[2024-01-24 13:58:25,709] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:25,711] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:25,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg4595de49-ac9e-48f9-a157-4935c6102274/dqc_reference
[2024-01-24 13:58:26,989] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:26,990] [INFO] Task started: Prodigal
[2024-01-24 13:58:26,991] [INFO] Running command: gunzip -c /var/lib/cwl/stg774311d4-c059-40de-95af-dedc34d2d958/GCF_031451735.1_ASM3145173v1_genomic.fna.gz | prodigal -d GCF_031451735.1_ASM3145173v1_genomic.fna/cds.fna -a GCF_031451735.1_ASM3145173v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:37,006] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:37,006] [INFO] Task started: HMMsearch
[2024-01-24 13:58:37,006] [INFO] Running command: hmmsearch --tblout GCF_031451735.1_ASM3145173v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4595de49-ac9e-48f9-a157-4935c6102274/dqc_reference/reference_markers.hmm GCF_031451735.1_ASM3145173v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:37,302] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:37,304] [INFO] Found 6/6 markers.
[2024-01-24 13:58:37,342] [INFO] Query marker FASTA was written to GCF_031451735.1_ASM3145173v1_genomic.fna/markers.fasta
[2024-01-24 13:58:37,342] [INFO] Task started: Blastn
[2024-01-24 13:58:37,342] [INFO] Running command: blastn -query GCF_031451735.1_ASM3145173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4595de49-ac9e-48f9-a157-4935c6102274/dqc_reference/reference_markers.fasta -out GCF_031451735.1_ASM3145173v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:38,452] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:38,455] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:38,455] [INFO] Target genome list was writen to GCF_031451735.1_ASM3145173v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:38,470] [INFO] Task started: fastANI
[2024-01-24 13:58:38,470] [INFO] Running command: fastANI --query /var/lib/cwl/stg774311d4-c059-40de-95af-dedc34d2d958/GCF_031451735.1_ASM3145173v1_genomic.fna.gz --refList GCF_031451735.1_ASM3145173v1_genomic.fna/target_genomes.txt --output GCF_031451735.1_ASM3145173v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:50,925] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:50,925] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4595de49-ac9e-48f9-a157-4935c6102274/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:50,926] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4595de49-ac9e-48f9-a157-4935c6102274/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:50,938] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:50,938] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:50,939] [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 halophila	strain=NBRC 102604	GCA_007989465.1	29573	29573	type	True	99.9603	1112	1156	95	conclusive
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	93.5221	914	1156	95	below_threshold
Halomonas organivorans	strain=CECT 5995	GCA_014192055.1	257772	257772	type	True	88.2777	984	1156	95	below_threshold
Halomonas borealis	strain=ATF 5.2	GCA_004798905.1	2508710	2508710	type	True	87.8796	832	1156	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	86.542	900	1156	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	85.9112	878	1156	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	85.477	839	1156	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	83.3647	747	1156	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	82.9535	757	1156	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	82.5273	716	1156	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	81.9495	715	1156	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	81.6849	674	1156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:50,942] [INFO] DFAST Taxonomy check result was written to GCF_031451735.1_ASM3145173v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:50,942] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:50,943] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:50,943] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4595de49-ac9e-48f9-a157-4935c6102274/dqc_reference/checkm_data
[2024-01-24 13:58:50,944] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:50,983] [INFO] Task started: CheckM
[2024-01-24 13:58:50,983] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_031451735.1_ASM3145173v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_031451735.1_ASM3145173v1_genomic.fna/checkm_input GCF_031451735.1_ASM3145173v1_genomic.fna/checkm_result
[2024-01-24 13:59:24,219] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:24,220] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:24,239] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:24,239] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:24,240] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_031451735.1_ASM3145173v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:24,240] [INFO] Task started: Blastn
[2024-01-24 13:59:24,240] [INFO] Running command: blastn -query GCF_031451735.1_ASM3145173v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4595de49-ac9e-48f9-a157-4935c6102274/dqc_reference/reference_markers_gtdb.fasta -out GCF_031451735.1_ASM3145173v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:26,281] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:26,286] [INFO] Selected 7 target genomes.
[2024-01-24 13:59:26,287] [INFO] Target genome list was writen to GCF_031451735.1_ASM3145173v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:26,301] [INFO] Task started: fastANI
[2024-01-24 13:59:26,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg774311d4-c059-40de-95af-dedc34d2d958/GCF_031451735.1_ASM3145173v1_genomic.fna.gz --refList GCF_031451735.1_ASM3145173v1_genomic.fna/target_genomes_gtdb.txt --output GCF_031451735.1_ASM3145173v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:33,300] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:33,307] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:33,307] [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_007989465.1	s__Halomonas halophila	99.9603	1112	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.43	97.59	0.92	0.89	4	conclusive
GCF_000265245.1	s__Halomonas smyrnensis	93.6055	910	1156	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_014192055.1	s__Halomonas organivorans	88.2449	987	1156	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	87.8956	831	1156	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	86.5286	901	1156	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	86.3179	896	1156	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	85.9243	877	1156	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 13:59:33,309] [INFO] GTDB search result was written to GCF_031451735.1_ASM3145173v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:33,310] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:33,313] [INFO] DFAST_QC result json was written to GCF_031451735.1_ASM3145173v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:33,314] [INFO] DFAST_QC completed!
[2024-01-24 13:59:33,314] [INFO] Total running time: 0h1m8s