[2024-01-24 12:44:52,526] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:44:52,527] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:44:52,528] [INFO] DQC Reference Directory: /var/lib/cwl/stgea0ba9c5-dda6-4afc-b799-9929f8a3d98c/dqc_reference
[2024-01-24 12:44:53,764] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:44:53,765] [INFO] Task started: Prodigal
[2024-01-24 12:44:53,765] [INFO] Running command: gunzip -c /var/lib/cwl/stg1531bd63-5cb3-44c1-9fbd-89c21842cba5/GCF_002970975.1_ASM297097v1_genomic.fna.gz | prodigal -d GCF_002970975.1_ASM297097v1_genomic.fna/cds.fna -a GCF_002970975.1_ASM297097v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:02,694] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:02,695] [INFO] Task started: HMMsearch
[2024-01-24 12:45:02,695] [INFO] Running command: hmmsearch --tblout GCF_002970975.1_ASM297097v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea0ba9c5-dda6-4afc-b799-9929f8a3d98c/dqc_reference/reference_markers.hmm GCF_002970975.1_ASM297097v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:02,948] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:02,950] [INFO] Found 6/6 markers.
[2024-01-24 12:45:02,982] [INFO] Query marker FASTA was written to GCF_002970975.1_ASM297097v1_genomic.fna/markers.fasta
[2024-01-24 12:45:02,982] [INFO] Task started: Blastn
[2024-01-24 12:45:02,982] [INFO] Running command: blastn -query GCF_002970975.1_ASM297097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea0ba9c5-dda6-4afc-b799-9929f8a3d98c/dqc_reference/reference_markers.fasta -out GCF_002970975.1_ASM297097v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:04,327] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:04,331] [INFO] Selected 18 target genomes.
[2024-01-24 12:45:04,331] [INFO] Target genome list was writen to GCF_002970975.1_ASM297097v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:04,387] [INFO] Task started: fastANI
[2024-01-24 12:45:04,387] [INFO] Running command: fastANI --query /var/lib/cwl/stg1531bd63-5cb3-44c1-9fbd-89c21842cba5/GCF_002970975.1_ASM297097v1_genomic.fna.gz --refList GCF_002970975.1_ASM297097v1_genomic.fna/target_genomes.txt --output GCF_002970975.1_ASM297097v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:16,172] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:16,172] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea0ba9c5-dda6-4afc-b799-9929f8a3d98c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:16,173] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea0ba9c5-dda6-4afc-b799-9929f8a3d98c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:16,186] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:16,187] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:16,187] [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
Microbacterium halophytorum	strain=YJYP 303	GCA_002970975.1	2067568	2067568	type	True	100.0	1101	1102	95	conclusive
Microbacterium halotolerans	strain=YIM 70130	GCA_003569805.1	246613	246613	type	True	82.1216	619	1102	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_004564075.1	904291	904291	type	True	81.0165	514	1102	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_001689915.1	904291	904291	type	True	81.0053	504	1102	95	below_threshold
Microbacterium sediminis	strain=YLB-01	GCA_002741995.1	904291	904291	type	True	80.9846	506	1102	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_014641475.1	1867410	1867410	type	True	80.6929	498	1102	95	below_threshold
Microbacterium sorbitolivorans	strain=CGMCC 1.15228	GCA_003327285.1	1867410	1867410	type	True	80.6506	498	1102	95	below_threshold
Microbacterium excoecariae	strain=CBS5P-1	GCA_011326725.1	2715210	2715210	type	True	80.3006	491	1102	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	80.1285	518	1102	95	below_threshold
Microbacterium album	strain=CGMCC 1.15794	GCA_014643695.1	2053191	2053191	type	True	79.9912	448	1102	95	below_threshold
Microbacterium marinilacus	strain=YM11-607	GCA_019753765.1	415209	415209	type	True	79.9506	503	1102	95	below_threshold
Microbacterium stercoris	strain=NEAU-LLB	GCA_017592545.1	2820289	2820289	type	True	79.9285	474	1102	95	below_threshold
Microbacterium nanhaiense	strain=CGMCC 4.7181	GCA_014646015.1	1301026	1301026	type	True	79.9218	497	1102	95	below_threshold
Microbacterium commune	strain=Re1	GCA_014836945.1	2762219	2762219	type	True	79.386	414	1102	95	below_threshold
Microbacterium hominis	strain=LCDC 84-0209	GCA_001553805.1	162426	162426	type	True	79.0899	422	1102	95	below_threshold
Microbacterium bovistercoris	strain=NEAU-LLE	GCA_003387575.1	2293570	2293570	type	True	79.0899	437	1102	95	below_threshold
