[2024-01-24 13:57:42,200] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,202] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,202] [INFO] DQC Reference Directory: /var/lib/cwl/stgd8d0bab4-87d1-40e3-88fc-2b3f7daa2918/dqc_reference
[2024-01-24 13:57:43,478] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:43,479] [INFO] Task started: Prodigal
[2024-01-24 13:57:43,479] [INFO] Running command: gunzip -c /var/lib/cwl/stg43e51d6d-458b-41de-b892-004b5626dd94/GCF_005298175.1_ASM529817v1_genomic.fna.gz | prodigal -d GCF_005298175.1_ASM529817v1_genomic.fna/cds.fna -a GCF_005298175.1_ASM529817v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:57,199] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:57,199] [INFO] Task started: HMMsearch
[2024-01-24 13:57:57,199] [INFO] Running command: hmmsearch --tblout GCF_005298175.1_ASM529817v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd8d0bab4-87d1-40e3-88fc-2b3f7daa2918/dqc_reference/reference_markers.hmm GCF_005298175.1_ASM529817v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:57,530] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:57,531] [INFO] Found 6/6 markers.
[2024-01-24 13:57:57,576] [INFO] Query marker FASTA was written to GCF_005298175.1_ASM529817v1_genomic.fna/markers.fasta
[2024-01-24 13:57:57,576] [INFO] Task started: Blastn
[2024-01-24 13:57:57,576] [INFO] Running command: blastn -query GCF_005298175.1_ASM529817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8d0bab4-87d1-40e3-88fc-2b3f7daa2918/dqc_reference/reference_markers.fasta -out GCF_005298175.1_ASM529817v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:58,571] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:58,575] [INFO] Selected 10 target genomes.
[2024-01-24 13:57:58,575] [INFO] Target genome list was writen to GCF_005298175.1_ASM529817v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:58,579] [INFO] Task started: fastANI
[2024-01-24 13:57:58,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg43e51d6d-458b-41de-b892-004b5626dd94/GCF_005298175.1_ASM529817v1_genomic.fna.gz --refList GCF_005298175.1_ASM529817v1_genomic.fna/target_genomes.txt --output GCF_005298175.1_ASM529817v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:08,156] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:08,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd8d0bab4-87d1-40e3-88fc-2b3f7daa2918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:08,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd8d0bab4-87d1-40e3-88fc-2b3f7daa2918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:08,167] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:58:08,167] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:58:08,167] [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
Marinobacter denitrificans	strain=JB02H27	GCA_008795955.1	2597703	2597703	type	True	86.5583	1162	1473	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_012956055.1	1928859	1928859	type	True	84.8821	1052	1473	95	below_threshold
Marinobacter orientalis	strain=W62	GCA_004792665.1	1928859	1928859	type	True	84.827	1038	1473	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_007559285.1	1928331	1928331	type	True	84.463	994	1473	95	below_threshold
Marinobacter vulgaris	strain=F01	GCA_003344045.1	1928331	1928331	type	True	84.4217	1007	1473	95	below_threshold
Marinobacter algicola	strain=DG893	GCA_000170835.1	236100	236100	type	True	82.0227	869	1473	95	below_threshold
Marinobacter arenosus	strain=CAU 1620	GCA_019264345.1	2856822	2856822	type	True	79.9736	604	1473	95	below_threshold
Marinobacter goseongensis	strain=KCTC 12515	GCA_023156235.1	453838	453838	type	True	79.7623	595	1473	95	below_threshold
Marinobacter similis	strain=A3d10	GCA_000830985.1	1420916	1420916	type	True	79.276	542	1473	95	below_threshold
Marinobacter koreensis	strain=DSM 17924	GCA_023156285.1	335974	335974	type	True	79.2006	495	1473	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:08,169] [INFO] DFAST Taxonomy check result was written to GCF_005298175.1_ASM529817v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:08,170] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:08,170] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:08,170] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd8d0bab4-87d1-40e3-88fc-2b3f7daa2918/dqc_reference/checkm_data
[2024-01-24 13:58:08,172] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:08,218] [INFO] Task started: CheckM
[2024-01-24 13:58:08,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005298175.1_ASM529817v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005298175.1_ASM529817v1_genomic.fna/checkm_input GCF_005298175.1_ASM529817v1_genomic.fna/checkm_result
[2024-01-24 13:58:52,272] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:52,273] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:52,298] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:52,298] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:52,299] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005298175.1_ASM529817v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:52,299] [INFO] Task started: Blastn
[2024-01-24 13:58:52,300] [INFO] Running command: blastn -query GCF_005298175.1_ASM529817v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd8d0bab4-87d1-40e3-88fc-2b3f7daa2918/dqc_reference/reference_markers_gtdb.fasta -out GCF_005298175.1_ASM529817v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:53,824] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:53,827] [INFO] Selected 9 target genomes.
[2024-01-24 13:58:53,827] [INFO] Target genome list was writen to GCF_005298175.1_ASM529817v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:53,837] [INFO] Task started: fastANI
[2024-01-24 13:58:53,838] [INFO] Running command: fastANI --query /var/lib/cwl/stg43e51d6d-458b-41de-b892-004b5626dd94/GCF_005298175.1_ASM529817v1_genomic.fna.gz --refList GCF_005298175.1_ASM529817v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005298175.1_ASM529817v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:04,150] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:04,162] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:04,163] [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_005298175.1	s__Marinobacter sp005298175	100.0	1473	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008795955.1	s__Marinobacter sp008795955	86.5583	1162	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004792665.1	s__Marinobacter orientalis	84.8114	1040	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003344045.1	s__Marinobacter vulgaris	84.423	1005	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000686085.1	s__Marinobacter sp000686085	84.1695	1049	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_000831005.1	s__Marinobacter salarius	82.2602	903	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	97.84	96.73	0.88	0.79	21	-
GCF_000170835.1	s__Marinobacter algicola	82.0194	870	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002726615.1	s__Marinobacter sp002726615	81.784	604	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	98.52	98.30	0.75	0.64	3	-
GCA_017643965.1	s__Marinobacter sp017643965	80.0162	462	1473	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Oleiphilaceae;g__Marinobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:04,164] [INFO] GTDB search result was written to GCF_005298175.1_ASM529817v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:04,165] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:04,168] [INFO] DFAST_QC result json was written to GCF_005298175.1_ASM529817v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:04,168] [INFO] DFAST_QC completed!
[2024-01-24 13:59:04,168] [INFO] Total running time: 0h1m22s