[2024-01-24 12:21:43,543] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:43,544] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:43,545] [INFO] DQC Reference Directory: /var/lib/cwl/stg343a37ca-10ed-4c6d-921a-77739019e114/dqc_reference
[2024-01-24 12:21:44,910] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:44,911] [INFO] Task started: Prodigal
[2024-01-24 12:21:44,911] [INFO] Running command: gunzip -c /var/lib/cwl/stg594e960f-eee5-4fa2-983e-0236cb9d542f/GCF_001482365.1_ASM148236v1_genomic.fna.gz | prodigal -d GCF_001482365.1_ASM148236v1_genomic.fna/cds.fna -a GCF_001482365.1_ASM148236v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:55,028] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:55,029] [INFO] Task started: HMMsearch
[2024-01-24 12:21:55,029] [INFO] Running command: hmmsearch --tblout GCF_001482365.1_ASM148236v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg343a37ca-10ed-4c6d-921a-77739019e114/dqc_reference/reference_markers.hmm GCF_001482365.1_ASM148236v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:55,311] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:55,313] [INFO] Found 6/6 markers.
[2024-01-24 12:21:55,350] [INFO] Query marker FASTA was written to GCF_001482365.1_ASM148236v1_genomic.fna/markers.fasta
[2024-01-24 12:21:55,351] [INFO] Task started: Blastn
[2024-01-24 12:21:55,351] [INFO] Running command: blastn -query GCF_001482365.1_ASM148236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg343a37ca-10ed-4c6d-921a-77739019e114/dqc_reference/reference_markers.fasta -out GCF_001482365.1_ASM148236v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:56,674] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:56,677] [INFO] Selected 12 target genomes.
[2024-01-24 12:21:56,678] [INFO] Target genome list was writen to GCF_001482365.1_ASM148236v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:56,680] [INFO] Task started: fastANI
[2024-01-24 12:21:56,680] [INFO] Running command: fastANI --query /var/lib/cwl/stg594e960f-eee5-4fa2-983e-0236cb9d542f/GCF_001482365.1_ASM148236v1_genomic.fna.gz --refList GCF_001482365.1_ASM148236v1_genomic.fna/target_genomes.txt --output GCF_001482365.1_ASM148236v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:07,545] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:07,545] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg343a37ca-10ed-4c6d-921a-77739019e114/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:07,546] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg343a37ca-10ed-4c6d-921a-77739019e114/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:07,557] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:07,558] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:07,558] [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
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	100.0	1210	1210	95	conclusive
Kocuria rosea	strain=DSM 20447	GCA_006717035.1	1275	1275	suspected-type	True	85.5112	875	1210	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_006094695.1	1275	1275	suspected-type	True	85.4764	897	1210	95	below_threshold
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	85.4584	902	1210	95	below_threshold
Kocuria rosea	strain=ATCC 186	GCA_003124035.1	1275	1275	suspected-type	True	85.3881	897	1210	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	85.3855	858	1210	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	85.0946	879	1210	95	below_threshold
Micrococcus luteus	strain=ATCC 4698	GCA_003417425.1	1270	1270	type	True	79.0872	320	1210	95	below_threshold
Arthrobacter mobilis	strain=E918	GCA_012395835.1	2724944	2724944	type	True	78.212	412	1210	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_018622995.1	2817475	2817475	type	True	77.9957	300	1210	95	below_threshold
Arthrobacter jiangjiafuii	strain=zg-ZUI227	GCA_017898065.1	2817475	2817475	type	True	77.6875	292	1210	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.9442	323	1210	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:07,561] [INFO] DFAST Taxonomy check result was written to GCF_001482365.1_ASM148236v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:07,562] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:07,562] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:07,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg343a37ca-10ed-4c6d-921a-77739019e114/dqc_reference/checkm_data
[2024-01-24 12:22:07,564] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:07,602] [INFO] Task started: CheckM
[2024-01-24 12:22:07,602] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001482365.1_ASM148236v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001482365.1_ASM148236v1_genomic.fna/checkm_input GCF_001482365.1_ASM148236v1_genomic.fna/checkm_result
[2024-01-24 12:23:09,748] [INFO] Task succeeded: CheckM
[2024-01-24 12:23:09,749] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:23:09,772] [INFO] ===== Completeness check finished =====
[2024-01-24 12:23:09,773] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:23:09,773] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001482365.1_ASM148236v1_genomic.fna/markers.fasta)
[2024-01-24 12:23:09,773] [INFO] Task started: Blastn
[2024-01-24 12:23:09,774] [INFO] Running command: blastn -query GCF_001482365.1_ASM148236v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg343a37ca-10ed-4c6d-921a-77739019e114/dqc_reference/reference_markers_gtdb.fasta -out GCF_001482365.1_ASM148236v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:11,878] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:11,882] [INFO] Selected 5 target genomes.
[2024-01-24 12:23:11,883] [INFO] Target genome list was writen to GCF_001482365.1_ASM148236v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:23:11,885] [INFO] Task started: fastANI
[2024-01-24 12:23:11,886] [INFO] Running command: fastANI --query /var/lib/cwl/stg594e960f-eee5-4fa2-983e-0236cb9d542f/GCF_001482365.1_ASM148236v1_genomic.fna.gz --refList GCF_001482365.1_ASM148236v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001482365.1_ASM148236v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:23:17,739] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:17,745] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:23:17,745] [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_001482365.1	s__Kocuria flava	100.0	1209	1210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.78	97.61	0.93	0.87	4	conclusive
GCF_001483755.1	s__Kocuria polaris_A	85.5339	887	1210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001580365.1	s__Kocuria turfanensis	85.4552	906	1210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	-
GCF_006094695.1	s__Kocuria rosea	85.4452	899	1210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.85	97.54	0.92	0.85	16	-
GCF_014636775.1	s__Kocuria dechangensis	85.117	876	1210	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:23:17,747] [INFO] GTDB search result was written to GCF_001482365.1_ASM148236v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:23:17,747] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:23:17,750] [INFO] DFAST_QC result json was written to GCF_001482365.1_ASM148236v1_genomic.fna/dqc_result.json
[2024-01-24 12:23:17,751] [INFO] DFAST_QC completed!
[2024-01-24 12:23:17,751] [INFO] Total running time: 0h1m34s