[2024-01-24 13:47:10,871] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:47:10,873] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:47:10,873] [INFO] DQC Reference Directory: /var/lib/cwl/stg749e9c8e-d4a3-4f44-a0b0-45a2a9715560/dqc_reference
[2024-01-24 13:47:12,110] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:47:12,111] [INFO] Task started: Prodigal
[2024-01-24 13:47:12,111] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f890472-0ced-472e-8c8f-8ee19f012c94/GCF_021295345.1_ASM2129534v1_genomic.fna.gz | prodigal -d GCF_021295345.1_ASM2129534v1_genomic.fna/cds.fna -a GCF_021295345.1_ASM2129534v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:24,017] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:24,018] [INFO] Task started: HMMsearch
[2024-01-24 13:47:24,018] [INFO] Running command: hmmsearch --tblout GCF_021295345.1_ASM2129534v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg749e9c8e-d4a3-4f44-a0b0-45a2a9715560/dqc_reference/reference_markers.hmm GCF_021295345.1_ASM2129534v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:24,321] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:24,322] [INFO] Found 6/6 markers.
[2024-01-24 13:47:24,366] [INFO] Query marker FASTA was written to GCF_021295345.1_ASM2129534v1_genomic.fna/markers.fasta
[2024-01-24 13:47:24,366] [INFO] Task started: Blastn
[2024-01-24 13:47:24,367] [INFO] Running command: blastn -query GCF_021295345.1_ASM2129534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg749e9c8e-d4a3-4f44-a0b0-45a2a9715560/dqc_reference/reference_markers.fasta -out GCF_021295345.1_ASM2129534v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:25,166] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:25,170] [INFO] Selected 23 target genomes.
[2024-01-24 13:47:25,170] [INFO] Target genome list was writen to GCF_021295345.1_ASM2129534v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:25,181] [INFO] Task started: fastANI
[2024-01-24 13:47:25,182] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f890472-0ced-472e-8c8f-8ee19f012c94/GCF_021295345.1_ASM2129534v1_genomic.fna.gz --refList GCF_021295345.1_ASM2129534v1_genomic.fna/target_genomes.txt --output GCF_021295345.1_ASM2129534v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:41,785] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:41,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg749e9c8e-d4a3-4f44-a0b0-45a2a9715560/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:41,787] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg749e9c8e-d4a3-4f44-a0b0-45a2a9715560/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:41,803] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:41,803] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:41,803] [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
Motilimonas eburnea	strain=YH6	GCA_021295345.1	1737488	1737488	type	True	100.0	1496	1497	95	conclusive
Motilimonas cestriensis	strain=MKS20	GCA_021295315.1	2742685	2742685	type	True	79.9787	582	1497	95	below_threshold
Motilimonas pumila	strain=PLHSC7-2	GCA_003596335.1	2303987	2303987	type	True	79.1015	234	1497	95	below_threshold
Vibrio rarus	strain=LMG 23674	GCA_024347075.1	413403	413403	type	True	77.1704	68	1497	95	below_threshold
Photobacterium lutimaris	strain=JCM 13586	GCA_003025555.1	388278	388278	type	True	77.1226	64	1497	95	below_threshold
Photobacterium lucens	strain=CAIM 1937	GCA_009873615.1	2562949	2562949	type	True	77.078	80	1497	95	below_threshold
Pseudoalteromonas ulvae	strain=UL12	GCA_014925405.1	107327	107327	type	True	76.9368	53	1497	95	below_threshold
Photobacterium leiognathi	strain=ATCC 25521	GCA_003026235.1	553611	553611	type	True	76.9208	88	1497	95	below_threshold
Grimontia celer	strain=CECT 9029	GCA_900055185.1	1796497	1796497	type	True	76.8572	59	1497	95	below_threshold
Vibrio cholerae	strain=ATCC 14035	GCA_000621645.1	666	666	type	True	76.736	67	1497	95	below_threshold
Grimontia marina	strain=CECT 8713	GCA_900060185.1	646534	646534	type	True	76.5804	58	1497	95	below_threshold
Shewanella denitrificans	strain=OS217	GCA_000013765.1	192073	192073	type	True	76.5589	63	1497	95	below_threshold
Shewanella surugensis	strain=DSM 17177	GCA_023284005.1	212020	212020	type	True	75.5982	51	1497	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:41,805] [INFO] DFAST Taxonomy check result was written to GCF_021295345.1_ASM2129534v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:41,806] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:41,806] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:41,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg749e9c8e-d4a3-4f44-a0b0-45a2a9715560/dqc_reference/checkm_data
[2024-01-24 13:47:41,807] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:41,861] [INFO] Task started: CheckM
[2024-01-24 13:47:41,862] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021295345.1_ASM2129534v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021295345.1_ASM2129534v1_genomic.fna/checkm_input GCF_021295345.1_ASM2129534v1_genomic.fna/checkm_result
[2024-01-24 13:48:21,298] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:21,299] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:21,322] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:21,323] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:21,323] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021295345.1_ASM2129534v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:21,323] [INFO] Task started: Blastn
[2024-01-24 13:48:21,324] [INFO] Running command: blastn -query GCF_021295345.1_ASM2129534v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg749e9c8e-d4a3-4f44-a0b0-45a2a9715560/dqc_reference/reference_markers_gtdb.fasta -out GCF_021295345.1_ASM2129534v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:22,533] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:22,538] [INFO] Selected 32 target genomes.
