[2024-01-24 13:41:10,722] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:10,724] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:10,724] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7177dba-c4ac-495c-87f1-1b1a1bde5966/dqc_reference
[2024-01-24 13:41:12,151] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:12,152] [INFO] Task started: Prodigal
[2024-01-24 13:41:12,153] [INFO] Running command: gunzip -c /var/lib/cwl/stg85578bb0-7132-454a-b69b-cc9f1dd0a18f/GCF_006540005.1_ASM654000v1_genomic.fna.gz | prodigal -d GCF_006540005.1_ASM654000v1_genomic.fna/cds.fna -a GCF_006540005.1_ASM654000v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:22,372] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:22,373] [INFO] Task started: HMMsearch
[2024-01-24 13:41:22,373] [INFO] Running command: hmmsearch --tblout GCF_006540005.1_ASM654000v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7177dba-c4ac-495c-87f1-1b1a1bde5966/dqc_reference/reference_markers.hmm GCF_006540005.1_ASM654000v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:22,662] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:22,664] [INFO] Found 6/6 markers.
[2024-01-24 13:41:22,702] [INFO] Query marker FASTA was written to GCF_006540005.1_ASM654000v1_genomic.fna/markers.fasta
[2024-01-24 13:41:22,703] [INFO] Task started: Blastn
[2024-01-24 13:41:22,703] [INFO] Running command: blastn -query GCF_006540005.1_ASM654000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7177dba-c4ac-495c-87f1-1b1a1bde5966/dqc_reference/reference_markers.fasta -out GCF_006540005.1_ASM654000v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:23,762] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:23,766] [INFO] Selected 18 target genomes.
[2024-01-24 13:41:23,767] [INFO] Target genome list was writen to GCF_006540005.1_ASM654000v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:23,770] [INFO] Task started: fastANI
[2024-01-24 13:41:23,771] [INFO] Running command: fastANI --query /var/lib/cwl/stg85578bb0-7132-454a-b69b-cc9f1dd0a18f/GCF_006540005.1_ASM654000v1_genomic.fna.gz --refList GCF_006540005.1_ASM654000v1_genomic.fna/target_genomes.txt --output GCF_006540005.1_ASM654000v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:38,175] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:38,176] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7177dba-c4ac-495c-87f1-1b1a1bde5966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:38,176] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7177dba-c4ac-495c-87f1-1b1a1bde5966/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:38,190] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:38,191] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:38,191] [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	100.0	1040	1042	95	conclusive
Halomonas elongata	strain=type strain: DSM 2581	GCA_000196875.2	2746	2746	type	True	83.1901	780	1042	95	below_threshold
Halomonas caseinilytica	strain=CGMCC 1.6773	GCA_900109905.1	438744	438744	type	True	82.7527	739	1042	95	below_threshold
Halomonas caseinilytica	strain=JCM 14802	GCA_001662305.1	438744	438744	type	True	82.7424	724	1042	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	81.9429	672	1042	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	81.8863	654	1042	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	81.7671	688	1042	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	81.7171	695	1042	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	81.5749	717	1042	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	81.1994	643	1042	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	80.9028	619	1042	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	80.8566	595	1042	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	80.6834	575	1042	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	80.4315	540	1042	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	80.1909	546	1042	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	80.1682	555	1042	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	79.7742	494	1042	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	79.7033	519	1042	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:38,193] [INFO] DFAST Taxonomy check result was written to GCF_006540005.1_ASM654000v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:38,193] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:38,193] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:38,194] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7177dba-c4ac-495c-87f1-1b1a1bde5966/dqc_reference/checkm_data
[2024-01-24 13:41:38,195] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:38,231] [INFO] Task started: CheckM
[2024-01-24 13:41:38,231] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006540005.1_ASM654000v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006540005.1_ASM654000v1_genomic.fna/checkm_input GCF_006540005.1_ASM654000v1_genomic.fna/checkm_result
[2024-01-24 13:42:12,162] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:12,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:12,191] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:12,192] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:12,192] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006540005.1_ASM654000v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:12,193] [INFO] Task started: Blastn
[2024-01-24 13:42:12,193] [INFO] Running command: blastn -query GCF_006540005.1_ASM654000v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7177dba-c4ac-495c-87f1-1b1a1bde5966/dqc_reference/reference_markers_gtdb.fasta -out GCF_006540005.1_ASM654000v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:13,921] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:13,926] [INFO] Selected 14 target genomes.
[2024-01-24 13:42:13,927] [INFO] Target genome list was writen to GCF_006540005.1_ASM654000v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:13,932] [INFO] Task started: fastANI
[2024-01-24 13:42:13,932] [INFO] Running command: fastANI --query /var/lib/cwl/stg85578bb0-7132-454a-b69b-cc9f1dd0a18f/GCF_006540005.1_ASM654000v1_genomic.fna.gz --refList GCF_006540005.1_ASM654000v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006540005.1_ASM654000v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:24,717] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:24,741] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:24,741] [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	100.0	1040	1042	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	83.1791	781	1042	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	82.7701	755	1042	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	82.7476	723	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.18	98.28	0.94	0.89	6	-
GCF_007989465.1	s__Halomonas halophila	81.9431	672	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_000265245.1	s__Halomonas smyrnensis	81.8686	657	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_003966155.1	s__Halomonas nitroreducens	81.7882	686	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192275.1	s__Halomonas stenophila	81.7103	696	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002549795.1	s__Halomonas beimenensis	81.6718	655	1042	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	81.5683	718	1042	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	81.2655	602	1042	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	81.1719	646	1042	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	80.9121	619	1042	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	80.6899	574	1042	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:24,744] [INFO] GTDB search result was written to GCF_006540005.1_ASM654000v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:24,744] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:24,748] [INFO] DFAST_QC result json was written to GCF_006540005.1_ASM654000v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:24,749] [INFO] DFAST_QC completed!
[2024-01-24 13:42:24,749] [INFO] Total running time: 0h1m14s