Microbacterium gallinarum	strain=Sa1CUA4	GCA_014837165.1	2762209	2762209	type	True	79.0859	438	1102	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	78.2028	441	1102	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:16,189] [INFO] DFAST Taxonomy check result was written to GCF_002970975.1_ASM297097v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:16,189] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:16,189] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:16,190] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea0ba9c5-dda6-4afc-b799-9929f8a3d98c/dqc_reference/checkm_data
[2024-01-24 12:45:16,191] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:16,224] [INFO] Task started: CheckM
[2024-01-24 12:45:16,224] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002970975.1_ASM297097v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002970975.1_ASM297097v1_genomic.fna/checkm_input GCF_002970975.1_ASM297097v1_genomic.fna/checkm_result
[2024-01-24 12:46:00,705] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:00,706] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:00,726] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:00,726] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:00,727] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002970975.1_ASM297097v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:00,727] [INFO] Task started: Blastn
[2024-01-24 12:46:00,728] [INFO] Running command: blastn -query GCF_002970975.1_ASM297097v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea0ba9c5-dda6-4afc-b799-9929f8a3d98c/dqc_reference/reference_markers_gtdb.fasta -out GCF_002970975.1_ASM297097v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:02,958] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:02,961] [INFO] Selected 14 target genomes.
[2024-01-24 12:46:02,961] [INFO] Target genome list was writen to GCF_002970975.1_ASM297097v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:02,978] [INFO] Task started: fastANI
[2024-01-24 12:46:02,979] [INFO] Running command: fastANI --query /var/lib/cwl/stg1531bd63-5cb3-44c1-9fbd-89c21842cba5/GCF_002970975.1_ASM297097v1_genomic.fna.gz --refList GCF_002970975.1_ASM297097v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002970975.1_ASM297097v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:13,073] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:13,088] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:13,089] [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_002970975.1	s__Microbacterium halophytorum	100.0	1101	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900163665.1	s__Microbacterium sp900163665	82.1922	635	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003569805.1	s__Microbacterium halotolerans	82.1133	620	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004564075.1	s__Microbacterium sediminis	81.074	508	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	99.95	99.95	1.00	1.00	3	-
GCF_003327285.1	s__Microbacterium sorbitolivorans	80.6881	495	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016805985.1	s__Microbacterium sp016805985	80.5023	504	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426925.1	s__Microbacterium sp001426925	80.4657	501	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	98.86	98.86	0.90	0.90	2	-
GCF_015235415.1	s__Microbacterium paludicola_A	80.3438	490	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011326725.1	s__Microbacterium excoecariae	80.3292	489	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	95.69	95.69	0.87	0.87	2	-
GCF_009735645.1	s__Microbacterium oryzae	80.1568	515	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014643695.1	s__Microbacterium album	80.0637	442	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646015.1	s__Microbacterium nanhaiense	79.9053	498	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314225.1	s__Microbacterium sp001314225	79.4163	484	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362195.1	s__Microbacterium sp004362195	78.8683	413	1102	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:13,091] [INFO] GTDB search result was written to GCF_002970975.1_ASM297097v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:13,092] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:13,095] [INFO] DFAST_QC result json was written to GCF_002970975.1_ASM297097v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:13,095] [INFO] DFAST_QC completed!
[2024-01-24 12:46:13,095] [INFO] Total running time: 0h1m21s