[2024-01-24 14:22:33,501] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:33,503] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:33,503] [INFO] DQC Reference Directory: /var/lib/cwl/stg234aa656-d44f-4609-8638-dd1d5cd8c6a3/dqc_reference
[2024-01-24 14:22:34,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:34,721] [INFO] Task started: Prodigal
[2024-01-24 14:22:34,721] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a805398-6d0b-4618-8949-1cabc147a2c0/GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/cds.fna -a GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:47,806] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:47,807] [INFO] Task started: HMMsearch
[2024-01-24 14:22:47,807] [INFO] Running command: hmmsearch --tblout GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg234aa656-d44f-4609-8638-dd1d5cd8c6a3/dqc_reference/reference_markers.hmm GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:48,253] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:48,254] [INFO] Found 6/6 markers.
[2024-01-24 14:22:48,312] [INFO] Query marker FASTA was written to GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:22:48,312] [INFO] Task started: Blastn
[2024-01-24 14:22:48,312] [INFO] Running command: blastn -query GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg234aa656-d44f-4609-8638-dd1d5cd8c6a3/dqc_reference/reference_markers.fasta -out GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:49,465] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:49,469] [INFO] Selected 14 target genomes.
[2024-01-24 14:22:49,469] [INFO] Target genome list was writen to GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:22:49,475] [INFO] Task started: fastANI
[2024-01-24 14:22:49,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a805398-6d0b-4618-8949-1cabc147a2c0/GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna.gz --refList GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:01,615] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:01,616] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg234aa656-d44f-4609-8638-dd1d5cd8c6a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:01,616] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg234aa656-d44f-4609-8638-dd1d5cd8c6a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:01,633] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:23:01,634] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:01,634] [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
Microbulbifer donghaiensis	strain=CGMCC 1.7063	GCA_900129095.1	494016	494016	type	True	100.0	1431	1431	95	conclusive
Microbulbifer marinus	strain=CGMCC 1.10657	GCA_900107725.1	658218	658218	type	True	86.3412	1087	1431	95	below_threshold
Microbulbifer taiwanensis	strain=LMG 26125	GCA_014904815.1	986746	986746	type	True	83.0931	920	1431	95	below_threshold
Microbulbifer hainanensis	strain=NBU-8HK146	GCA_014904735.1	2735675	2735675	type	True	81.3858	812	1431	95	below_threshold
Microbulbifer rhizosphaerae	strain=CECT 8799	GCA_014191725.1	1562603	1562603	type	True	80.9124	750	1431	95	below_threshold
Microbulbifer yueqingensis	strain=CGMCC 1.10658	GCA_900100355.1	658219	658219	type	True	80.4798	654	1431	95	below_threshold
Microbulbifer flavimaris	strain=WRN-8	GCA_001641755.2	1781068	1781068	type	True	80.2773	599	1431	95	below_threshold
Microbulbifer aggregans	strain=CCB-MM1	GCA_001750105.1	1769779	1769779	type	True	80.1722	602	1431	95	below_threshold
Microbulbifer harenosus	strain=HB161719	GCA_005771435.1	2576840	2576840	type	True	79.7572	585	1431	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	79.4308	491	1431	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	79.4109	502	1431	95	below_threshold
Microbulbifer celer	strain=KCTC 12973	GCA_020991125.1	435905	435905	type	True	79.2967	520	1431	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	76.8808	155	1431	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	76.8017	158	1431	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:01,635] [INFO] DFAST Taxonomy check result was written to GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:23:01,638] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:01,638] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:01,639] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg234aa656-d44f-4609-8638-dd1d5cd8c6a3/dqc_reference/checkm_data
[2024-01-24 14:23:01,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:01,691] [INFO] Task started: CheckM
[2024-01-24 14:23:01,691] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/checkm_input GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:23:41,053] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:41,054] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:41,081] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:41,081] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:41,082] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:23:41,082] [INFO] Task started: Blastn
[2024-01-24 14:23:41,083] [INFO] Running command: blastn -query GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg234aa656-d44f-4609-8638-dd1d5cd8c6a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:42,800] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:42,803] [INFO] Selected 9 target genomes.
[2024-01-24 14:23:42,803] [INFO] Target genome list was writen to GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:42,811] [INFO] Task started: fastANI
[2024-01-24 14:23:42,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a805398-6d0b-4618-8949-1cabc147a2c0/GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna.gz --refList GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:51,827] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:51,893] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:51,894] [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_900129095.1	s__Microbulbifer donghaiensis	100.0	1431	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900107725.1	s__Microbulbifer marinus	86.3412	1087	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904815.1	s__Microbulbifer taiwanensis	83.0886	921	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014904735.1	s__Microbulbifer hainanensis	81.3937	811	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014191725.1	s__Microbulbifer rhizosphaerae	80.9154	749	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100355.1	s__Microbulbifer yueqingensis	80.4798	654	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641755.2	s__Microbulbifer flavimaris	80.2618	601	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001750105.1	s__Microbulbifer aggregans	80.1671	603	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005771435.1	s__Microbulbifer harenosus	79.7615	585	1431	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Cellvibrionaceae;g__Microbulbifer	95.0	98.17	98.17	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:23:51,896] [INFO] GTDB search result was written to GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:51,896] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:51,899] [INFO] DFAST_QC result json was written to GCF_900129095.1_IMG-taxon_2619618825_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:23:51,900] [INFO] DFAST_QC completed!
[2024-01-24 14:23:51,900] [INFO] Total running time: 0h1m18s