[2024-01-24 13:21:57,423] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:21:57,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:21:57,424] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3c1736e-3674-49aa-a784-386e6c4abd05/dqc_reference
[2024-01-24 13:21:58,681] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:21:58,682] [INFO] Task started: Prodigal
[2024-01-24 13:21:58,682] [INFO] Running command: gunzip -c /var/lib/cwl/stgb19430a1-7cbb-402e-8115-cb0164421709/GCF_006337105.1_ASM633710v1_genomic.fna.gz | prodigal -d GCF_006337105.1_ASM633710v1_genomic.fna/cds.fna -a GCF_006337105.1_ASM633710v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:08,303] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:08,304] [INFO] Task started: HMMsearch
[2024-01-24 13:22:08,304] [INFO] Running command: hmmsearch --tblout GCF_006337105.1_ASM633710v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3c1736e-3674-49aa-a784-386e6c4abd05/dqc_reference/reference_markers.hmm GCF_006337105.1_ASM633710v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:08,591] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:08,593] [INFO] Found 6/6 markers.
[2024-01-24 13:22:08,620] [INFO] Query marker FASTA was written to GCF_006337105.1_ASM633710v1_genomic.fna/markers.fasta
[2024-01-24 13:22:08,620] [INFO] Task started: Blastn
[2024-01-24 13:22:08,620] [INFO] Running command: blastn -query GCF_006337105.1_ASM633710v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3c1736e-3674-49aa-a784-386e6c4abd05/dqc_reference/reference_markers.fasta -out GCF_006337105.1_ASM633710v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:09,747] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:09,750] [INFO] Selected 15 target genomes.
[2024-01-24 13:22:09,751] [INFO] Target genome list was writen to GCF_006337105.1_ASM633710v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:09,754] [INFO] Task started: fastANI
[2024-01-24 13:22:09,754] [INFO] Running command: fastANI --query /var/lib/cwl/stgb19430a1-7cbb-402e-8115-cb0164421709/GCF_006337105.1_ASM633710v1_genomic.fna.gz --refList GCF_006337105.1_ASM633710v1_genomic.fna/target_genomes.txt --output GCF_006337105.1_ASM633710v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:23,623] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:23,623] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3c1736e-3674-49aa-a784-386e6c4abd05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:23,623] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3c1736e-3674-49aa-a784-386e6c4abd05/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:23,636] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:23,636] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:23,636] [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
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	100.0	1001	1001	95	conclusive
Thermomonas carbonis	strain=KCTC 42013	GCA_014652775.1	1463158	1463158	type	True	85.0744	760	1001	95	below_threshold
Thermomonas carbonis	strain=KCTC 42013	GCA_014396975.1	1463158	1463158	type	True	85.0639	756	1001	95	below_threshold
Thermomonas fusca	strain=DSM 15424	GCA_000423885.1	215690	215690	type	True	84.5216	673	1001	95	below_threshold
Thermomonas haemolytica	strain=LMG 19653	GCA_006352395.1	141949	141949	type	True	84.2525	600	1001	95	below_threshold
Thermomonas haemolytica	strain=DSM 13605	GCA_004346265.1	141949	141949	type	True	84.1517	620	1001	95	below_threshold
Vulcaniibacterium gelatinicum	strain=R-5-52-3	GCA_008033445.1	2598725	2598725	type	True	82.6185	576	1001	95	below_threshold
Pseudoxanthomonas helianthi	strain=110414	GCA_017939625.1	1453541	1453541	type	True	82.3431	635	1001	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	82.2585	604	1001	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	82.0516	632	1001	95	below_threshold
Luteimonas cucumeris	strain=CGMCC 1.10821	GCA_007830035.1	985012	985012	type	True	81.5449	608	1001	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	81.5226	628	1001	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	81.4605	631	1001	95	below_threshold
Luteimonas panaciterrae	strain=Gsoil 068	GCA_020511115.1	363885	363885	type	True	80.8484	550	1001	95	below_threshold
Luteimonas terrae	strain=THG-MD21	GCA_004358165.1	1530191	1530191	type	True	80.8151	545	1001	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:23,638] [INFO] DFAST Taxonomy check result was written to GCF_006337105.1_ASM633710v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:23,640] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:23,640] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:23,641] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3c1736e-3674-49aa-a784-386e6c4abd05/dqc_reference/checkm_data
[2024-01-24 13:22:23,642] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:23,680] [INFO] Task started: CheckM
[2024-01-24 13:22:23,680] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006337105.1_ASM633710v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006337105.1_ASM633710v1_genomic.fna/checkm_input GCF_006337105.1_ASM633710v1_genomic.fna/checkm_result
[2024-01-24 13:23:08,515] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:08,518] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:08,545] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:08,545] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:08,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006337105.1_ASM633710v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:08,547] [INFO] Task started: Blastn
[2024-01-24 13:23:08,547] [INFO] Running command: blastn -query GCF_006337105.1_ASM633710v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3c1736e-3674-49aa-a784-386e6c4abd05/dqc_reference/reference_markers_gtdb.fasta -out GCF_006337105.1_ASM633710v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:10,625] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:10,629] [INFO] Selected 11 target genomes.
[2024-01-24 13:23:10,630] [INFO] Target genome list was writen to GCF_006337105.1_ASM633710v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:10,651] [INFO] Task started: fastANI
[2024-01-24 13:23:10,651] [INFO] Running command: fastANI --query /var/lib/cwl/stgb19430a1-7cbb-402e-8115-cb0164421709/GCF_006337105.1_ASM633710v1_genomic.fna.gz --refList GCF_006337105.1_ASM633710v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006337105.1_ASM633710v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:19,012] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:19,022] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:19,023] [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_006337105.1	s__Thermomonas sp006337105	100.0	1001	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011302915.1	s__Thermomonas sp011302915	87.3105	763	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016720345.1	s__Thermomonas sp016720345	87.2033	727	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.48	99.08	0.97	0.93	11	-
GCF_014395425.1	s__Thermomonas brevis	85.3414	728	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017302075.1	s__Thermomonas sp017302075	85.3391	621	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014396975.1	s__Thermomonas carbonis	85.0507	760	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	1.00	1.00	2	-
GCA_017302095.1	s__Thermomonas sp017302095	85.0429	461	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423885.1	s__Thermomonas fusca	84.4886	675	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	96.57	96.57	0.92	0.92	2	-
GCF_004346265.1	s__Thermomonas haemolytica	84.1442	621	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Thermomonas	95.0	99.99	99.99	0.99	0.99	3	-
GCA_005502915.1	s__SCMT01 sp005502915	81.8761	613	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__SCMT01	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004284655.1	s__Pseudoxanthomonas_A spadix_A	81.0137	552	1001	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas_A	95.0	98.46	98.41	0.91	0.91	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:19,025] [INFO] GTDB search result was written to GCF_006337105.1_ASM633710v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:19,025] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:19,029] [INFO] DFAST_QC result json was written to GCF_006337105.1_ASM633710v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:19,029] [INFO] DFAST_QC completed!
[2024-01-24 13:23:19,029] [INFO] Total running time: 0h1m22s