[2024-01-24 13:31:33,610] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:31:33,612] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:31:33,613] [INFO] DQC Reference Directory: /var/lib/cwl/stgec4b6716-6ce6-41d0-b0a2-edcd6d29980e/dqc_reference
[2024-01-24 13:31:34,887] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:31:34,888] [INFO] Task started: Prodigal
[2024-01-24 13:31:34,888] [INFO] Running command: gunzip -c /var/lib/cwl/stgae983e62-b558-4c99-a4d3-537dbd561397/GCF_013425525.1_ASM1342552v1_genomic.fna.gz | prodigal -d GCF_013425525.1_ASM1342552v1_genomic.fna/cds.fna -a GCF_013425525.1_ASM1342552v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:31:47,504] [INFO] Task succeeded: Prodigal
[2024-01-24 13:31:47,505] [INFO] Task started: HMMsearch
[2024-01-24 13:31:47,505] [INFO] Running command: hmmsearch --tblout GCF_013425525.1_ASM1342552v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec4b6716-6ce6-41d0-b0a2-edcd6d29980e/dqc_reference/reference_markers.hmm GCF_013425525.1_ASM1342552v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:31:47,826] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:31:47,830] [INFO] Found 6/6 markers.
[2024-01-24 13:31:47,867] [INFO] Query marker FASTA was written to GCF_013425525.1_ASM1342552v1_genomic.fna/markers.fasta
[2024-01-24 13:31:47,867] [INFO] Task started: Blastn
[2024-01-24 13:31:47,867] [INFO] Running command: blastn -query GCF_013425525.1_ASM1342552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec4b6716-6ce6-41d0-b0a2-edcd6d29980e/dqc_reference/reference_markers.fasta -out GCF_013425525.1_ASM1342552v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:31:48,890] [INFO] Task succeeded: Blastn
[2024-01-24 13:31:48,896] [INFO] Selected 22 target genomes.
[2024-01-24 13:31:48,897] [INFO] Target genome list was writen to GCF_013425525.1_ASM1342552v1_genomic.fna/target_genomes.txt
[2024-01-24 13:31:48,905] [INFO] Task started: fastANI
[2024-01-24 13:31:48,905] [INFO] Running command: fastANI --query /var/lib/cwl/stgae983e62-b558-4c99-a4d3-537dbd561397/GCF_013425525.1_ASM1342552v1_genomic.fna.gz --refList GCF_013425525.1_ASM1342552v1_genomic.fna/target_genomes.txt --output GCF_013425525.1_ASM1342552v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:08,222] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:08,223] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec4b6716-6ce6-41d0-b0a2-edcd6d29980e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:08,223] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec4b6716-6ce6-41d0-b0a2-edcd6d29980e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:08,240] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:08,240] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:08,240] [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 salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	100.0	1456	1462	95	conclusive
Luteimonas huabeiensis	strain=HB2	GCA_000559025.1	1244513	1244513	type	True	83.1169	805	1462	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	82.468	799	1462	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	82.0969	622	1462	95	below_threshold
Luteimonas arsenica	strain=26-35	GCA_004352825.1	1586242	1586242	type	True	82.0666	673	1462	95	below_threshold
Luteimonas wenzhouensis	strain=YD-1	GCA_007859305.1	2599615	2599615	type	True	82.0131	749	1462	95	below_threshold
Luteimonas yindakuii	strain=S-1072	GCA_004803715.2	2565782	2565782	type	True	81.9809	696	1462	95	below_threshold
Luteimonas colneyensis	strain=Sa2BVA3	GCA_014836665.1	2762230	2762230	type	True	81.9535	675	1462	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	81.8995	731	1462	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	81.8707	540	1462	95	below_threshold
Luteimonas mephitis	strain=DSM 12574	GCA_000422305.1	83615	83615	type	True	81.8404	675	1462	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	81.8364	853	1462	95	below_threshold
Luteimonas viscosa	strain=XBU10	GCA_008244685.1	1132694	1132694	type	True	81.7782	861	1462	95	below_threshold
Luteimonas terricola	strain=BZ92r	GCA_004352845.1	645597	645597	type	True	81.7377	637	1462	95	below_threshold
Luteimonas terricola	strain=CGMCC 1.8985	GCA_014645675.1	645597	645597	type	True	81.7309	643	1462	95	below_threshold
Luteimonas granuli	strain=Gr-4	GCA_007795095.1	1176533	1176533	type	True	81.562	644	1462	95	below_threshold
Pseudoxanthomonas taiwanensis	strain=DSM 22914	GCA_010093135.1	176598	176598	type	True	81.4912	631	1462	95	below_threshold
Pseudoxanthomonas jiangsuensis	strain=DSM 22398	GCA_010093185.1	619688	619688	type	True	81.2652	704	1462	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_014202435.1	83619	83619	type	True	81.2291	656	1462	95	below_threshold
Pseudoxanthomonas sangjuensis	strain=DSM 28345	GCA_010211755.1	1503750	1503750	type	True	81.2253	631	1462	95	below_threshold
Pseudoxanthomonas broegbernensis	strain=DSM 12573	GCA_010093165.1	83619	83619	type	True	81.2243	650	1462	95	below_threshold
