[2024-01-24 13:48:59,712] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,714] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,714] [INFO] DQC Reference Directory: /var/lib/cwl/stgc94bf296-ef9a-455b-ac0f-f2ff30f4540a/dqc_reference
[2024-01-24 13:49:01,039] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,040] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,040] [INFO] Running command: gunzip -c /var/lib/cwl/stg46ec264e-f04f-4cc7-a6d0-48c73f47b81b/GCF_900155385.1_PRJEB18749_genomic.fna.gz | prodigal -d GCF_900155385.1_PRJEB18749_genomic.fna/cds.fna -a GCF_900155385.1_PRJEB18749_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:11,298] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:11,299] [INFO] Task started: HMMsearch
[2024-01-24 13:49:11,299] [INFO] Running command: hmmsearch --tblout GCF_900155385.1_PRJEB18749_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc94bf296-ef9a-455b-ac0f-f2ff30f4540a/dqc_reference/reference_markers.hmm GCF_900155385.1_PRJEB18749_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:11,571] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:11,573] [INFO] Found 6/6 markers.
[2024-01-24 13:49:11,606] [INFO] Query marker FASTA was written to GCF_900155385.1_PRJEB18749_genomic.fna/markers.fasta
[2024-01-24 13:49:11,607] [INFO] Task started: Blastn
[2024-01-24 13:49:11,607] [INFO] Running command: blastn -query GCF_900155385.1_PRJEB18749_genomic.fna/markers.fasta -db /var/lib/cwl/stgc94bf296-ef9a-455b-ac0f-f2ff30f4540a/dqc_reference/reference_markers.fasta -out GCF_900155385.1_PRJEB18749_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:12,359] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:12,362] [INFO] Selected 21 target genomes.
[2024-01-24 13:49:12,362] [INFO] Target genome list was writen to GCF_900155385.1_PRJEB18749_genomic.fna/target_genomes.txt
[2024-01-24 13:49:12,381] [INFO] Task started: fastANI
[2024-01-24 13:49:12,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg46ec264e-f04f-4cc7-a6d0-48c73f47b81b/GCF_900155385.1_PRJEB18749_genomic.fna.gz --refList GCF_900155385.1_PRJEB18749_genomic.fna/target_genomes.txt --output GCF_900155385.1_PRJEB18749_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:27,017] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:27,018] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc94bf296-ef9a-455b-ac0f-f2ff30f4540a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:27,018] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc94bf296-ef9a-455b-ac0f-f2ff30f4540a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:27,040] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:27,040] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:27,040] [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 massiliensis	strain=Marseille-P2426	GCA_900155385.1	1816686	1816686	type	True	100.0	1135	1135	95	conclusive
Halomonas salicampi	strain=BH103	GCA_013415105.1	1449798	1449798	type	True	82.7638	761	1135	95	below_threshold
Halomonas aquamarina	strain=558	GCA_900110265.1	77097	77097	type	True	79.2354	374	1135	95	below_threshold
Halomonas meridiana	strain=ACAM 246	GCA_900129255.1	29570	29570	type	True	79.2083	389	1135	95	below_threshold
Halomonas songnenensis	strain=CGMCC 1.12152	GCA_003002925.1	1176243	1176243	type	True	79.1068	394	1135	95	below_threshold
Halomonas meridiana	strain=NBRC 15608	GCA_006540125.1	29570	29570	type	True	79.0585	362	1135	95	below_threshold
Halomonas arcis	strain=CGMCC 1.6494	GCA_900103865.1	416873	416873	type	True	79.0583	359	1135	95	below_threshold
Halomonas subglaciescola	strain=ACAM 12	GCA_900142895.1	29571	29571	type	True	78.9767	394	1135	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	78.9317	340	1135	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	78.8856	324	1135	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	78.8249	293	1135	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	78.822	369	1135	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	78.7364	373	1135	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	78.6758	354	1135	95	below_threshold
Halomonas halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	78.6555	310	1135	95	below_threshold
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	78.5712	365	1135	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	78.5314	351	1135	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	78.5251	331	1135	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	78.5101	311	1135	95	below_threshold
Halomonas zhaodongensis	strain=NEAU-ST10-25	GCA_013415115.1	1176240	1176240	type	True	78.4929	263	1135	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	78.4055	306	1135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:27,042] [INFO] DFAST Taxonomy check result was written to GCF_900155385.1_PRJEB18749_genomic.fna/tc_result.tsv
