[2024-01-24 12:15:04,095] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:04,097] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:04,097] [INFO] DQC Reference Directory: /var/lib/cwl/stg55d7f0a0-cc42-400b-8ad7-0b45f9ccc963/dqc_reference
[2024-01-24 12:15:05,437] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:05,438] [INFO] Task started: Prodigal
[2024-01-24 12:15:05,438] [INFO] Running command: gunzip -c /var/lib/cwl/stg81d96ceb-88bc-4ab4-8d2b-b8e6bc5f65a3/GCF_006476065.1_ASM647606v1_genomic.fna.gz | prodigal -d GCF_006476065.1_ASM647606v1_genomic.fna/cds.fna -a GCF_006476065.1_ASM647606v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:12,979] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:12,980] [INFO] Task started: HMMsearch
[2024-01-24 12:15:12,980] [INFO] Running command: hmmsearch --tblout GCF_006476065.1_ASM647606v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55d7f0a0-cc42-400b-8ad7-0b45f9ccc963/dqc_reference/reference_markers.hmm GCF_006476065.1_ASM647606v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:13,250] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:13,252] [INFO] Found 6/6 markers.
[2024-01-24 12:15:13,277] [INFO] Query marker FASTA was written to GCF_006476065.1_ASM647606v1_genomic.fna/markers.fasta
[2024-01-24 12:15:13,277] [INFO] Task started: Blastn
[2024-01-24 12:15:13,278] [INFO] Running command: blastn -query GCF_006476065.1_ASM647606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55d7f0a0-cc42-400b-8ad7-0b45f9ccc963/dqc_reference/reference_markers.fasta -out GCF_006476065.1_ASM647606v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:14,394] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:14,399] [INFO] Selected 18 target genomes.
[2024-01-24 12:15:14,399] [INFO] Target genome list was writen to GCF_006476065.1_ASM647606v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:14,410] [INFO] Task started: fastANI
[2024-01-24 12:15:14,410] [INFO] Running command: fastANI --query /var/lib/cwl/stg81d96ceb-88bc-4ab4-8d2b-b8e6bc5f65a3/GCF_006476065.1_ASM647606v1_genomic.fna.gz --refList GCF_006476065.1_ASM647606v1_genomic.fna/target_genomes.txt --output GCF_006476065.1_ASM647606v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:27,216] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:27,217] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55d7f0a0-cc42-400b-8ad7-0b45f9ccc963/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:27,217] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55d7f0a0-cc42-400b-8ad7-0b45f9ccc963/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:27,236] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:15:27,236] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:15:27,236] [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
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	100.0	785	785	95	conclusive
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	84.8358	601	785	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	83.5939	529	785	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	83.0683	527	785	95	below_threshold
Lysobacter arseniciresistens	strain=ZS79	GCA_000768335.1	1385522	1385522	type	True	83.0668	550	785	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	82.9782	565	785	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	82.9685	566	785	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	82.9149	563	785	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	82.8195	546	785	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	82.7825	532	785	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	82.6405	515	785	95	below_threshold
Luteimonas granuli	strain=Gr-4	GCA_007795095.1	1176533	1176533	type	True	82.546	526	785	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	82.3316	561	785	95	below_threshold
Lysobacter defluvii	strain=IMMIB APB-9	GCA_000769985.1	391738	391738	type	True	82.2559	408	785	95	below_threshold
Lysobacter defluvii	strain=DSM 18482	GCA_000423325.1	391738	391738	type	True	82.1671	485	785	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	82.0502	514	785	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	81.9751	555	785	95	below_threshold
Lysobacter chinensis	strain=TLK-CK17	GCA_021725675.1	2912247	2912247	type	True	81.6087	531	785	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:27,239] [INFO] DFAST Taxonomy check result was written to GCF_006476065.1_ASM647606v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:27,240] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:27,240] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:27,241] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55d7f0a0-cc42-400b-8ad7-0b45f9ccc963/dqc_reference/checkm_data
[2024-01-24 12:15:27,242] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:27,275] [INFO] Task started: CheckM
[2024-01-24 12:15:27,275] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006476065.1_ASM647606v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006476065.1_ASM647606v1_genomic.fna/checkm_input GCF_006476065.1_ASM647606v1_genomic.fna/checkm_result
[2024-01-24 12:15:56,544] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:56,546] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:56,569] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:56,569] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:56,570] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006476065.1_ASM647606v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:56,570] [INFO] Task started: Blastn
[2024-01-24 12:15:56,570] [INFO] Running command: blastn -query GCF_006476065.1_ASM647606v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55d7f0a0-cc42-400b-8ad7-0b45f9ccc963/dqc_reference/reference_markers_gtdb.fasta -out GCF_006476065.1_ASM647606v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:58,729] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:58,734] [INFO] Selected 19 target genomes.
[2024-01-24 12:15:58,734] [INFO] Target genome list was writen to GCF_006476065.1_ASM647606v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:58,750] [INFO] Task started: fastANI
[2024-01-24 12:15:58,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg81d96ceb-88bc-4ab4-8d2b-b8e6bc5f65a3/GCF_006476065.1_ASM647606v1_genomic.fna.gz --refList GCF_006476065.1_ASM647606v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006476065.1_ASM647606v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:11,947] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:11,969] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:11,969] [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_006476065.1	s__Luteimonas_B lumbrici	100.0	785	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004297225.1	s__Luteimonas_B sp004297225	85.3439	545	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003416885.1	s__Luteimonas_B sp003416885	84.8592	599	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008033445.1	s__Vulcaniibacterium_B gelatinicum	83.569	530	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Vulcaniibacterium_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859325.1	s__Luteimonas marina	83.0085	563	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422305.1	s__Luteimonas mephitis	82.9597	567	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014652935.1	s__Luteimonas padinae	82.9443	561	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014836665.1	s__Luteimonas sp014836665	82.8329	545	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000472505.1	s__Luteimonas sp000472505	82.6677	543	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.95	99.95	0.99	0.99	2	-
GCF_004352845.1	s__Luteimonas terricola	82.622	516	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007795095.1	s__Luteimonas granuli	82.5918	523	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016615955.1	s__Luteimonas sp016615955	82.4891	520	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.39	98.78	0.97	0.95	3	-
GCF_007859305.1	s__Luteimonas wenzhouensis	82.3316	561	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.47	99.47	0.98	0.98	2	-
GCA_013362405.1	s__JABFWF01 sp013362405	82.3314	426	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__JABFWF01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011320095.1	s__Luteimonas_B telluris	82.2359	497	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001442515.1	s__Lysobacter enzymogenes_B	82.233	549	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Lysobacter	95.0	97.93	95.70	0.94	0.91	4	-
GCF_010211755.1	s__Pseudoxanthomonas_A sangjuensis	82.1405	512	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013425525.1	s__Luteimonas sp013425525	81.9562	557	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001683895.1	s__Luteimonas sp001683895	81.0702	456	785	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:11,971] [INFO] GTDB search result was written to GCF_006476065.1_ASM647606v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:11,972] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:11,976] [INFO] DFAST_QC result json was written to GCF_006476065.1_ASM647606v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:11,977] [INFO] DFAST_QC completed!
[2024-01-24 12:16:11,977] [INFO] Total running time: 0h1m8s