Luteimonas aestuarii	strain=B9	GCA_004357985.1	453837	453837	type	True	81.1517	698	1462	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:08,242] [INFO] DFAST Taxonomy check result was written to GCF_013425525.1_ASM1342552v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:08,243] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:08,243] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:08,243] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec4b6716-6ce6-41d0-b0a2-edcd6d29980e/dqc_reference/checkm_data
[2024-01-24 13:32:08,245] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:08,293] [INFO] Task started: CheckM
[2024-01-24 13:32:08,293] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013425525.1_ASM1342552v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013425525.1_ASM1342552v1_genomic.fna/checkm_input GCF_013425525.1_ASM1342552v1_genomic.fna/checkm_result
[2024-01-24 13:32:51,075] [INFO] Task succeeded: CheckM
[2024-01-24 13:32:51,076] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:32:51,095] [INFO] ===== Completeness check finished =====
[2024-01-24 13:32:51,096] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:32:51,096] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013425525.1_ASM1342552v1_genomic.fna/markers.fasta)
[2024-01-24 13:32:51,097] [INFO] Task started: Blastn
[2024-01-24 13:32:51,097] [INFO] Running command: blastn -query GCF_013425525.1_ASM1342552v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgec4b6716-6ce6-41d0-b0a2-edcd6d29980e/dqc_reference/reference_markers_gtdb.fasta -out GCF_013425525.1_ASM1342552v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:53,308] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:53,311] [INFO] Selected 19 target genomes.
[2024-01-24 13:32:53,312] [INFO] Target genome list was writen to GCF_013425525.1_ASM1342552v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:32:53,328] [INFO] Task started: fastANI
[2024-01-24 13:32:53,328] [INFO] Running command: fastANI --query /var/lib/cwl/stgae983e62-b558-4c99-a4d3-537dbd561397/GCF_013425525.1_ASM1342552v1_genomic.fna.gz --refList GCF_013425525.1_ASM1342552v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013425525.1_ASM1342552v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:12,331] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:12,350] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:12,351] [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_013425525.1	s__Luteimonas sp013425525	100.0	1456	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008312895.1	s__Luteimonas sp008312895	85.549	1015	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000559025.1	s__Luteimonas huabeiensis	83.1441	803	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859325.1	s__Luteimonas marina	82.4929	796	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004118975.1	s__Luteimonas sp004118975	82.1529	716	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002798175.1	s__Luteimonas sp002798175	82.1015	712	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004352825.1	s__Luteimonas arsenica	82.0438	675	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859305.1	s__Luteimonas wenzhouensis	82.0132	749	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.47	99.47	0.98	0.98	2	-
GCF_000472505.1	s__Luteimonas sp000472505	81.9918	747	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.95	99.95	0.99	0.99	2	-
GCF_006476065.1	s__Luteimonas_B lumbrici	81.8981	538	1462	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_016774335.1	s__Luteimonas sp016774335	81.8786	848	1462	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	81.7996	679	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008244685.1	s__Luteimonas sp008244685	81.7717	861	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010093135.1	s__Pseudoxanthomonas taiwanensis	81.5013	630	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.04	99.04	0.90	0.90	2	-
GCF_001014645.1	s__Luteimonas sp001014645	81.4204	742	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202435.1	s__Pseudoxanthomonas broegbernensis	81.2596	653	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Pseudoxanthomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_004357985.1	s__Luteimonas aestuarii	81.1804	695	1462	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	80.5885	679	1462	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	80.5056	665	1462	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 13:33:12,352] [INFO] GTDB search result was written to GCF_013425525.1_ASM1342552v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:12,353] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:12,357] [INFO] DFAST_QC result json was written to GCF_013425525.1_ASM1342552v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:12,358] [INFO] DFAST_QC completed!
[2024-01-24 13:33:12,358] [INFO] Total running time: 0h1m39s