[2024-01-24 13:13:31,795] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:31,796] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:31,797] [INFO] DQC Reference Directory: /var/lib/cwl/stge78a0c97-318d-4768-b764-42fd2903cbd8/dqc_reference
[2024-01-24 13:13:33,322] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:33,323] [INFO] Task started: Prodigal
[2024-01-24 13:13:33,323] [INFO] Running command: gunzip -c /var/lib/cwl/stgb145c66b-1edc-4f7c-a428-7556ac58765a/GCF_003045775.1_ASM304577v1_genomic.fna.gz | prodigal -d GCF_003045775.1_ASM304577v1_genomic.fna/cds.fna -a GCF_003045775.1_ASM304577v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:48,868] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:48,869] [INFO] Task started: HMMsearch
[2024-01-24 13:13:48,869] [INFO] Running command: hmmsearch --tblout GCF_003045775.1_ASM304577v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge78a0c97-318d-4768-b764-42fd2903cbd8/dqc_reference/reference_markers.hmm GCF_003045775.1_ASM304577v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:49,224] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:49,226] [INFO] Found 6/6 markers.
[2024-01-24 13:13:49,267] [INFO] Query marker FASTA was written to GCF_003045775.1_ASM304577v1_genomic.fna/markers.fasta
[2024-01-24 13:13:49,268] [INFO] Task started: Blastn
[2024-01-24 13:13:49,268] [INFO] Running command: blastn -query GCF_003045775.1_ASM304577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge78a0c97-318d-4768-b764-42fd2903cbd8/dqc_reference/reference_markers.fasta -out GCF_003045775.1_ASM304577v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:50,296] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:50,300] [INFO] Selected 18 target genomes.
[2024-01-24 13:13:50,300] [INFO] Target genome list was writen to GCF_003045775.1_ASM304577v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:50,306] [INFO] Task started: fastANI
[2024-01-24 13:13:50,306] [INFO] Running command: fastANI --query /var/lib/cwl/stgb145c66b-1edc-4f7c-a428-7556ac58765a/GCF_003045775.1_ASM304577v1_genomic.fna.gz --refList GCF_003045775.1_ASM304577v1_genomic.fna/target_genomes.txt --output GCF_003045775.1_ASM304577v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:14:07,061] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:07,062] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge78a0c97-318d-4768-b764-42fd2903cbd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:14:07,063] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge78a0c97-318d-4768-b764-42fd2903cbd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:14:07,082] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:14:07,082] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:14:07,082] [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 litopenaei	strain=SYSU ZJ2214	GCA_003045775.1	2109328	2109328	type	True	100.0	1584	1586	95	conclusive
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	82.1692	717	1586	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	82.1429	710	1586	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	81.8755	778	1586	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	81.7953	697	1586	95	below_threshold
Halomonas saccharevitans	strain=CGMCC 1.6493	GCA_900116405.1	416872	416872	type	True	81.6102	686	1586	95	below_threshold
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	81.6033	694	1586	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	81.5837	722	1586	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	81.4871	760	1586	95	below_threshold
Halomonas urmiana	strain=TBZ3	GCA_005780185.1	490901	490901	type	True	81.3866	742	1586	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	81.3331	795	1586	95	below_threshold
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	81.1638	737	1586	95	below_threshold
Halomonas heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	81.0978	760	1586	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	80.9891	672	1586	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	80.9744	660	1586	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	80.5685	636	1586	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	80.518	612	1586	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	80.2115	574	1586	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:14:07,084] [INFO] DFAST Taxonomy check result was written to GCF_003045775.1_ASM304577v1_genomic.fna/tc_result.tsv
[2024-01-24 13:14:07,085] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:14:07,085] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:14:07,086] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge78a0c97-318d-4768-b764-42fd2903cbd8/dqc_reference/checkm_data
[2024-01-24 13:14:07,087] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:14:07,148] [INFO] Task started: CheckM
[2024-01-24 13:14:07,149] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003045775.1_ASM304577v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003045775.1_ASM304577v1_genomic.fna/checkm_input GCF_003045775.1_ASM304577v1_genomic.fna/checkm_result
[2024-01-24 13:14:53,477] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:53,478] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:53,501] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:53,501] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:53,502] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003045775.1_ASM304577v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:53,502] [INFO] Task started: Blastn
[2024-01-24 13:14:53,502] [INFO] Running command: blastn -query GCF_003045775.1_ASM304577v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge78a0c97-318d-4768-b764-42fd2903cbd8/dqc_reference/reference_markers_gtdb.fasta -out GCF_003045775.1_ASM304577v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:55,356] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:55,361] [INFO] Selected 15 target genomes.
[2024-01-24 13:14:55,361] [INFO] Target genome list was writen to GCF_003045775.1_ASM304577v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:55,376] [INFO] Task started: fastANI
[2024-01-24 13:14:55,377] [INFO] Running command: fastANI --query /var/lib/cwl/stgb145c66b-1edc-4f7c-a428-7556ac58765a/GCF_003045775.1_ASM304577v1_genomic.fna.gz --refList GCF_003045775.1_ASM304577v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003045775.1_ASM304577v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:09,777] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:09,797] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:09,797] [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_003045775.1	s__Halomonas litopenaei	100.0	1584	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.31	97.80	0.93	0.89	11	conclusive
GCA_002433675.1	s__Halomonas salina_B	94.7167	1124	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.49	99.49	0.75	0.75	2	-
GCF_017303055.1	s__Halomonas litopenaei_A	82.979	1106	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	82.1621	719	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_007989465.1	s__Halomonas halophila	82.1268	712	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	-
GCF_003056305.1	s__Halomonas denitrificans	81.8753	778	1586	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	81.8208	764	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116405.1	s__Halomonas saccharevitans	81.5934	686	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	81.5658	698	1586	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	81.5083	762	1586	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	81.4849	761	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182195.1	s__Halomonas sp003182195	81.3848	612	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
GCF_014192055.1	s__Halomonas organivorans	81.3385	794	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859505.1	s__Halomonas sp014859505	81.0272	566	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010977575.1	s__Halomonas_B socia	80.4146	683	1586	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:09,801] [INFO] GTDB search result was written to GCF_003045775.1_ASM304577v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:09,802] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:09,810] [INFO] DFAST_QC result json was written to GCF_003045775.1_ASM304577v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:09,810] [INFO] DFAST_QC completed!
[2024-01-24 13:15:09,810] [INFO] Total running time: 0h1m38s