[2024-01-25 19:55:21,022] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:55:21,023] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:55:21,023] [INFO] DQC Reference Directory: /var/lib/cwl/stgef8c1d84-9fcd-44f6-b07b-732dcde432f4/dqc_reference
[2024-01-25 19:55:22,214] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:55:22,215] [INFO] Task started: Prodigal
[2024-01-25 19:55:22,215] [INFO] Running command: gunzip -c /var/lib/cwl/stgc05fa5e2-d3d7-46d4-a950-5521dc609500/GCF_030409265.1_ASM3040926v1_genomic.fna.gz | prodigal -d GCF_030409265.1_ASM3040926v1_genomic.fna/cds.fna -a GCF_030409265.1_ASM3040926v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:55:31,907] [INFO] Task succeeded: Prodigal
[2024-01-25 19:55:31,908] [INFO] Task started: HMMsearch
[2024-01-25 19:55:31,908] [INFO] Running command: hmmsearch --tblout GCF_030409265.1_ASM3040926v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef8c1d84-9fcd-44f6-b07b-732dcde432f4/dqc_reference/reference_markers.hmm GCF_030409265.1_ASM3040926v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:55:32,109] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:55:32,110] [INFO] Found 6/6 markers.
[2024-01-25 19:55:32,137] [INFO] Query marker FASTA was written to GCF_030409265.1_ASM3040926v1_genomic.fna/markers.fasta
[2024-01-25 19:55:32,137] [INFO] Task started: Blastn
[2024-01-25 19:55:32,138] [INFO] Running command: blastn -query GCF_030409265.1_ASM3040926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef8c1d84-9fcd-44f6-b07b-732dcde432f4/dqc_reference/reference_markers.fasta -out GCF_030409265.1_ASM3040926v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:32,927] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:32,929] [INFO] Selected 19 target genomes.
[2024-01-25 19:55:32,930] [INFO] Target genome list was writen to GCF_030409265.1_ASM3040926v1_genomic.fna/target_genomes.txt
[2024-01-25 19:55:32,957] [INFO] Task started: fastANI
[2024-01-25 19:55:32,957] [INFO] Running command: fastANI --query /var/lib/cwl/stgc05fa5e2-d3d7-46d4-a950-5521dc609500/GCF_030409265.1_ASM3040926v1_genomic.fna.gz --refList GCF_030409265.1_ASM3040926v1_genomic.fna/target_genomes.txt --output GCF_030409265.1_ASM3040926v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:55:48,225] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:48,226] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef8c1d84-9fcd-44f6-b07b-732dcde432f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:55:48,226] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef8c1d84-9fcd-44f6-b07b-732dcde432f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:55:48,237] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:55:48,237] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:55:48,238] [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 halmophila	strain=NBRC 15537	GCA_006540005.1	252	252	type	True	95.6087	946	1140	95	conclusive
Halomonas elongata	strain=type strain: DSM 2581	GCA_000196875.2	2746	2746	type	True	83.5284	813	1140	95	below_threshold
Halomonas caseinilytica	strain=CGMCC 1.6773	GCA_900109905.1	438744	438744	type	True	83.0725	758	1140	95	below_threshold
Halomonas caseinilytica	strain=JCM 14802	GCA_001662305.1	438744	438744	type	True	82.9744	765	1140	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	82.2979	656	1140	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	82.0746	703	1140	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	82.0449	707	1140	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	81.8296	709	1140	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	81.6958	734	1140	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	81.4861	647	1140	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	81.2603	629	1140	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	80.9992	574	1140	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	80.498	578	1140	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	80.48	579	1140	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	80.2704	582	1140	95	below_threshold
Halomonas aerodenitrificans	strain=MCCC 1A11058	GCA_021404405.1	2733483	2733483	type	True	79.862	544	1140	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	79.7518	546	1140	95	below_threshold
Chromohalobacter japonicus	strain=CECT 7219	GCA_023061175.1	223900	223900	type	True	79.2235	360	1140	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:55:48,239] [INFO] DFAST Taxonomy check result was written to GCF_030409265.1_ASM3040926v1_genomic.fna/tc_result.tsv
