[2024-01-24 14:14:46,980] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:46,986] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:46,988] [INFO] DQC Reference Directory: /var/lib/cwl/stgaae1cea3-d2bc-4b58-a867-2b172e5be006/dqc_reference
[2024-01-24 14:14:49,420] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:49,423] [INFO] Task started: Prodigal
[2024-01-24 14:14:49,424] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ea62d94-d588-4635-a621-bc23922faaca/GCF_006094695.1_ASM609469v1_genomic.fna.gz | prodigal -d GCF_006094695.1_ASM609469v1_genomic.fna/cds.fna -a GCF_006094695.1_ASM609469v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:01,610] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:01,610] [INFO] Task started: HMMsearch
[2024-01-24 14:15:01,611] [INFO] Running command: hmmsearch --tblout GCF_006094695.1_ASM609469v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaae1cea3-d2bc-4b58-a867-2b172e5be006/dqc_reference/reference_markers.hmm GCF_006094695.1_ASM609469v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:01,909] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:01,911] [INFO] Found 6/6 markers.
[2024-01-24 14:15:01,948] [INFO] Query marker FASTA was written to GCF_006094695.1_ASM609469v1_genomic.fna/markers.fasta
[2024-01-24 14:15:01,949] [INFO] Task started: Blastn
[2024-01-24 14:15:01,949] [INFO] Running command: blastn -query GCF_006094695.1_ASM609469v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaae1cea3-d2bc-4b58-a867-2b172e5be006/dqc_reference/reference_markers.fasta -out GCF_006094695.1_ASM609469v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:03,347] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:03,353] [INFO] Selected 12 target genomes.
[2024-01-24 14:15:03,353] [INFO] Target genome list was writen to GCF_006094695.1_ASM609469v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:03,364] [INFO] Task started: fastANI
[2024-01-24 14:15:03,364] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea62d94-d588-4635-a621-bc23922faaca/GCF_006094695.1_ASM609469v1_genomic.fna.gz --refList GCF_006094695.1_ASM609469v1_genomic.fna/target_genomes.txt --output GCF_006094695.1_ASM609469v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:14,953] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:14,953] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaae1cea3-d2bc-4b58-a867-2b172e5be006/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:14,954] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaae1cea3-d2bc-4b58-a867-2b172e5be006/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:14,971] [INFO] Found 12 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:15:14,972] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:15:14,972] [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 rosea	strain=ATCC 186	GCA_006094695.1	1275	1275	suspected-type	True	100.0	1314	1315	95	conclusive
Kocuria rosea	strain=DSM 20447	GCA_006717035.1	1275	1275	suspected-type	True	99.9894	1277	1315	95	conclusive
Kocuria rosea	strain=ATCC 186	GCA_003124035.1	1275	1275	suspected-type	True	99.9817	1272	1315	95	conclusive
Kocuria turfanensis	strain=HO-9042	GCA_001580365.1	388357	388357	type	True	88.6675	1014	1315	95	below_threshold
Kocuria sediminis	strain=JCM 17929	GCA_009735315.1	1038857	1038857	type	True	88.2004	982	1315	95	below_threshold
Kocuria dechangensis	strain=CGMCC 1.12187	GCA_014636775.1	1176249	1176249	type	True	86.1841	934	1315	95	below_threshold
Kocuria flava	strain=HO-9041	GCA_001482365.1	446860	446860	type	True	85.4521	899	1315	95	below_threshold
Micrococcus flavus	strain=DSM 19079	GCA_022348285.1	384602	384602	type	True	78.5447	375	1315	95	below_threshold
Arthrobacter sedimenti	strain=MIC A30	GCA_011750795.2	2694931	2694931	type	True	78.0616	331	1315	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	77.7189	314	1315	95	below_threshold
Arthrobacter sunyaminii	strain=zg-ZUI122	GCA_018866305.1	2816859	2816859	type	True	77.581	253	1315	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	77.217	304	1315	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:15:14,974] [INFO] DFAST Taxonomy check result was written to GCF_006094695.1_ASM609469v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:14,975] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:14,975] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:14,976] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaae1cea3-d2bc-4b58-a867-2b172e5be006/dqc_reference/checkm_data
[2024-01-24 14:15:14,977] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:15,017] [INFO] Task started: CheckM
[2024-01-24 14:15:15,017] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006094695.1_ASM609469v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006094695.1_ASM609469v1_genomic.fna/checkm_input GCF_006094695.1_ASM609469v1_genomic.fna/checkm_result
[2024-01-24 14:16:24,431] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:24,432] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:24,455] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:24,455] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:24,456] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006094695.1_ASM609469v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:24,456] [INFO] Task started: Blastn
[2024-01-24 14:16:24,456] [INFO] Running command: blastn -query GCF_006094695.1_ASM609469v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaae1cea3-d2bc-4b58-a867-2b172e5be006/dqc_reference/reference_markers_gtdb.fasta -out GCF_006094695.1_ASM609469v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:26,513] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:26,517] [INFO] Selected 5 target genomes.
[2024-01-24 14:16:26,517] [INFO] Target genome list was writen to GCF_006094695.1_ASM609469v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:26,524] [INFO] Task started: fastANI
[2024-01-24 14:16:26,524] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea62d94-d588-4635-a621-bc23922faaca/GCF_006094695.1_ASM609469v1_genomic.fna.gz --refList GCF_006094695.1_ASM609469v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006094695.1_ASM609469v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:16:32,873] [INFO] Task succeeded: fastANI
[2024-01-24 14:16:32,881] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:16:32,881] [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_006094695.1	s__Kocuria rosea	100.0	1314	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.85	97.54	0.92	0.85	16	conclusive
GCF_001483755.1	s__Kocuria polaris_A	92.3559	1028	1315	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	88.6465	1015	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	96.38	95.01	0.87	0.80	5	-
GCF_014636775.1	s__Kocuria dechangensis	86.1778	935	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001482365.1	s__Kocuria flava	85.4514	904	1315	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.78	97.61	0.93	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 14:16:32,883] [INFO] GTDB search result was written to GCF_006094695.1_ASM609469v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:16:32,883] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:16:32,886] [INFO] DFAST_QC result json was written to GCF_006094695.1_ASM609469v1_genomic.fna/dqc_result.json
[2024-01-24 14:16:32,886] [INFO] DFAST_QC completed!
[2024-01-24 14:16:32,886] [INFO] Total running time: 0h1m46s