[2024-01-24 13:18:32,574] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:32,576] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:32,576] [INFO] DQC Reference Directory: /var/lib/cwl/stg9ac652ed-b2d3-4040-9529-cbf23b56ef82/dqc_reference
[2024-01-24 13:18:33,973] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:33,974] [INFO] Task started: Prodigal
[2024-01-24 13:18:33,974] [INFO] Running command: gunzip -c /var/lib/cwl/stgeb67a350-5f7a-45ee-8760-495f01727417/GCF_014395645.1_ASM1439564v1_genomic.fna.gz | prodigal -d GCF_014395645.1_ASM1439564v1_genomic.fna/cds.fna -a GCF_014395645.1_ASM1439564v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:43,431] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:43,431] [INFO] Task started: HMMsearch
[2024-01-24 13:18:43,431] [INFO] Running command: hmmsearch --tblout GCF_014395645.1_ASM1439564v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9ac652ed-b2d3-4040-9529-cbf23b56ef82/dqc_reference/reference_markers.hmm GCF_014395645.1_ASM1439564v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:43,727] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:43,728] [INFO] Found 6/6 markers.
[2024-01-24 13:18:43,756] [INFO] Query marker FASTA was written to GCF_014395645.1_ASM1439564v1_genomic.fna/markers.fasta
[2024-01-24 13:18:43,756] [INFO] Task started: Blastn
[2024-01-24 13:18:43,756] [INFO] Running command: blastn -query GCF_014395645.1_ASM1439564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ac652ed-b2d3-4040-9529-cbf23b56ef82/dqc_reference/reference_markers.fasta -out GCF_014395645.1_ASM1439564v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:45,107] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:45,110] [INFO] Selected 12 target genomes.
[2024-01-24 13:18:45,110] [INFO] Target genome list was writen to GCF_014395645.1_ASM1439564v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:45,120] [INFO] Task started: fastANI
[2024-01-24 13:18:45,120] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb67a350-5f7a-45ee-8760-495f01727417/GCF_014395645.1_ASM1439564v1_genomic.fna.gz --refList GCF_014395645.1_ASM1439564v1_genomic.fna/target_genomes.txt --output GCF_014395645.1_ASM1439564v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:55,651] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:55,651] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9ac652ed-b2d3-4040-9529-cbf23b56ef82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:55,651] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9ac652ed-b2d3-4040-9529-cbf23b56ef82/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:55,662] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:55,662] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:55,662] [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 endophyticus	strain=CGMCC 4.7300	GCA_014646175.1	1690220	1690220	type	True	99.9787	1065	1079	95	conclusive
Phycicoccus endophyticus	strain=IP6SC6	GCA_011326735.1	1690220	1690220	type	True	99.9757	1044	1079	95	conclusive
Phycicoccus mangrovi	strain=KQZ13P-1	GCA_018729305.1	2840470	2840470	type	True	84.0882	798	1079	95	below_threshold
Phycicoccus jejuensis	strain=NRRL B-24460	GCA_000720925.1	367299	367299	type	True	84.0697	796	1079	95	below_threshold
Phycicoccus flavus	strain=CMS6Z-2	GCA_004025965.2	2502783	2502783	type	True	83.6398	767	1079	95	below_threshold
Phycicoccus duodecadis	strain=DSM 12806	GCA_002846495.1	173053	173053	type	True	82.8728	727	1079	95	below_threshold
Knoellia remsis	strain=ATCC BAA-1496	GCA_003002895.1	407159	407159	type	True	80.4161	566	1079	95	below_threshold
Janibacter melonis	strain=NBRC107855	GCA_020567375.1	262209	262209	type	True	79.9316	551	1079	95	below_threshold
Janibacter endophyticus	strain=YIM B02568	GCA_016888335.1	2806261	2806261	type	True	79.713	491	1079	95	below_threshold
Arsenicicoccus bolidensis	strain=DSM 15745	GCA_000426385.1	229480	229480	type	True	78.5707	426	1079	95	below_threshold
Arsenicicoccus cauae	strain=MKL-02	GCA_009707125.1	2663847	2663847	type	True	78.5591	413	1079	95	below_threshold
Arsenicicoccus dermatophilus	strain=DSM 25571	GCA_022568795.1	1076331	1076331	type	True	78.4383	412	1079	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:55,664] [INFO] DFAST Taxonomy check result was written to GCF_014395645.1_ASM1439564v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:55,665] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:55,665] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:55,665] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9ac652ed-b2d3-4040-9529-cbf23b56ef82/dqc_reference/checkm_data
[2024-01-24 13:18:55,666] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:55,704] [INFO] Task started: CheckM
[2024-01-24 13:18:55,704] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014395645.1_ASM1439564v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014395645.1_ASM1439564v1_genomic.fna/checkm_input GCF_014395645.1_ASM1439564v1_genomic.fna/checkm_result
[2024-01-24 13:19:47,416] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:47,417] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:47,436] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:47,437] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:47,437] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014395645.1_ASM1439564v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:47,438] [INFO] Task started: Blastn
[2024-01-24 13:19:47,438] [INFO] Running command: blastn -query GCF_014395645.1_ASM1439564v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9ac652ed-b2d3-4040-9529-cbf23b56ef82/dqc_reference/reference_markers_gtdb.fasta -out GCF_014395645.1_ASM1439564v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:49,506] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:49,512] [INFO] Selected 10 target genomes.
[2024-01-24 13:19:49,512] [INFO] Target genome list was writen to GCF_014395645.1_ASM1439564v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:49,521] [INFO] Task started: fastANI
[2024-01-24 13:19:49,521] [INFO] Running command: fastANI --query /var/lib/cwl/stgeb67a350-5f7a-45ee-8760-495f01727417/GCF_014395645.1_ASM1439564v1_genomic.fna.gz --refList GCF_014395645.1_ASM1439564v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014395645.1_ASM1439564v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:59,097] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:59,112] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:59,113] [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_011326735.1	s__Phycicoccus endophyticus	99.9757	1044	1079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	99.99	99.99	1.00	1.00	3	conclusive
GCF_016887965.1	s__Phycicoccus sp016887965	84.2669	797	1079	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	84.2015	790	1079	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	84.1049	602	1079	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	84.0818	795	1079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	96.36	95.39	0.88	0.87	4	-
GCF_011383005.1	s__Phycicoccus sp011383005	83.8968	820	1079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004025965.2	s__Phycicoccus flavus	83.5658	774	1079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018139485.1	s__Phycicoccus sp018139485	83.1252	728	1079	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	82.9387	721	1079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428065.1	s__Phycicoccus sp001428065	82.7151	718	1079	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Phycicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:59,115] [INFO] GTDB search result was written to GCF_014395645.1_ASM1439564v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:59,115] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:59,118] [INFO] DFAST_QC result json was written to GCF_014395645.1_ASM1439564v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:59,118] [INFO] DFAST_QC completed!
[2024-01-24 13:19:59,119] [INFO] Total running time: 0h1m27s