[2024-01-24 11:19:53,710] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:53,711] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:53,712] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7163fd2-24c1-4930-9a6c-2a7f7d34f397/dqc_reference
[2024-01-24 11:19:55,151] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:55,154] [INFO] Task started: Prodigal
[2024-01-24 11:19:55,154] [INFO] Running command: gunzip -c /var/lib/cwl/stgb4e2ed3b-2aab-4024-87e1-44c83e7f0c0b/GCF_013425765.1_ASM1342576v1_genomic.fna.gz | prodigal -d GCF_013425765.1_ASM1342576v1_genomic.fna/cds.fna -a GCF_013425765.1_ASM1342576v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:06,577] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:06,577] [INFO] Task started: HMMsearch
[2024-01-24 11:20:06,578] [INFO] Running command: hmmsearch --tblout GCF_013425765.1_ASM1342576v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7163fd2-24c1-4930-9a6c-2a7f7d34f397/dqc_reference/reference_markers.hmm GCF_013425765.1_ASM1342576v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:06,848] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:06,849] [INFO] Found 6/6 markers.
[2024-01-24 11:20:06,881] [INFO] Query marker FASTA was written to GCF_013425765.1_ASM1342576v1_genomic.fna/markers.fasta
[2024-01-24 11:20:06,882] [INFO] Task started: Blastn
[2024-01-24 11:20:06,882] [INFO] Running command: blastn -query GCF_013425765.1_ASM1342576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7163fd2-24c1-4930-9a6c-2a7f7d34f397/dqc_reference/reference_markers.fasta -out GCF_013425765.1_ASM1342576v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:07,953] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:07,956] [INFO] Selected 14 target genomes.
[2024-01-24 11:20:07,957] [INFO] Target genome list was writen to GCF_013425765.1_ASM1342576v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:07,962] [INFO] Task started: fastANI
[2024-01-24 11:20:07,963] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4e2ed3b-2aab-4024-87e1-44c83e7f0c0b/GCF_013425765.1_ASM1342576v1_genomic.fna.gz --refList GCF_013425765.1_ASM1342576v1_genomic.fna/target_genomes.txt --output GCF_013425765.1_ASM1342576v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:20,136] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:20,137] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7163fd2-24c1-4930-9a6c-2a7f7d34f397/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:20,137] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7163fd2-24c1-4930-9a6c-2a7f7d34f397/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:20,155] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:20:20,155] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:20:20,156] [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 deserti	strain=SJ-16	GCA_013425765.1	2752306	2752306	type	True	100.0	1231	1233	95	conclusive
Luteimonas fraxinea	strain=D4P002	GCA_021233355.1	2901869	2901869	type	True	84.0636	838	1233	95	below_threshold
Luteimonas terrae	strain=THG-MD21	GCA_004358165.1	1530191	1530191	type	True	84.0535	838	1233	95	below_threshold
Luteimonas chenhongjianii	strain=100111	GCA_002327105.1	2006110	2006110	type	True	83.8317	797	1233	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	81.8275	681	1233	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	81.0777	609	1233	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	81.0768	698	1233	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	81.0558	711	1233	95	below_threshold
Luteimonas terricola	strain=CGMCC 1.8985	GCA_014645675.1	645597	645597	type	True	81.0396	544	1233	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	81.0344	595	1233	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	81.0031	553	1233	95	below_threshold
Luteimonas granuli	strain=Gr-4	GCA_007795095.1	1176533	1176533	type	True	80.6555	549	1233	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	80.4829	673	1233	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	80.3099	511	1233	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:20,158] [INFO] DFAST Taxonomy check result was written to GCF_013425765.1_ASM1342576v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:20,158] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:20,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:20,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7163fd2-24c1-4930-9a6c-2a7f7d34f397/dqc_reference/checkm_data
[2024-01-24 11:20:20,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:20,207] [INFO] Task started: CheckM
[2024-01-24 11:20:20,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013425765.1_ASM1342576v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013425765.1_ASM1342576v1_genomic.fna/checkm_input GCF_013425765.1_ASM1342576v1_genomic.fna/checkm_result
[2024-01-24 11:21:08,453] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:08,455] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:08,473] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:08,473] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:08,474] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013425765.1_ASM1342576v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:08,474] [INFO] Task started: Blastn
[2024-01-24 11:21:08,474] [INFO] Running command: blastn -query GCF_013425765.1_ASM1342576v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7163fd2-24c1-4930-9a6c-2a7f7d34f397/dqc_reference/reference_markers_gtdb.fasta -out GCF_013425765.1_ASM1342576v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:10,613] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:10,618] [INFO] Selected 12 target genomes.
[2024-01-24 11:21:10,618] [INFO] Target genome list was writen to GCF_013425765.1_ASM1342576v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:10,633] [INFO] Task started: fastANI
[2024-01-24 11:21:10,634] [INFO] Running command: fastANI --query /var/lib/cwl/stgb4e2ed3b-2aab-4024-87e1-44c83e7f0c0b/GCF_013425765.1_ASM1342576v1_genomic.fna.gz --refList GCF_013425765.1_ASM1342576v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013425765.1_ASM1342576v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:21,223] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:21,247] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:21,248] [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_013425765.1	s__Luteimonas sp013425765	100.0	1230	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002324875.1	s__Luteimonas sp002324875	85.7183	918	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_902506295.1	s__Luteimonas sp902506295	84.4878	823	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002307375.1	s__Luteimonas sp002307375	84.094	834	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004358165.1	s__Luteimonas terrae	84.0245	841	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	96.65	96.65	0.95	0.95	2	-
GCF_002849595.1	s__Luteimonas sp002849595	83.851	863	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.97	99.97	0.99	0.99	2	-
GCF_002327105.1	s__Luteimonas chenhongjianii	83.8309	794	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	98.75	98.75	0.95	0.95	2	-
GCF_001014645.1	s__Luteimonas sp001014645	83.7856	825	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014192745.1	s__Luteimonas sp014192745	82.9932	807	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002240395.1	s__Luteimonas citri_A	82.8105	785	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352845.1	s__Luteimonas terricola	80.9883	553	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_011320095.1	s__Luteimonas_B telluris	79.9836	455	1233	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:21,250] [INFO] GTDB search result was written to GCF_013425765.1_ASM1342576v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:21,250] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:21,255] [INFO] DFAST_QC result json was written to GCF_013425765.1_ASM1342576v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:21,256] [INFO] DFAST_QC completed!
[2024-01-24 11:21:21,256] [INFO] Total running time: 0h1m28s