[2024-01-25 20:03:05,521] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:03:05,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:03:05,525] [INFO] DQC Reference Directory: /var/lib/cwl/stgd21e27fc-6519-4224-b525-02911461fbfe/dqc_reference
[2024-01-25 20:03:06,656] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:03:06,657] [INFO] Task started: Prodigal
[2024-01-25 20:03:06,657] [INFO] Running command: gunzip -c /var/lib/cwl/stg35d3c484-3985-4a06-abff-13f702b35ce3/GCF_003971195.1_ASM397119v1_genomic.fna.gz | prodigal -d GCF_003971195.1_ASM397119v1_genomic.fna/cds.fna -a GCF_003971195.1_ASM397119v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:03:14,170] [INFO] Task succeeded: Prodigal
[2024-01-25 20:03:14,170] [INFO] Task started: HMMsearch
[2024-01-25 20:03:14,170] [INFO] Running command: hmmsearch --tblout GCF_003971195.1_ASM397119v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd21e27fc-6519-4224-b525-02911461fbfe/dqc_reference/reference_markers.hmm GCF_003971195.1_ASM397119v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:03:14,361] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:03:14,362] [INFO] Found 6/6 markers.
[2024-01-25 20:03:14,384] [INFO] Query marker FASTA was written to GCF_003971195.1_ASM397119v1_genomic.fna/markers.fasta
[2024-01-25 20:03:14,385] [INFO] Task started: Blastn
[2024-01-25 20:03:14,385] [INFO] Running command: blastn -query GCF_003971195.1_ASM397119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd21e27fc-6519-4224-b525-02911461fbfe/dqc_reference/reference_markers.fasta -out GCF_003971195.1_ASM397119v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:15,137] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:15,139] [INFO] Selected 21 target genomes.
[2024-01-25 20:03:15,140] [INFO] Target genome list was writen to GCF_003971195.1_ASM397119v1_genomic.fna/target_genomes.txt
[2024-01-25 20:03:15,154] [INFO] Task started: fastANI
[2024-01-25 20:03:15,154] [INFO] Running command: fastANI --query /var/lib/cwl/stg35d3c484-3985-4a06-abff-13f702b35ce3/GCF_003971195.1_ASM397119v1_genomic.fna.gz --refList GCF_003971195.1_ASM397119v1_genomic.fna/target_genomes.txt --output GCF_003971195.1_ASM397119v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:03:29,171] [INFO] Task succeeded: fastANI
[2024-01-25 20:03:29,171] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd21e27fc-6519-4224-b525-02911461fbfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:03:29,172] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd21e27fc-6519-4224-b525-02911461fbfe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:03:29,181] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:03:29,181] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:03:29,181] [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
Flaviflexus ciconiae	strain=H23T48	GCA_003971195.1	2496867	2496867	type	True	100.0	942	943	95	conclusive
Flaviflexus massiliensis	strain=SIT4	GCA_001375495.1	1522309	1522309	type	True	80.269	394	943	95	below_threshold
Flaviflexus equikiangi	strain=dk850	GCA_014069875.1	2758573	2758573	type	True	79.4203	304	943	95	below_threshold
Flaviflexus salsibiostraticola	strain=KCTC 33148	GCA_003952265.1	1282737	1282737	type	True	79.0961	344	943	95	below_threshold
Flaviflexus huanghaiensis	strain=CICC 10486	GCA_014118685.1	1111473	1111473	type	True	78.5872	238	943	95	below_threshold
Sanguibacter keddieii	strain=DSM 10542	GCA_000024925.1	60920	60920	type	True	78.0244	67	943	95	below_threshold
Nocardioides jishulii	strain=dk3136	GCA_006007965.1	2575440	2575440	type	True	77.875	52	943	95	below_threshold
Cellulomonas shaoxiangyii	strain=Z28	GCA_004798685.1	2566013	2566013	type	True	77.7435	67	943	95	below_threshold
Georgenia soli	strain=DSM 21838	GCA_002563695.1	638953	638953	type	True	77.7144	101	943	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	77.181	62	943	95	below_threshold
Ruania zhangjianzhongii	strain=HY168	GCA_008000995.1	2603206	2603206	type	True	76.9317	67	943	95	below_threshold
Actinomyces urogenitalis	strain=DSM 15434	GCA_000159035.1	103621	103621	type	True	76.6932	61	943	95	below_threshold
