609015	79.1737	539	1445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000743715.1	s__Palleronia rufa	79.155	546	1445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358695.1	s__Palleronia sp004358695	79.0417	481	1445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003340555.1	s__Jannaschia formosa	78.2872	372	1445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Jannaschia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000744955.1	s__Actibacterium sp000744955	78.2759	337	1445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Actibacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003253995.1	s__Palleronia aestuarii	78.0962	374	1445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358185.1	s__Antarcticimicrobium luteum	77.9581	353	1445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Antarcticimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007004065.1	s__Palleronia caenipelagi	77.7131	295	1445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__Palleronia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012070395.1	s__CLL3-39 sp012070395	77.6391	291	1445	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhodobacterales;f__Rhodobacteraceae;g__CLL3-39	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:21:21,531] [INFO] GTDB search result was written to GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/result_gtdb.tsv
[2024-01-24 14:21:21,531] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:21:21,535] [INFO] DFAST_QC result json was written to GCF_900302445.1_P.abyssalisCECT8504_Spades_Prokka_genomic.fna/dqc_result.json
[2024-01-24 14:21:21,535] [INFO] DFAST_QC completed!
[2024-01-24 14:21:21,535] [INFO] Total running time: 0h1m21s