[2024-01-24 13:40:44,251] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:44,253] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:44,253] [INFO] DQC Reference Directory: /var/lib/cwl/stgfda93e73-24d5-443a-977f-84298d76bef8/dqc_reference
[2024-01-24 13:40:45,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:45,675] [INFO] Task started: Prodigal
[2024-01-24 13:40:45,675] [INFO] Running command: gunzip -c /var/lib/cwl/stgdac8028a-919b-4e5f-b624-e21f072edae3/GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/cds.fna -a GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:53,608] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:53,608] [INFO] Task started: HMMsearch
[2024-01-24 13:40:53,608] [INFO] Running command: hmmsearch --tblout GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfda93e73-24d5-443a-977f-84298d76bef8/dqc_reference/reference_markers.hmm GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:53,883] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:53,884] [INFO] Found 6/6 markers.
[2024-01-24 13:40:53,911] [INFO] Query marker FASTA was written to GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:40:53,911] [INFO] Task started: Blastn
[2024-01-24 13:40:53,911] [INFO] Running command: blastn -query GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgfda93e73-24d5-443a-977f-84298d76bef8/dqc_reference/reference_markers.fasta -out GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:54,527] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:54,530] [INFO] Selected 17 target genomes.
[2024-01-24 13:40:54,530] [INFO] Target genome list was writen to GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:40:54,544] [INFO] Task started: fastANI
[2024-01-24 13:40:54,545] [INFO] Running command: fastANI --query /var/lib/cwl/stgdac8028a-919b-4e5f-b624-e21f072edae3/GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna.gz --refList GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:04,326] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:04,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfda93e73-24d5-443a-977f-84298d76bef8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:04,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfda93e73-24d5-443a-977f-84298d76bef8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:04,335] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:04,335] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:04,335] [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
Salinicoccus halodurans	strain=CGMCC 1.6501	GCA_900114445.1	407035	407035	type	True	100.0	905	906	95	conclusive
Salinicoccus sediminis	strain=SV-16	GCA_000986795.1	1432562	1432562	type	True	82.4924	617	906	95	below_threshold
Salinicoccus carnicancri	strain=Crm	GCA_000330705.1	558170	558170	type	True	81.6891	579	906	95	below_threshold
Salinicoccus cyprini	strain=CT19	GCA_007713705.1	2493691	2493691	type	True	78.6747	227	906	95	below_threshold
Salinicoccus albus	strain=YIM-Y21	GCA_000385175.1	418756	418756	type	True	78.4769	248	906	95	below_threshold
Salinicoccus hispanicus	strain=J-82	GCA_009831115.1	157225	157225	type	True	78.062	225	906	95	below_threshold
Jeotgalicoccus aerolatus	strain=CCM 7679	GCA_014635205.1	709510	709510	type	True	77.7149	68	906	95	below_threshold
Jeotgalicoccus aerolatus	strain=DSM 22420	GCA_017873755.1	709510	709510	type	True	77.6966	70	906	95	below_threshold
Salinicoccus qingdaonensis	strain=CGMCC 1.8895	GCA_900101075.1	576118	576118	type	True	77.5362	127	906	95	below_threshold
Salinicoccus alkaliphilus	strain=DSM 16010	GCA_900142805.1	148453	148453	type	True	77.0329	118	906	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:04,337] [INFO] DFAST Taxonomy check result was written to GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:41:04,338] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:04,338] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:04,338] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfda93e73-24d5-443a-977f-84298d76bef8/dqc_reference/checkm_data
[2024-01-24 13:41:04,339] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:04,371] [INFO] Task started: CheckM
[2024-01-24 13:41:04,371] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/checkm_input GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:41:34,285] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:34,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:34,305] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:34,305] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:34,306] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:41:34,306] [INFO] Task started: Blastn
[2024-01-24 13:41:34,306] [INFO] Running command: blastn -query GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgfda93e73-24d5-443a-977f-84298d76bef8/dqc_reference/reference_markers_gtdb.fasta -out GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:35,113] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:35,117] [INFO] Selected 15 target genomes.
[2024-01-24 13:41:35,117] [INFO] Target genome list was writen to GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:35,146] [INFO] Task started: fastANI
[2024-01-24 13:41:35,147] [INFO] Running command: fastANI --query /var/lib/cwl/stgdac8028a-919b-4e5f-b624-e21f072edae3/GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna.gz --refList GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:43,609] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:43,624] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:43,625] [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_900114445.1	s__Salinicoccus halodurans	100.0	905	906	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000986795.1	s__Salinicoccus sediminis	82.4924	617	906	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113295.1	s__Salinicoccus stercoripullorum	81.9105	545	906	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000330705.1	s__Salinicoccus carnicancri	81.6846	579	906	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003814515.1	s__Salinicoccus roseus	79.1397	235	906	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	97.90	96.75	0.92	0.87	5	-
GCF_000385175.1	s__Salinicoccus albus	78.4769	248	906	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009831115.1	s__Salinicoccus hispanicus	78.0465	226	906	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014635205.1	s__Jeotgalicoccus aerolatus	77.7515	69	906	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Jeotgalicoccus	95.0	99.67	99.03	0.98	0.93	4	-
GCF_900101075.1	s__Salinicoccus qingdaonensis	77.5362	127	906	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142805.1	s__Salinicoccus alkaliphilus	77.0323	117	906	d__Bacteria;p__Firmicutes;c__Bacilli;o__Staphylococcales;f__Salinicoccaceae;g__Salinicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:43,627] [INFO] GTDB search result was written to GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:43,628] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:43,633] [INFO] DFAST_QC result json was written to GCF_900114445.1_IMG-taxon_2687453789_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:41:43,633] [INFO] DFAST_QC completed!
[2024-01-24 13:41:43,633] [INFO] Total running time: 0h0m59s