[2024-01-24 13:46:03,739] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:03,741] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:03,742] [INFO] DQC Reference Directory: /var/lib/cwl/stg7046ddd6-07b8-49a4-8bee-762ffa1eebf3/dqc_reference
[2024-01-24 13:46:05,125] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:05,126] [INFO] Task started: Prodigal
[2024-01-24 13:46:05,127] [INFO] Running command: gunzip -c /var/lib/cwl/stg335936ae-411b-45a6-b5ee-e0a776c4c921/GCF_021233355.1_ASM2123335v1_genomic.fna.gz | prodigal -d GCF_021233355.1_ASM2123335v1_genomic.fna/cds.fna -a GCF_021233355.1_ASM2123335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:17,773] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:17,774] [INFO] Task started: HMMsearch
[2024-01-24 13:46:17,774] [INFO] Running command: hmmsearch --tblout GCF_021233355.1_ASM2123335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7046ddd6-07b8-49a4-8bee-762ffa1eebf3/dqc_reference/reference_markers.hmm GCF_021233355.1_ASM2123335v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:18,046] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:18,047] [INFO] Found 6/6 markers.
[2024-01-24 13:46:18,085] [INFO] Query marker FASTA was written to GCF_021233355.1_ASM2123335v1_genomic.fna/markers.fasta
[2024-01-24 13:46:18,086] [INFO] Task started: Blastn
[2024-01-24 13:46:18,086] [INFO] Running command: blastn -query GCF_021233355.1_ASM2123335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7046ddd6-07b8-49a4-8bee-762ffa1eebf3/dqc_reference/reference_markers.fasta -out GCF_021233355.1_ASM2123335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:19,216] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:19,219] [INFO] Selected 15 target genomes.
[2024-01-24 13:46:19,219] [INFO] Target genome list was writen to GCF_021233355.1_ASM2123335v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:19,226] [INFO] Task started: fastANI
[2024-01-24 13:46:19,226] [INFO] Running command: fastANI --query /var/lib/cwl/stg335936ae-411b-45a6-b5ee-e0a776c4c921/GCF_021233355.1_ASM2123335v1_genomic.fna.gz --refList GCF_021233355.1_ASM2123335v1_genomic.fna/target_genomes.txt --output GCF_021233355.1_ASM2123335v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:32,610] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:32,610] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7046ddd6-07b8-49a4-8bee-762ffa1eebf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:32,611] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7046ddd6-07b8-49a4-8bee-762ffa1eebf3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:32,623] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:32,623] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:32,624] [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 fraxinea	strain=D4P002	GCA_021233355.1	2901869	2901869	type	True	100.0	1335	1336	95	conclusive
Luteimonas terrae	strain=THG-MD21	GCA_004358165.1	1530191	1530191	type	True	87.2322	1002	1336	95	below_threshold
Luteimonas chenhongjianii	strain=100111	GCA_002327105.1	2006110	2006110	type	True	85.2536	875	1336	95	below_threshold
Luteimonas deserti	strain=SJ-16	GCA_013425765.1	2752306	2752306	type	True	84.0459	837	1336	95	below_threshold
Luteimonas marina	strain=FR1330	GCA_007859325.1	488485	488485	type	True	81.9977	714	1336	95	below_threshold
Luteimonas saliphila	strain=SJ-9	GCA_016774335.1	2804919	2804919	type	True	81.0821	712	1336	95	below_threshold
Luteimonas yindakuii	strain=S-1072	GCA_004803715.2	2565782	2565782	type	True	81.0374	652	1336	95	below_threshold
Luteimonas padinae	strain=KCTC 52403	GCA_014652935.1	1714359	1714359	type	True	80.9427	606	1336	95	below_threshold
Luteimonas terricola	strain=CGMCC 1.8985	GCA_014645675.1	645597	645597	type	True	80.7111	579	1336	95	below_threshold
Luteimonas weifangensis	strain=WF-2	GCA_003416885.1	2303539	2303539	type	True	80.3708	507	1336	95	below_threshold
Luteimonas aquatica	strain=RIB1-20	GCA_022662575.1	450364	450364	type	True	80.3501	629	1336	95	below_threshold
Thermomonas aquatica	strain=SY21	GCA_006337105.1	2202149	2202149	type	True	80.1923	541	1336	95	below_threshold
Luteimonas lumbrici	strain=1.1416	GCA_006476065.1	2559601	2559601	type	True	80.0872	465	1336	95	below_threshold
Luteimonas salinisoli	strain=SJ-92	GCA_013425525.1	2752307	2752307	type	True	80.0188	657	1336	95	below_threshold
Lysobacter capsici	strain=VKM B-2533	GCA_014779555.2	435897	435897	type	True	79.9999	670	1336	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:32,625] [INFO] DFAST Taxonomy check result was written to GCF_021233355.1_ASM2123335v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:32,626] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:32,626] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:32,626] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7046ddd6-07b8-49a4-8bee-762ffa1eebf3/dqc_reference/checkm_data
[2024-01-24 13:46:32,627] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:32,667] [INFO] Task started: CheckM
[2024-01-24 13:46:32,668] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021233355.1_ASM2123335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021233355.1_ASM2123335v1_genomic.fna/checkm_input GCF_021233355.1_ASM2123335v1_genomic.fna/checkm_result
[2024-01-24 13:47:23,444] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:23,446] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:23,462] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:23,462] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:23,462] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021233355.1_ASM2123335v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:23,463] [INFO] Task started: Blastn
[2024-01-24 13:47:23,463] [INFO] Running command: blastn -query GCF_021233355.1_ASM2123335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7046ddd6-07b8-49a4-8bee-762ffa1eebf3/dqc_reference/reference_markers_gtdb.fasta -out GCF_021233355.1_ASM2123335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:25,339] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:25,342] [INFO] Selected 8 target genomes.
[2024-01-24 13:47:25,342] [INFO] Target genome list was writen to GCF_021233355.1_ASM2123335v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:25,353] [INFO] Task started: fastANI
[2024-01-24 13:47:25,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg335936ae-411b-45a6-b5ee-e0a776c4c921/GCF_021233355.1_ASM2123335v1_genomic.fna.gz --refList GCF_021233355.1_ASM2123335v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021233355.1_ASM2123335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:32,572] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:32,582] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:47:32,582] [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_902506295.1	s__Luteimonas sp902506295	89.6281	1021	1336	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	87.2276	1002	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	96.65	96.65	0.95	0.95	2	-
GCA_002307375.1	s__Luteimonas sp002307375	85.8492	937	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002327105.1	s__Luteimonas chenhongjianii	85.299	873	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	98.75	98.75	0.95	0.95	2	-
GCA_002324875.1	s__Luteimonas sp002324875	85.155	887	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.99	99.99	0.99	0.99	3	-
GCF_002849595.1	s__Luteimonas sp002849595	85.0533	895	1336	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Xanthomonadaceae;g__Luteimonas	95.0	99.97	99.97	0.99	0.99	2	-
GCF_013425765.1	s__Luteimonas sp013425765	84.0251	839	1336	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	83.289	863	1336	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 13:47:32,584] [INFO] GTDB search result was written to GCF_021233355.1_ASM2123335v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:32,584] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:32,588] [INFO] DFAST_QC result json was written to GCF_021233355.1_ASM2123335v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:32,588] [INFO] DFAST_QC completed!
[2024-01-24 13:47:32,588] [INFO] Total running time: 0h1m29s