[2024-01-24 13:30:11,127] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:30:11,129] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:30:11,130] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d73b0a4-8312-4879-a334-c356a8a5178a/dqc_reference
[2024-01-24 13:30:12,427] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:30:12,428] [INFO] Task started: Prodigal
[2024-01-24 13:30:12,428] [INFO] Running command: gunzip -c /var/lib/cwl/stg018b8d1f-6a53-4b55-8657-8ea28ebb9441/GCF_022008365.1_ASM2200836v1_genomic.fna.gz | prodigal -d GCF_022008365.1_ASM2200836v1_genomic.fna/cds.fna -a GCF_022008365.1_ASM2200836v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:30:26,591] [INFO] Task succeeded: Prodigal
[2024-01-24 13:30:26,592] [INFO] Task started: HMMsearch
[2024-01-24 13:30:26,592] [INFO] Running command: hmmsearch --tblout GCF_022008365.1_ASM2200836v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d73b0a4-8312-4879-a334-c356a8a5178a/dqc_reference/reference_markers.hmm GCF_022008365.1_ASM2200836v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:30:26,907] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:30:26,916] [INFO] Found 6/6 markers.
[2024-01-24 13:30:26,962] [INFO] Query marker FASTA was written to GCF_022008365.1_ASM2200836v1_genomic.fna/markers.fasta
[2024-01-24 13:30:26,962] [INFO] Task started: Blastn
[2024-01-24 13:30:26,962] [INFO] Running command: blastn -query GCF_022008365.1_ASM2200836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d73b0a4-8312-4879-a334-c356a8a5178a/dqc_reference/reference_markers.fasta -out GCF_022008365.1_ASM2200836v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:30:27,744] [INFO] Task succeeded: Blastn
[2024-01-24 13:30:27,748] [INFO] Selected 16 target genomes.
[2024-01-24 13:30:27,748] [INFO] Target genome list was writen to GCF_022008365.1_ASM2200836v1_genomic.fna/target_genomes.txt
[2024-01-24 13:30:27,755] [INFO] Task started: fastANI
[2024-01-24 13:30:27,756] [INFO] Running command: fastANI --query /var/lib/cwl/stg018b8d1f-6a53-4b55-8657-8ea28ebb9441/GCF_022008365.1_ASM2200836v1_genomic.fna.gz --refList GCF_022008365.1_ASM2200836v1_genomic.fna/target_genomes.txt --output GCF_022008365.1_ASM2200836v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:30:38,043] [INFO] Task succeeded: fastANI
[2024-01-24 13:30:38,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d73b0a4-8312-4879-a334-c356a8a5178a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:30:38,044] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d73b0a4-8312-4879-a334-c356a8a5178a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:30:38,058] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:30:38,059] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:30:38,059] [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
Aequorivita aquimaris	strain=D-24	GCA_001573155.1	1548749	1548749	type	True	80.1153	570	1144	95	below_threshold
Aequorivita vladivostokensis	strain=KMM 3516	GCA_000952855.1	171194	171194	type	True	80.1047	543	1144	95	below_threshold
Aequorivita lipolytica	strain=Y10-2	GCA_007997135.1	153267	153267	type	True	79.8763	594	1144	95	below_threshold
Aequorivita soesokkakensis	strain=RSSK-12	GCA_001641085.1	1385699	1385699	type	True	79.7533	570	1144	95	below_threshold
Aequorivita sublithincola	strain=DSM 14238	GCA_000265385.1	101385	101385	type	True	79.7501	565	1144	95	below_threshold
Aequorivita iocasae	strain=KX20305	GCA_016757735.1	2803865	2803865	type	True	79.684	546	1144	95	below_threshold
Aequorivita antarctica	strain=SW49	GCA_007997155.1	153266	153266	type	True	79.657	615	1144	95	below_threshold
Aequorivita capsosiphonis	strain=DSM 23843	GCA_000429125.1	487317	487317	type	True	78.979	509	1144	95	below_threshold
Aequorivita sinensis	strain=S1-10	GCA_006346335.1	1382458	1382458	type	True	78.686	374	1144	95	below_threshold
Aequorivita viscosa	strain=CGMCC 1.11023	GCA_900106795.1	797419	797419	type	True	78.4689	351	1144	95	below_threshold
Aequorivita viscosa	strain=DSM 26349	GCA_900141955.1	797419	797419	type	True	78.4406	352	1144	95	below_threshold
Aequorivita echinoideorum	strain=JCM30378	GCA_018476645.1	1549647	1549647	type	True	77.832	287	1144	95	below_threshold
Halomarinibacterium sedimenti	strain=CAU 1614	GCA_019312585.1	2857106	2857106	type	True	76.826	147	1144	95	below_threshold
Aestuariivivens insulae	strain=AH-MY3	GCA_022662195.1	1621988	1621988	type	True	76.4836	58	1144	95	below_threshold
Tenacibaculum haliotis	strain=KCTC 52419	GCA_025215075.1	1888914	1888914	type	True	76.0035	57	1144	95	below_threshold
