[2024-01-24 14:56:23,821] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:56:23,823] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:56:23,823] [INFO] DQC Reference Directory: /var/lib/cwl/stg127d16e6-8c09-4034-aa00-29a1d23e803e/dqc_reference
[2024-01-24 14:56:26,558] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:56:26,560] [INFO] Task started: Prodigal
[2024-01-24 14:56:26,561] [INFO] Running command: gunzip -c /var/lib/cwl/stg1769ce01-0c3f-4455-84ab-798c9a8ef836/GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/cds.fna -a GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:56:49,903] [INFO] Task succeeded: Prodigal
[2024-01-24 14:56:49,903] [INFO] Task started: HMMsearch
[2024-01-24 14:56:49,903] [INFO] Running command: hmmsearch --tblout GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg127d16e6-8c09-4034-aa00-29a1d23e803e/dqc_reference/reference_markers.hmm GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:56:50,265] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:56:50,266] [INFO] Found 6/6 markers.
[2024-01-24 14:56:50,308] [INFO] Query marker FASTA was written to GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:56:50,308] [INFO] Task started: Blastn
[2024-01-24 14:56:50,308] [INFO] Running command: blastn -query GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg127d16e6-8c09-4034-aa00-29a1d23e803e/dqc_reference/reference_markers.fasta -out GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:50,972] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:50,977] [INFO] Selected 15 target genomes.
[2024-01-24 14:56:50,977] [INFO] Target genome list was writen to GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:56:50,987] [INFO] Task started: fastANI
[2024-01-24 14:56:50,987] [INFO] Running command: fastANI --query /var/lib/cwl/stg1769ce01-0c3f-4455-84ab-798c9a8ef836/GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna.gz --refList GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:57:03,181] [INFO] Task succeeded: fastANI
[2024-01-24 14:57:03,182] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg127d16e6-8c09-4034-aa00-29a1d23e803e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:57:03,183] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg127d16e6-8c09-4034-aa00-29a1d23e803e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:57:03,192] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:57:03,192] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:57:03,192] [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
Gracilimonas mengyeensis	strain=DSM 21985	GCA_900182705.1	1302730	1302730	type	True	100.0	1539	1540	95	conclusive
Gracilimonas tropica	strain=DSM 19535	GCA_000375425.1	454600	454600	type	True	77.8317	232	1540	95	below_threshold
Gracilimonas amylolytica	strain=LA399	GCA_002911695.1	1749045	1749045	type	True	77.762	182	1540	95	below_threshold
Balneola vulgaris	strain=DSM 17893	GCA_000375465.1	287535	287535	type	True	76.549	50	1540	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:57:03,194] [INFO] DFAST Taxonomy check result was written to GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:57:03,195] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:57:03,195] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:57:03,195] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg127d16e6-8c09-4034-aa00-29a1d23e803e/dqc_reference/checkm_data
[2024-01-24 14:57:03,196] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:57:03,244] [INFO] Task started: CheckM
[2024-01-24 14:57:03,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/checkm_input GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:58:10,319] [INFO] Task succeeded: CheckM
[2024-01-24 14:58:10,320] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 97.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:58:10,339] [INFO] ===== Completeness check finished =====
[2024-01-24 14:58:10,340] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:58:10,340] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:58:10,340] [INFO] Task started: Blastn
[2024-01-24 14:58:10,341] [INFO] Running command: blastn -query GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg127d16e6-8c09-4034-aa00-29a1d23e803e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:58:11,243] [INFO] Task succeeded: Blastn
[2024-01-24 14:58:11,246] [INFO] Selected 15 target genomes.
[2024-01-24 14:58:11,246] [INFO] Target genome list was writen to GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:58:11,272] [INFO] Task started: fastANI
[2024-01-24 14:58:11,272] [INFO] Running command: fastANI --query /var/lib/cwl/stg1769ce01-0c3f-4455-84ab-798c9a8ef836/GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna.gz --refList GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:58:22,817] [INFO] Task succeeded: fastANI
[2024-01-24 14:58:22,831] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:58:22,832] [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_900182705.1	s__Gracilimonas mengyeensis	100.0	1539	1540	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000375425.1	s__Gracilimonas tropica	77.8611	230	1540	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002911695.1	s__Gracilimonas amylolytica	77.7981	180	1540	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002696035.1	s__Gracilimonas sp002696035	77.772	266	1540	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCA_017641085.1	s__Gracilimonas sp017641085	77.6036	261	1540	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002694685.1	s__Gracilimonas sp002694685	77.5688	223	1540	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	99.97	99.87	0.99	0.97	9	-
GCA_014762685.1	s__Gracilimonas sp014762685	77.5616	209	1540	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Gracilimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002364085.1	s__Balneola sp002364085	76.5345	52	1540	d__Bacteria;p__Bacteroidota;c__Rhodothermia;o__Balneolales;f__Balneolaceae;g__Balneola	95.0	99.57	98.41	0.97	0.85	26	-
--------------------------------------------------------------------------------
[2024-01-24 14:58:22,833] [INFO] GTDB search result was written to GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:58:22,834] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:58:22,836] [INFO] DFAST_QC result json was written to GCF_900182705.1_IMG-taxon_2724679790_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:58:22,837] [INFO] DFAST_QC completed!
[2024-01-24 14:58:22,837] [INFO] Total running time: 0h1m59s