[2024-01-24 13:48:22,539] [INFO] Target genome list was writen to GCF_021295345.1_ASM2129534v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:22,577] [INFO] Task started: fastANI
[2024-01-24 13:48:22,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f890472-0ced-472e-8c8f-8ee19f012c94/GCF_021295345.1_ASM2129534v1_genomic.fna.gz --refList GCF_021295345.1_ASM2129534v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021295345.1_ASM2129534v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:45,385] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:45,403] [INFO] Found 22 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:48:45,404] [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_003596335.1	s__Motilimonas pumila	79.1171	233	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Motilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900185615.1	s__Photobacterium malacitanum	77.3699	60	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	95.08	95.06	0.91	0.91	6	-
GCF_003025555.1	s__Photobacterium lutimaris	77.1557	63	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009873615.1	s__Photobacterium lucens	77.078	80	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	98.83	97.58	0.96	0.94	5	-
GCF_003026215.1	s__Photobacterium indicum	77.0354	63	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002749895.1	s__Vibrio fujianensis	77.0247	57	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	99.21	99.14	0.95	0.93	8	-
GCF_002964765.1	s__Pseudoalteromonas sp002964765	76.9912	51	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.33	98.12	0.95	0.94	4	-
GCF_014925405.1	s__Pseudoalteromonas ulvae	76.9368	53	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	98.81	98.81	0.93	0.93	2	-
GCF_000696385.1	s__Vibrio metoecus	76.9034	61	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.79	97.58	0.93	0.89	26	-
GCF_000950415.1	s__Photobacterium leiognathi	76.8517	81	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.0	97.11	96.59	0.91	0.88	15	-
GCF_900055185.1	s__Enterovibrio celer	76.8311	58	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004120195.1	s__Enterovibrio baiacu	76.7999	65	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001471585.2	s__Vibrio cholerae	76.7984	64	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Vibrio	95.0	97.72	95.09	0.90	0.82	1544	-
GCF_002964785.1	s__Pseudoalteromonas sp002964785	76.7386	55	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196255.1	s__Photobacterium profundum_A	76.733	54	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Photobacterium	95.5718	N/A	N/A	N/A	N/A	1	-
GCF_000333895.2	s__Enterovibrio indicus	76.6369	66	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	96.52	96.52	0.90	0.90	2	-
GCF_900060185.1	s__Enterovibrio marinus	76.5764	56	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Vibrionaceae;g__Enterovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000013765.1	s__Shewanella denitrificans	76.5275	64	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014163735.1	s__Shewanella sp014163735	76.4157	56	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Shewanellaceae;g__Shewanella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013619145.1	s__Psychromonas sp013619145	76.2425	62	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Psychromonadaceae;g__Psychromonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000170855.1	s__Moritella sp000170855	76.1868	65	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Moritellaceae;g__Moritella	95.0	97.45	95.37	0.88	0.83	4	-
GCF_008808095.1	s__Pseudoalteromonas ruthenica	75.9951	52	1497	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Enterobacterales;f__Alteromonadaceae;g__Pseudoalteromonas	95.0	97.93	97.29	0.94	0.91	18	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:45,406] [INFO] GTDB search result was written to GCF_021295345.1_ASM2129534v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:45,406] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:45,414] [INFO] DFAST_QC result json was written to GCF_021295345.1_ASM2129534v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:45,414] [INFO] DFAST_QC completed!
[2024-01-24 13:48:45,414] [INFO] Total running time: 0h1m35s