[2024-01-24 12:06:34,601] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:34,603] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:34,604] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b073d79-f18f-48c5-a799-71e3990590db/dqc_reference
[2024-01-24 12:06:35,903] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:35,904] [INFO] Task started: Prodigal
[2024-01-24 12:06:35,904] [INFO] Running command: gunzip -c /var/lib/cwl/stgde69670b-0b36-4505-87d6-6c894e329759/GCF_006539885.1_ASM653988v1_genomic.fna.gz | prodigal -d GCF_006539885.1_ASM653988v1_genomic.fna/cds.fna -a GCF_006539885.1_ASM653988v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:44,753] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:44,754] [INFO] Task started: HMMsearch
[2024-01-24 12:06:44,754] [INFO] Running command: hmmsearch --tblout GCF_006539885.1_ASM653988v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b073d79-f18f-48c5-a799-71e3990590db/dqc_reference/reference_markers.hmm GCF_006539885.1_ASM653988v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:45,010] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:45,012] [INFO] Found 6/6 markers.
[2024-01-24 12:06:45,041] [INFO] Query marker FASTA was written to GCF_006539885.1_ASM653988v1_genomic.fna/markers.fasta
[2024-01-24 12:06:45,042] [INFO] Task started: Blastn
[2024-01-24 12:06:45,042] [INFO] Running command: blastn -query GCF_006539885.1_ASM653988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b073d79-f18f-48c5-a799-71e3990590db/dqc_reference/reference_markers.fasta -out GCF_006539885.1_ASM653988v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:46,229] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:46,233] [INFO] Selected 11 target genomes.
[2024-01-24 12:06:46,233] [INFO] Target genome list was writen to GCF_006539885.1_ASM653988v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:46,237] [INFO] Task started: fastANI
[2024-01-24 12:06:46,238] [INFO] Running command: fastANI --query /var/lib/cwl/stgde69670b-0b36-4505-87d6-6c894e329759/GCF_006539885.1_ASM653988v1_genomic.fna.gz --refList GCF_006539885.1_ASM653988v1_genomic.fna/target_genomes.txt --output GCF_006539885.1_ASM653988v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:53,103] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:53,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b073d79-f18f-48c5-a799-71e3990590db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:53,104] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b073d79-f18f-48c5-a799-71e3990590db/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:53,114] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:53,114] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:53,114] [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 varians	strain=NBRC 15358	GCA_006539885.1	1272	1272	type	True	100.0	922	925	95	conclusive
Kocuria tytonicola	strain=DSM 104133	GCA_003687455.1	2055946	2055946	type	True	86.4596	637	925	95	below_threshold
Kocuria rhizophila	strain=TA68	GCA_003667225.1	72000	72000	type	True	85.9605	673	925	95	below_threshold
Kocuria tytonis	strain=442	GCA_003226895.2	2054280	2054280	type	True	85.9148	738	925	95	below_threshold
Kocuria indica	strain=NIO-1021	GCA_003667205.1	1049583	1049583	type	True	84.6685	693	925	95	below_threshold
Kocuria indica	strain=DSM 25126	GCA_002237805.1	1049583	1049583	type	True	84.6186	701	925	95	below_threshold
Arthrobacter stackebrandtii	strain=DSM 16005	GCA_017876675.1	272161	272161	type	True	77.5887	219	925	95	below_threshold
Sinomonas notoginsengisoli	strain=KCTC 29237	GCA_021554725.1	1457311	1457311	type	True	77.5177	237	925	95	below_threshold
Garicola koreensis	strain=DSM 28238	GCA_014195445.1	1262554	1262554	type	True	77.1911	139	925	95	below_threshold
Georgenia yuyongxinii	strain=Z443	GCA_006352065.1	2589797	2589797	type	True	76.8009	234	925	95	below_threshold
Cellulomonas palmilytica	strain=EW123	GCA_021590045.1	2608402	2608402	type	True	76.774	226	925	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:53,117] [INFO] DFAST Taxonomy check result was written to GCF_006539885.1_ASM653988v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:53,118] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:53,118] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:53,118] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b073d79-f18f-48c5-a799-71e3990590db/dqc_reference/checkm_data
[2024-01-24 12:06:53,120] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:53,154] [INFO] Task started: CheckM
[2024-01-24 12:06:53,154] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539885.1_ASM653988v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539885.1_ASM653988v1_genomic.fna/checkm_input GCF_006539885.1_ASM653988v1_genomic.fna/checkm_result
[2024-01-24 12:07:28,892] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:28,893] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:28,913] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:28,913] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:28,914] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539885.1_ASM653988v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:28,914] [INFO] Task started: Blastn
[2024-01-24 12:07:28,914] [INFO] Running command: blastn -query GCF_006539885.1_ASM653988v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b073d79-f18f-48c5-a799-71e3990590db/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539885.1_ASM653988v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:30,961] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:30,966] [INFO] Selected 7 target genomes.
[2024-01-24 12:07:30,966] [INFO] Target genome list was writen to GCF_006539885.1_ASM653988v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:30,973] [INFO] Task started: fastANI
[2024-01-24 12:07:30,973] [INFO] Running command: fastANI --query /var/lib/cwl/stgde69670b-0b36-4505-87d6-6c894e329759/GCF_006539885.1_ASM653988v1_genomic.fna.gz --refList GCF_006539885.1_ASM653988v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539885.1_ASM653988v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:35,831] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:35,843] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:35,843] [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_006539885.1	s__Kocuria varians	100.0	922	925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	99.47	99.47	0.94	0.94	2	conclusive
GCF_007681555.1	s__Kocuria salsicia	88.0919	795	925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.09	95.42	0.92	0.89	8	-
GCF_000010285.1	s__Kocuria rhizophila_A	86.5692	749	925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.71	97.98	0.95	0.89	9	-
GCF_003687455.1	s__Kocuria tytonicola	86.4572	637	925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	98.95	98.95	0.94	0.94	2	-
GCF_003667225.1	s__Kocuria rhizophila	85.9945	671	925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	97.80	97.11	0.92	0.85	19	-
GCF_003226895.2	s__Kocuria tytonis	85.905	738	925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014652975.1	s__Kocuria marina	84.5202	717	925	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Micrococcaceae;g__Kocuria	95.811	98.16	96.52	0.91	0.86	16	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:35,845] [INFO] GTDB search result was written to GCF_006539885.1_ASM653988v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:35,845] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:35,848] [INFO] DFAST_QC result json was written to GCF_006539885.1_ASM653988v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:35,848] [INFO] DFAST_QC completed!
[2024-01-24 12:07:35,848] [INFO] Total running time: 0h1m1s