Abyssalbus ytuae	strain=MT3330	GCA_022807975.1	2926907	2926907	type	True	75.9975	56	1144	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:30:38,061] [INFO] DFAST Taxonomy check result was written to GCF_022008365.1_ASM2200836v1_genomic.fna/tc_result.tsv
[2024-01-24 13:30:38,061] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:30:38,061] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:30:38,062] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d73b0a4-8312-4879-a334-c356a8a5178a/dqc_reference/checkm_data
[2024-01-24 13:30:38,063] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:30:38,102] [INFO] Task started: CheckM
[2024-01-24 13:30:38,103] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022008365.1_ASM2200836v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022008365.1_ASM2200836v1_genomic.fna/checkm_input GCF_022008365.1_ASM2200836v1_genomic.fna/checkm_result
[2024-01-24 13:31:21,281] [INFO] Task succeeded: CheckM
[2024-01-24 13:31:21,283] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:31:21,333] [INFO] ===== Completeness check finished =====
[2024-01-24 13:31:21,333] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:31:21,334] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022008365.1_ASM2200836v1_genomic.fna/markers.fasta)
[2024-01-24 13:31:21,334] [INFO] Task started: Blastn
[2024-01-24 13:31:21,335] [INFO] Running command: blastn -query GCF_022008365.1_ASM2200836v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d73b0a4-8312-4879-a334-c356a8a5178a/dqc_reference/reference_markers_gtdb.fasta -out GCF_022008365.1_ASM2200836v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:22,169] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:22,173] [INFO] Selected 15 target genomes.
[2024-01-24 13:31:22,173] [INFO] Target genome list was writen to GCF_022008365.1_ASM2200836v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:31:22,196] [INFO] Task started: fastANI
[2024-01-24 13:31:22,196] [INFO] Running command: fastANI --query /var/lib/cwl/stg018b8d1f-6a53-4b55-8657-8ea28ebb9441/GCF_022008365.1_ASM2200836v1_genomic.fna.gz --refList GCF_022008365.1_ASM2200836v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022008365.1_ASM2200836v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:31:31,640] [INFO] Task succeeded: fastANI
[2024-01-24 13:31:31,668] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:31:31,669] [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
GCA_002364215.1	s__Aequorivita sp002364215	80.258	583	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.66	98.55	0.97	0.89	12	-
GCF_001573155.1	s__Aequorivita aquimaris	80.1061	571	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000952855.1	s__Aequorivita vladivostokensis	80.1047	543	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	98.24	98.00	0.93	0.90	7	-
GCA_002375695.1	s__Aequorivita sp002375695	79.9457	553	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007997135.1	s__Aequorivita lipolytica	79.8763	594	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000265385.1	s__Aequorivita sublithincola	79.7556	564	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641085.1	s__Aequorivita soesokkakensis	79.744	571	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.26	97.26	0.92	0.92	2	-
GCF_016757735.1	s__Aequorivita sp016757735	79.6882	546	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007997155.1	s__Aequorivita antarctica	79.653	616	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.98	99.98	0.99	0.99	2	-
GCF_900489465.1	s__Aequorivita sp900489465	79.6164	571	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002715485.1	s__Aequorivita sp002715485	79.5808	473	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.49	99.49	0.87	0.87	2	-
GCA_016649715.1	s__Aequorivita sp016649715	79.5585	540	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002733915.1	s__Aequorivita sp002733915	79.5201	541	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006346335.1	s__Aequorivita sinensis	78.686	374	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	97.40	96.22	0.90	0.88	3	-
GCF_900106795.1	s__Aequorivita viscosa	78.4689	351	1144	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Flavobacteriales;f__Flavobacteriaceae;g__Aequorivita	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:31:31,670] [INFO] GTDB search result was written to GCF_022008365.1_ASM2200836v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:31:31,671] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:31:31,675] [INFO] DFAST_QC result json was written to GCF_022008365.1_ASM2200836v1_genomic.fna/dqc_result.json
[2024-01-24 13:31:31,675] [INFO] DFAST_QC completed!
[2024-01-24 13:31:31,675] [INFO] Total running time: 0h1m21s