[2024-01-25 19:55:48,239] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:55:48,239] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:55:48,240] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef8c1d84-9fcd-44f6-b07b-732dcde432f4/dqc_reference/checkm_data
[2024-01-25 19:55:48,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:55:48,285] [INFO] Task started: CheckM
[2024-01-25 19:55:48,285] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030409265.1_ASM3040926v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030409265.1_ASM3040926v1_genomic.fna/checkm_input GCF_030409265.1_ASM3040926v1_genomic.fna/checkm_result
[2024-01-25 19:56:23,369] [INFO] Task succeeded: CheckM
[2024-01-25 19:56:23,370] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:56:23,399] [INFO] ===== Completeness check finished =====
[2024-01-25 19:56:23,400] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:56:23,403] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030409265.1_ASM3040926v1_genomic.fna/markers.fasta)
[2024-01-25 19:56:23,403] [INFO] Task started: Blastn
[2024-01-25 19:56:23,403] [INFO] Running command: blastn -query GCF_030409265.1_ASM3040926v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef8c1d84-9fcd-44f6-b07b-732dcde432f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_030409265.1_ASM3040926v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:56:24,800] [INFO] Task succeeded: Blastn
[2024-01-25 19:56:24,805] [INFO] Selected 18 target genomes.
[2024-01-25 19:56:24,806] [INFO] Target genome list was writen to GCF_030409265.1_ASM3040926v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:56:24,835] [INFO] Task started: fastANI
[2024-01-25 19:56:24,835] [INFO] Running command: fastANI --query /var/lib/cwl/stgc05fa5e2-d3d7-46d4-a950-5521dc609500/GCF_030409265.1_ASM3040926v1_genomic.fna.gz --refList GCF_030409265.1_ASM3040926v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030409265.1_ASM3040926v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:56:39,157] [INFO] Task succeeded: fastANI
[2024-01-25 19:56:39,169] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:56:39,169] [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_006540005.1	s__Halomonas halmophila	95.6174	945	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000196875.2	s__Halomonas elongata	83.5215	813	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.75	98.56	0.95	0.92	4	-
GCF_008274785.1	s__Halomonas eurihalina	83.0131	773	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001662305.1	s__Halomonas caseinilytica	82.9664	766	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.18	98.28	0.94	0.89	6	-
GCF_000265245.1	s__Halomonas smyrnensis	82.3096	655	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_014192275.1	s__Halomonas stenophila	82.0821	702	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007989465.1	s__Halomonas halophila	82.0666	705	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_002549795.1	s__Halomonas beimenensis	82.0541	653	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966155.1	s__Halomonas nitroreducens	81.8114	710	1140	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	81.7645	727	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003056305.1	s__Halomonas denitrificans	81.5075	645	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	81.3958	634	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363555.1	s__Halomonas ventosae	81.2754	628	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCF_900104135.1	s__Halomonas shengliensis	80.9975	575	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_009902005.1	s__Halomonas alimentaria	80.6476	551	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001556105.1	s__Pseudoxanthomonas_A mexicana_A	76.134	73	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	98.72	98.63	0.92	0.88	3	-
GCF_014851815.1	s__Pseudoxanthomonas_A sp014851815	75.6173	98	1140	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:56:39,171] [INFO] GTDB search result was written to GCF_030409265.1_ASM3040926v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:56:39,171] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:56:39,175] [INFO] DFAST_QC result json was written to GCF_030409265.1_ASM3040926v1_genomic.fna/dqc_result.json
[2024-01-25 19:56:39,176] [INFO] DFAST_QC completed!
[2024-01-25 19:56:39,176] [INFO] Total running time: 0h1m18s