[2024-01-24 13:49:27,043] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:27,043] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:27,043] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc94bf296-ef9a-455b-ac0f-f2ff30f4540a/dqc_reference/checkm_data
[2024-01-24 13:49:27,044] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:27,084] [INFO] Task started: CheckM
[2024-01-24 13:49:27,084] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900155385.1_PRJEB18749_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900155385.1_PRJEB18749_genomic.fna/checkm_input GCF_900155385.1_PRJEB18749_genomic.fna/checkm_result
[2024-01-24 13:50:01,191] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:01,192] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:01,215] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:01,215] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:01,216] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900155385.1_PRJEB18749_genomic.fna/markers.fasta)
[2024-01-24 13:50:01,216] [INFO] Task started: Blastn
[2024-01-24 13:50:01,217] [INFO] Running command: blastn -query GCF_900155385.1_PRJEB18749_genomic.fna/markers.fasta -db /var/lib/cwl/stgc94bf296-ef9a-455b-ac0f-f2ff30f4540a/dqc_reference/reference_markers_gtdb.fasta -out GCF_900155385.1_PRJEB18749_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:02,349] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:02,355] [INFO] Selected 21 target genomes.
[2024-01-24 13:50:02,355] [INFO] Target genome list was writen to GCF_900155385.1_PRJEB18749_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:02,504] [INFO] Task started: fastANI
[2024-01-24 13:50:02,504] [INFO] Running command: fastANI --query /var/lib/cwl/stg46ec264e-f04f-4cc7-a6d0-48c73f47b81b/GCF_900155385.1_PRJEB18749_genomic.fna.gz --refList GCF_900155385.1_PRJEB18749_genomic.fna/target_genomes_gtdb.txt --output GCF_900155385.1_PRJEB18749_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:17,688] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:17,710] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:17,711] [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_900155385.1	s__Halomonas massiliensis	100.0	1135	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.38	98.38	0.88	0.88	2	conclusive
GCF_013415105.1	s__Halomonas salicampi	82.7468	764	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686925.1	s__Halomonas sp000686925	79.4425	398	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900110265.1	s__Halomonas aquamarina	79.2421	374	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.65	97.09	0.84	0.80	25	-
GCF_009846525.1	s__Halomonas sp002696125	79.2372	410	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.53	98.53	0.95	0.95	2	-
GCF_012427705.1	s__Halomonas piezotolerans	79.2093	369	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	98.70	0.97	0.94	3	-
GCF_900103865.1	s__Halomonas arcis	79.033	361	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014263395.1	s__Halomonas sp014263395	79.0061	368	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111305.1	s__Halomonas subterranea	78.9671	388	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.10	95.10	0.84	0.84	2	-
GCF_900142895.1	s__Halomonas subglaciescola	78.9639	393	1135	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	78.8995	323	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCA_001507855.1	s__Halomonas sp001507855	78.8388	364	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	0.98	0.98	2	-
GCF_002257525.1	s__Halomonas ventosae_B	78.7998	394	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.23	97.92	0.94	0.87	4	-
GCF_002211105.1	s__Halomonas campaniensis_A	78.772	349	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.13	98.13	0.90	0.90	2	-
GCF_000236035.1	s__Halomonas boliviensis	78.7476	372	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.96	99.96	0.99	0.99	2	-
GCF_900104135.1	s__Halomonas shengliensis	78.6821	354	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_004364445.1	s__Halomonas alkaliantarctica	78.6144	380	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCF_003202205.1	s__Halomonas sp003202205	78.5465	331	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014779595.1	s__Halomonas_B sp014779595	78.4673	312	1135	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_003182195.1	s__Halomonas sp003182195	78.4477	346	1135	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:17,713] [INFO] GTDB search result was written to GCF_900155385.1_PRJEB18749_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:17,714] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:17,722] [INFO] DFAST_QC result json was written to GCF_900155385.1_PRJEB18749_genomic.fna/dqc_result.json
[2024-01-24 13:50:17,723] [INFO] DFAST_QC completed!
[2024-01-24 13:50:17,723] [INFO] Total running time: 0h1m18s