Actinomyces ruminicola	strain=DSM 27982	GCA_900103885.1	332524	332524	type	True	76.3717	75	943	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:03:29,182] [INFO] DFAST Taxonomy check result was written to GCF_003971195.1_ASM397119v1_genomic.fna/tc_result.tsv
[2024-01-25 20:03:29,182] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:03:29,183] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:03:29,183] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd21e27fc-6519-4224-b525-02911461fbfe/dqc_reference/checkm_data
[2024-01-25 20:03:29,183] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:03:29,218] [INFO] Task started: CheckM
[2024-01-25 20:03:29,218] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003971195.1_ASM397119v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003971195.1_ASM397119v1_genomic.fna/checkm_input GCF_003971195.1_ASM397119v1_genomic.fna/checkm_result
[2024-01-25 20:03:55,420] [INFO] Task succeeded: CheckM
[2024-01-25 20:03:55,421] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:03:55,437] [INFO] ===== Completeness check finished =====
[2024-01-25 20:03:55,437] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:03:55,438] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003971195.1_ASM397119v1_genomic.fna/markers.fasta)
[2024-01-25 20:03:55,438] [INFO] Task started: Blastn
[2024-01-25 20:03:55,438] [INFO] Running command: blastn -query GCF_003971195.1_ASM397119v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd21e27fc-6519-4224-b525-02911461fbfe/dqc_reference/reference_markers_gtdb.fasta -out GCF_003971195.1_ASM397119v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:03:56,562] [INFO] Task succeeded: Blastn
[2024-01-25 20:03:56,567] [INFO] Selected 19 target genomes.
[2024-01-25 20:03:56,567] [INFO] Target genome list was writen to GCF_003971195.1_ASM397119v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:03:56,583] [INFO] Task started: fastANI
[2024-01-25 20:03:56,583] [INFO] Running command: fastANI --query /var/lib/cwl/stg35d3c484-3985-4a06-abff-13f702b35ce3/GCF_003971195.1_ASM397119v1_genomic.fna.gz --refList GCF_003971195.1_ASM397119v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003971195.1_ASM397119v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:04:08,206] [INFO] Task succeeded: fastANI
[2024-01-25 20:04:08,214] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:04:08,214] [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_003971195.1	s__Flaviflexus sp003971195	100.0	942	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001375495.1	s__Flaviflexus massiliensis	80.2232	393	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014069875.1	s__Flaviflexus sp014069875	79.4505	303	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	99.13	99.13	0.93	0.93	3	-
GCF_003952265.1	s__Flaviflexus salsibiostraticola	79.1475	347	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014118685.1	s__Flaviflexus huanghaiensis	78.5872	238	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Flaviflexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004798685.1	s__Cellulomonas shaoxiangyii	77.7435	67	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002563695.1	s__Georgenia soli	77.7383	102	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Georgenia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009930875.1	s__Actinomyces sp009930875	77.2535	66	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	98.69	98.69	0.97	0.97	2	-
GCF_001553565.1	s__Actinomyces radicidentis	77.0759	101	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000159035.1	s__Actinomyces urogenitalis	76.6932	61	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	99.08	98.90	0.93	0.88	7	-
GCF_900103885.1	s__Actinomyces ruminicola	76.3717	75	943	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Actinomyces	95.0	96.80	96.66	0.89	0.87	3	-
--------------------------------------------------------------------------------
[2024-01-25 20:04:08,216] [INFO] GTDB search result was written to GCF_003971195.1_ASM397119v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:04:08,216] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:04:08,219] [INFO] DFAST_QC result json was written to GCF_003971195.1_ASM397119v1_genomic.fna/dqc_result.json
[2024-01-25 20:04:08,219] [INFO] DFAST_QC completed!
[2024-01-25 20:04:08,219] [INFO] Total running time: 0h1m3s