[2024-01-24 13:41:19,067] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:19,073] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:19,073] [INFO] DQC Reference Directory: /var/lib/cwl/stg3d704989-20af-4583-8f5a-e671490ea779/dqc_reference
[2024-01-24 13:41:20,416] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:20,418] [INFO] Task started: Prodigal
[2024-01-24 13:41:20,419] [INFO] Running command: gunzip -c /var/lib/cwl/stg55fd66ca-5399-494f-a4d3-b5c8c798fb00/GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/cds.fna -a GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:37,161] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:37,162] [INFO] Task started: HMMsearch
[2024-01-24 13:41:37,162] [INFO] Running command: hmmsearch --tblout GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3d704989-20af-4583-8f5a-e671490ea779/dqc_reference/reference_markers.hmm GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:37,490] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:37,491] [INFO] Found 6/6 markers.
[2024-01-24 13:41:37,546] [INFO] Query marker FASTA was written to GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:41:37,547] [INFO] Task started: Blastn
[2024-01-24 13:41:37,547] [INFO] Running command: blastn -query GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d704989-20af-4583-8f5a-e671490ea779/dqc_reference/reference_markers.fasta -out GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:38,427] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:38,431] [INFO] Selected 17 target genomes.
[2024-01-24 13:41:38,431] [INFO] Target genome list was writen to GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:41:38,436] [INFO] Task started: fastANI
[2024-01-24 13:41:38,436] [INFO] Running command: fastANI --query /var/lib/cwl/stg55fd66ca-5399-494f-a4d3-b5c8c798fb00/GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna.gz --refList GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:53,284] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:53,284] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3d704989-20af-4583-8f5a-e671490ea779/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:53,284] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3d704989-20af-4583-8f5a-e671490ea779/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:53,298] [INFO] Found 14 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:53,298] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:53,298] [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
Halomonas cupida	strain=DSM 4740	GCA_900142755.1	44933	44933	type	True	100.0	1636	1636	95	conclusive
Halomonas cupida	strain=NBRC 102219	GCA_007991155.1	44933	44933	type	True	99.8723	1509	1636	95	conclusive
Halomonas huangheensis	strain=BJGMM-B45	GCA_001431725.1	1178482	1178482	type	True	81.9666	1076	1636	95	below_threshold
Halomonas huangheensis	strain=BJGMM-B45	GCA_000470745.1	1178482	1178482	type	True	81.8945	1073	1636	95	below_threshold
Halomonas litopenaei	strain=SYSU ZJ2214	GCA_003045775.1	2109328	2109328	type	True	79.8546	711	1636	95	below_threshold
Halomonas borealis	strain=ATF 5.2	GCA_004798905.1	2508710	2508710	type	True	79.2659	474	1636	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	78.8922	428	1636	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	78.8122	452	1636	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.7967	470	1636	95	below_threshold
Halomonas saliphila	strain=LCB169	GCA_002930105.1	1848458	1848458	type	True	78.6167	438	1636	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.6066	454	1636	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.5619	467	1636	95	below_threshold
Yangia pacifica	strain=CGMCC 1.3455	GCA_900100725.1	311180	311180	suspected-type	True	75.5435	58	1636	95	below_threshold
Yangia pacifica	strain=DSM 26894	GCA_900116195.1	311180	311180	suspected-type	True	75.513	58	1636	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:53,300] [INFO] DFAST Taxonomy check result was written to GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:41:53,301] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:53,301] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:53,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3d704989-20af-4583-8f5a-e671490ea779/dqc_reference/checkm_data
[2024-01-24 13:41:53,303] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:53,358] [INFO] Task started: CheckM
[2024-01-24 13:41:53,359] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/checkm_input GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:42:41,945] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:41,946] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:41,969] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:41,969] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:41,969] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:42:41,970] [INFO] Task started: Blastn
[2024-01-24 13:42:41,970] [INFO] Running command: blastn -query GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg3d704989-20af-4583-8f5a-e671490ea779/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:43,426] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:43,430] [INFO] Selected 17 target genomes.
[2024-01-24 13:42:43,431] [INFO] Target genome list was writen to GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:43,441] [INFO] Task started: fastANI
[2024-01-24 13:42:43,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg55fd66ca-5399-494f-a4d3-b5c8c798fb00/GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna.gz --refList GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:57,982] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:58,009] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:58,009] [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_900142755.1	s__Halomonas cupida	100.0	1636	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_001431725.1	s__Halomonas huangheensis	81.9715	1074	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_003045775.1	s__Halomonas litopenaei	79.8667	709	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.31	97.80	0.93	0.89	11	-
GCF_008329985.2	s__Halomonas sp008329985	79.8198	642	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798905.1	s__Halomonas borealis	79.2669	474	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017303055.1	s__Halomonas litopenaei_A	79.2252	590	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192055.1	s__Halomonas organivorans	79.2217	584	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104135.1	s__Halomonas shengliensis	79.0846	433	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_003254665.1	s__Halomonas lactosivorans	78.8594	478	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001971685.1	s__Halomonas_B sp001971685	78.8414	448	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010994375.1	s__Halomonas sp010994375	78.7946	444	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000246875.1	s__Halomonas sp000246875	78.7673	440	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013697085.1	s__Halomonas kenyensis	78.7086	407	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000761475.1	s__Chromohalobacter israelensis	78.6264	358	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Chromohalobacter	95.0	98.07	97.76	0.86	0.85	6	-
GCF_002930105.1	s__Halomonas saliphila	78.6169	438	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991175.1	s__Halomonas variabilis	77.0037	172	1636	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:58,011] [INFO] GTDB search result was written to GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:58,011] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:58,015] [INFO] DFAST_QC result json was written to GCF_900142755.1_IMG-taxon_2599185207_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:42:58,016] [INFO] DFAST_QC completed!
[2024-01-24 13:42:58,016] [INFO] Total running time: 0h1m39s