[2024-01-24 11:26:12,968] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:12,970] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:12,970] [INFO] DQC Reference Directory: /var/lib/cwl/stg3318ff06-37b0-4be1-be6b-651ece0d0429/dqc_reference
[2024-01-24 11:26:14,326] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:14,327] [INFO] Task started: Prodigal
[2024-01-24 11:26:14,327] [INFO] Running command: gunzip -c /var/lib/cwl/stg36916722-b261-4e3a-8766-d5ed686de927/GCF_003002895.1_ASM300289v1_genomic.fna.gz | prodigal -d GCF_003002895.1_ASM300289v1_genomic.fna/cds.fna -a GCF_003002895.1_ASM300289v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:24,756] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:24,757] [INFO] Task started: HMMsearch
[2024-01-24 11:26:24,757] [INFO] Running command: hmmsearch --tblout GCF_003002895.1_ASM300289v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3318ff06-37b0-4be1-be6b-651ece0d0429/dqc_reference/reference_markers.hmm GCF_003002895.1_ASM300289v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:25,087] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:25,089] [INFO] Found 6/6 markers.
[2024-01-24 11:26:25,135] [INFO] Query marker FASTA was written to GCF_003002895.1_ASM300289v1_genomic.fna/markers.fasta
[2024-01-24 11:26:25,136] [INFO] Task started: Blastn
[2024-01-24 11:26:25,136] [INFO] Running command: blastn -query GCF_003002895.1_ASM300289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3318ff06-37b0-4be1-be6b-651ece0d0429/dqc_reference/reference_markers.fasta -out GCF_003002895.1_ASM300289v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:26,374] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:26,377] [INFO] Selected 16 target genomes.
[2024-01-24 11:26:26,378] [INFO] Target genome list was writen to GCF_003002895.1_ASM300289v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:26,383] [INFO] Task started: fastANI
[2024-01-24 11:26:26,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg36916722-b261-4e3a-8766-d5ed686de927/GCF_003002895.1_ASM300289v1_genomic.fna.gz --refList GCF_003002895.1_ASM300289v1_genomic.fna/target_genomes.txt --output GCF_003002895.1_ASM300289v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:39,628] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:39,629] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3318ff06-37b0-4be1-be6b-651ece0d0429/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:39,629] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3318ff06-37b0-4be1-be6b-651ece0d0429/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:39,642] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:26:39,643] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:39,643] [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
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	100.0	1159	1160	95	conclusive
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	84.4149	790	1160	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	84.3764	822	1160	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	83.6795	732	1160	95	below_threshold
Knoellia subterranea	strain=KCTC 19937	GCA_000768685.1	184882	184882	type	True	83.2926	767	1160	95	below_threshold
Knoellia sinensis	strain=KCTC 19936	GCA_000768705.1	136100	136100	type	True	82.4534	730	1160	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	80.141	487	1160	95	below_threshold
Janibacter massiliensis	strain=Marseille-P4121	GCA_900289115.1	2058291	2058291	type	True	79.6304	434	1160	95	below_threshold
Arsenicicoccus piscis	strain=DSM 22760	GCA_022568835.1	673954	673954	type	True	79.0643	412	1160	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.7846	432	1160	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.6818	437	1160	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.603	392	1160	95	below_threshold
Flexivirga oryzae	strain=DSM 105369	GCA_014190805.1	1794944	1794944	type	True	78.2024	362	1160	95	below_threshold
Flexivirga caeni	strain=BO-16	GCA_003724155.1	2294115	2294115	type	True	78.0973	318	1160	95	below_threshold
Ornithinimicrobium ciconiae	strain=H23M54	GCA_007197575.1	2594265	2594265	type	True	78.0179	298	1160	95	below_threshold
Cellulosimicrobium marinum	strain=NBRC 110994	GCA_020551945.1	1638992	1638992	type	True	77.4015	353	1160	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:39,645] [INFO] DFAST Taxonomy check result was written to GCF_003002895.1_ASM300289v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:39,645] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:39,646] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:39,646] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3318ff06-37b0-4be1-be6b-651ece0d0429/dqc_reference/checkm_data
[2024-01-24 11:26:39,647] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:39,684] [INFO] Task started: CheckM
[2024-01-24 11:26:39,685] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003002895.1_ASM300289v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003002895.1_ASM300289v1_genomic.fna/checkm_input GCF_003002895.1_ASM300289v1_genomic.fna/checkm_result
[2024-01-24 11:27:33,517] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:33,518] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:33,540] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:33,540] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:33,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003002895.1_ASM300289v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:33,541] [INFO] Task started: Blastn
[2024-01-24 11:27:33,541] [INFO] Running command: blastn -query GCF_003002895.1_ASM300289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3318ff06-37b0-4be1-be6b-651ece0d0429/dqc_reference/reference_markers_gtdb.fasta -out GCF_003002895.1_ASM300289v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:35,473] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:35,477] [INFO] Selected 13 target genomes.
[2024-01-24 11:27:35,478] [INFO] Target genome list was writen to GCF_003002895.1_ASM300289v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:35,486] [INFO] Task started: fastANI
[2024-01-24 11:27:35,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg36916722-b261-4e3a-8766-d5ed686de927/GCF_003002895.1_ASM300289v1_genomic.fna.gz --refList GCF_003002895.1_ASM300289v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003002895.1_ASM300289v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:46,953] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:46,975] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:46,976] [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_003002895.1	s__Knoellia remsis	100.0	1159	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000768675.1	s__Knoellia flava	84.4022	790	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007992835.1	s__Knoellia locipacati	84.2359	799	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768695.1	s__Knoellia aerolata	83.6919	731	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768685.1	s__Knoellia subterranea	83.2776	768	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001427985.1	s__Knoellia sp001427985	82.8853	731	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768705.1	s__Knoellia sinensis	82.4422	731	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016887965.1	s__Phycicoccus sp016887965	81.0638	658	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858245.1	s__Ornithinibacter aureus	80.6819	570	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001046855.1	s__Tetrasphaera japonica	79.6165	570	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Tetrasphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012518475.1	s__F2B08 sp012518475	79.4682	360	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__F2B08	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009184895.1	s__F2B08 sp009184895	79.1786	491	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__F2B08	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012838445.1	s__F2B08 sp012838445	79.128	414	1160	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__F2B08	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:46,978] [INFO] GTDB search result was written to GCF_003002895.1_ASM300289v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:46,978] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:46,982] [INFO] DFAST_QC result json was written to GCF_003002895.1_ASM300289v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:46,982] [INFO] DFAST_QC completed!
[2024-01-24 11:27:46,982] [INFO] Total running time: 0h1m34s