[2024-01-24 12:29:28,818] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dd87e3d-256e-4653-91f6-061360da5935/dqc_reference
[2024-01-24 12:29:30,167] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:30,168] [INFO] Task started: Prodigal
[2024-01-24 12:29:30,169] [INFO] Running command: gunzip -c /var/lib/cwl/stgdea5a108-ad85-4d40-879d-bf7cafb24a0b/GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/cds.fna -a GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:36,692] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:36,693] [INFO] Task started: HMMsearch
[2024-01-24 12:29:36,693] [INFO] Running command: hmmsearch --tblout GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dd87e3d-256e-4653-91f6-061360da5935/dqc_reference/reference_markers.hmm GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:37,067] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:37,071] [INFO] Found 6/6 markers.
[2024-01-24 12:29:37,099] [INFO] Query marker FASTA was written to GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:29:37,099] [INFO] Task started: Blastn
[2024-01-24 12:29:37,099] [INFO] Running command: blastn -query GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dd87e3d-256e-4653-91f6-061360da5935/dqc_reference/reference_markers.fasta -out GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:37,699] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:37,703] [INFO] Selected 11 target genomes.
[2024-01-24 12:29:37,703] [INFO] Target genome list was writen to GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:29:37,709] [INFO] Task started: fastANI
[2024-01-24 12:29:37,709] [INFO] Running command: fastANI --query /var/lib/cwl/stgdea5a108-ad85-4d40-879d-bf7cafb24a0b/GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna.gz --refList GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:44,985] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:44,986] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dd87e3d-256e-4653-91f6-061360da5935/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:44,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dd87e3d-256e-4653-91f6-061360da5935/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:44,993] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:29:44,993] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:44,993] [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
Halolactibacillus miurensis	strain=DSM 17074	GCA_900116255.1	306541	306541	type	True	100.0	1025	1028	95	conclusive
Halolactibacillus miurensis	strain=NBRC 100873	GCA_007990305.1	306541	306541	type	True	99.9537	972	1028	95	conclusive
Halolactibacillus halophilus	strain=NBRC 100868	GCA_007990285.1	306540	306540	type	True	84.6371	646	1028	95	below_threshold
Halolactibacillus halophilus	strain=DSM 17073	GCA_900115605.1	306540	306540	type	True	84.6243	659	1028	95	below_threshold
Halolactibacillus alkaliphilus	strain=NBRC 103919	GCA_007991355.1	442899	442899	type	True	81.7182	497	1028	95	below_threshold
Amphibacillus marinus	strain=CGMCC 1.10434	GCA_900110345.1	872970	872970	type	True	77.7418	102	1028	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:44,996] [INFO] DFAST Taxonomy check result was written to GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:29:44,997] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:44,997] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:44,997] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dd87e3d-256e-4653-91f6-061360da5935/dqc_reference/checkm_data
[2024-01-24 12:29:44,998] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:45,034] [INFO] Task started: CheckM
[2024-01-24 12:29:45,034] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/checkm_input GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:30:12,964] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:12,965] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:12,987] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:12,988] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:12,988] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:30:12,989] [INFO] Task started: Blastn
[2024-01-24 12:30:12,989] [INFO] Running command: blastn -query GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dd87e3d-256e-4653-91f6-061360da5935/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:13,774] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:13,777] [INFO] Selected 15 target genomes.
[2024-01-24 12:30:13,778] [INFO] Target genome list was writen to GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:13,788] [INFO] Task started: fastANI
[2024-01-24 12:30:13,788] [INFO] Running command: fastANI --query /var/lib/cwl/stgdea5a108-ad85-4d40-879d-bf7cafb24a0b/GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna.gz --refList GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:23,065] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:23,075] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:23,075] [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_900116255.1	s__Halolactibacillus miurensis	100.0	1025	1028	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	99.76	99.51	0.98	0.95	3	conclusive
GCF_900115605.1	s__Halolactibacillus halophilus	84.6268	658	1028	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900115465.1	s__Halolactibacillus alkaliphilus	81.8125	495	1028	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Halolactibacillus	95.0	99.99	99.98	0.99	0.99	3	-
GCF_003201605.1	s__Streptohalobacillus salinus	78.9478	219	1028	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Streptohalobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003315295.1	s__Paraliobacillus ryukyuensis	78.0915	73	1028	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus	95.0	98.18	98.18	0.92	0.92	2	-
GCF_900110345.1	s__Amphibacillus_D marinus	77.7418	102	1028	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003426025.1	s__Paraliobacillus_A quinghaiensis	77.7145	89	1028	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.99	99.99	0.99	0.99	2	-
GCF_016908375.1	s__Amphibacillus_C cookii	77.6164	106	1028	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018919165.1	s__Amphibacillus sp018919165	77.5924	71	1028	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Amphibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003268595.1	s__Paraliobacillus_A zengyii	77.4459	81	1028	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Paraliobacillus_A	95.0	99.46	99.36	0.95	0.93	3	-
GCF_017599345.1	s__Gracilibacillus sp017599345	77.3209	56	1028	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Amphibacillaceae;g__Gracilibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:30:23,077] [INFO] GTDB search result was written to GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:23,078] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:23,082] [INFO] DFAST_QC result json was written to GCF_900116255.1_IMG-taxon_2675903221_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:30:23,082] [INFO] DFAST_QC completed!
[2024-01-24 12:30:23,082] [INFO] Total running time: 0h0m54s