[2024-01-24 13:13:11,822] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:11,825] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:11,825] [INFO] DQC Reference Directory: /var/lib/cwl/stgf23b9d7c-d0bc-42a3-9c8b-bb1a1f24e52b/dqc_reference
[2024-01-24 13:13:13,399] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:13,400] [INFO] Task started: Prodigal
[2024-01-24 13:13:13,400] [INFO] Running command: gunzip -c /var/lib/cwl/stg91a9bac7-7817-42e2-b9c0-0305ed8ae92c/GCF_009858245.1_ASM985824v1_genomic.fna.gz | prodigal -d GCF_009858245.1_ASM985824v1_genomic.fna/cds.fna -a GCF_009858245.1_ASM985824v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:25,077] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:25,077] [INFO] Task started: HMMsearch
[2024-01-24 13:13:25,077] [INFO] Running command: hmmsearch --tblout GCF_009858245.1_ASM985824v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf23b9d7c-d0bc-42a3-9c8b-bb1a1f24e52b/dqc_reference/reference_markers.hmm GCF_009858245.1_ASM985824v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:25,371] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:25,372] [INFO] Found 6/6 markers.
[2024-01-24 13:13:25,409] [INFO] Query marker FASTA was written to GCF_009858245.1_ASM985824v1_genomic.fna/markers.fasta
[2024-01-24 13:13:25,409] [INFO] Task started: Blastn
[2024-01-24 13:13:25,409] [INFO] Running command: blastn -query GCF_009858245.1_ASM985824v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf23b9d7c-d0bc-42a3-9c8b-bb1a1f24e52b/dqc_reference/reference_markers.fasta -out GCF_009858245.1_ASM985824v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:26,708] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:26,712] [INFO] Selected 16 target genomes.
[2024-01-24 13:13:26,712] [INFO] Target genome list was writen to GCF_009858245.1_ASM985824v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:27,294] [INFO] Task started: fastANI
[2024-01-24 13:13:27,294] [INFO] Running command: fastANI --query /var/lib/cwl/stg91a9bac7-7817-42e2-b9c0-0305ed8ae92c/GCF_009858245.1_ASM985824v1_genomic.fna.gz --refList GCF_009858245.1_ASM985824v1_genomic.fna/target_genomes.txt --output GCF_009858245.1_ASM985824v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:39,197] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:39,198] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf23b9d7c-d0bc-42a3-9c8b-bb1a1f24e52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:39,198] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf23b9d7c-d0bc-42a3-9c8b-bb1a1f24e52b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:39,212] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:13:39,212] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:13:39,212] [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
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	82.036	729	1231	95	below_threshold
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	81.9542	719	1231	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	81.7977	687	1231	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	81.2909	670	1231	95	below_threshold
Phycicoccus endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	81.193	640	1231	95	below_threshold
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	81.1927	631	1231	95	below_threshold
Knoellia flava	strain=CGMCC 1.10749	GCA_014636255.1	913969	913969	type	True	80.8451	606	1231	95	below_threshold
Knoellia aerolata	strain=DSM 18566	GCA_000768695.1	442954	442954	type	True	80.8201	573	1231	95	below_threshold
Knoellia flava	strain=TL1	GCA_000768675.1	913969	913969	type	True	80.7042	598	1231	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	80.659	570	1231	95	below_threshold
Knoellia sinensis	strain=KCTC 19936	GCA_000768705.1	136100	136100	type	True	79.8604	502	1231	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.6041	471	1231	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	79.5999	492	1231	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.9045	389	1231	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.8128	416	1231	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.5378	398	1231	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:39,214] [INFO] DFAST Taxonomy check result was written to GCF_009858245.1_ASM985824v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:39,214] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:39,214] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:39,215] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf23b9d7c-d0bc-42a3-9c8b-bb1a1f24e52b/dqc_reference/checkm_data
[2024-01-24 13:13:39,216] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:39,252] [INFO] Task started: CheckM
[2024-01-24 13:13:39,253] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009858245.1_ASM985824v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009858245.1_ASM985824v1_genomic.fna/checkm_input GCF_009858245.1_ASM985824v1_genomic.fna/checkm_result
[2024-01-24 13:14:55,677] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:55,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:55,702] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:55,703] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:55,703] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009858245.1_ASM985824v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:55,703] [INFO] Task started: Blastn
[2024-01-24 13:14:55,704] [INFO] Running command: blastn -query GCF_009858245.1_ASM985824v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf23b9d7c-d0bc-42a3-9c8b-bb1a1f24e52b/dqc_reference/reference_markers_gtdb.fasta -out GCF_009858245.1_ASM985824v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:57,672] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:57,676] [INFO] Selected 15 target genomes.
[2024-01-24 13:14:57,676] [INFO] Target genome list was writen to GCF_009858245.1_ASM985824v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:57,695] [INFO] Task started: fastANI
[2024-01-24 13:14:57,695] [INFO] Running command: fastANI --query /var/lib/cwl/stg91a9bac7-7817-42e2-b9c0-0305ed8ae92c/GCF_009858245.1_ASM985824v1_genomic.fna.gz --refList GCF_009858245.1_ASM985824v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009858245.1_ASM985824v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:15:09,623] [INFO] Task succeeded: fastANI
[2024-01-24 13:15:09,639] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:15:09,639] [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_009858245.1	s__Ornithinibacter aureus	100.0	1228	1231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017989115.1	s__Ornithinibacter sp017989115	93.3451	681	1231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011383005.1	s__Phycicoccus sp011383005	82.4491	746	1231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201035.1	s__Phycicoccus sp013201035	82.222	729	1231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016887965.1	s__Phycicoccus sp016887965	82.0523	760	1231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000720925.1	s__Phycicoccus jejuensis	82.0255	730	1231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_001428065.1	s__Phycicoccus sp001428065	81.9044	680	1231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763705.1	s__Phycicoccus sp014763705	81.85	533	1231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002846495.1	s__Phycicoccus duodecadis	81.8392	681	1231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011326735.1	s__Phycicoccus endophyticus	81.1835	632	1231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	99.99	99.99	1.00	1.00	3	-
GCF_018139485.1	s__Phycicoccus sp018139485	80.9837	626	1231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768695.1	s__Knoellia aerolata	80.787	576	1231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000768675.1	s__Knoellia flava	80.7356	595	1231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003002895.1	s__Knoellia remsis	80.6396	573	1231	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	79.8608	502	1231	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Knoellia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:15:09,641] [INFO] GTDB search result was written to GCF_009858245.1_ASM985824v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:15:09,641] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:15:09,645] [INFO] DFAST_QC result json was written to GCF_009858245.1_ASM985824v1_genomic.fna/dqc_result.json
[2024-01-24 13:15:09,646] [INFO] DFAST_QC completed!
[2024-01-24 13:15:09,646] [INFO] Total running time: 0h1m58s