[2024-01-24 11:34:55,089] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:34:55,091] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:34:55,091] [INFO] DQC Reference Directory: /var/lib/cwl/stgfbc4ebfa-26e4-487b-b179-d0fd23287d8f/dqc_reference
[2024-01-24 11:34:56,595] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:34:56,596] [INFO] Task started: Prodigal
[2024-01-24 11:34:56,596] [INFO] Running command: gunzip -c /var/lib/cwl/stg4618be1b-07a6-42ac-85f1-bc635b718b60/GCF_006352285.1_ASM635228v1_genomic.fna.gz | prodigal -d GCF_006352285.1_ASM635228v1_genomic.fna/cds.fna -a GCF_006352285.1_ASM635228v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:06,413] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:06,413] [INFO] Task started: HMMsearch
[2024-01-24 11:35:06,414] [INFO] Running command: hmmsearch --tblout GCF_006352285.1_ASM635228v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfbc4ebfa-26e4-487b-b179-d0fd23287d8f/dqc_reference/reference_markers.hmm GCF_006352285.1_ASM635228v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:06,691] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:06,692] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4618be1b-07a6-42ac-85f1-bc635b718b60/GCF_006352285.1_ASM635228v1_genomic.fna.gz]
[2024-01-24 11:35:06,729] [INFO] Query marker FASTA was written to GCF_006352285.1_ASM635228v1_genomic.fna/markers.fasta
[2024-01-24 11:35:06,729] [INFO] Task started: Blastn
[2024-01-24 11:35:06,730] [INFO] Running command: blastn -query GCF_006352285.1_ASM635228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbc4ebfa-26e4-487b-b179-d0fd23287d8f/dqc_reference/reference_markers.fasta -out GCF_006352285.1_ASM635228v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:07,864] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:07,867] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:07,868] [INFO] Target genome list was writen to GCF_006352285.1_ASM635228v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:07,873] [INFO] Task started: fastANI
[2024-01-24 11:35:07,874] [INFO] Running command: fastANI --query /var/lib/cwl/stg4618be1b-07a6-42ac-85f1-bc635b718b60/GCF_006352285.1_ASM635228v1_genomic.fna.gz --refList GCF_006352285.1_ASM635228v1_genomic.fna/target_genomes.txt --output GCF_006352285.1_ASM635228v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:20,785] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:20,786] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfbc4ebfa-26e4-487b-b179-d0fd23287d8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:20,786] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfbc4ebfa-26e4-487b-b179-d0fd23287d8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:20,797] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:35:20,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:20,797] [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
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	100.0	1144	1152	95	conclusive
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	99.9865	1139	1152	95	conclusive
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	84.5665	761	1152	95	below_threshold
Frateuria terrea	strain=DSM 26515	GCA_900109025.1	529704	529704	type	True	84.204	747	1152	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	84.1598	754	1152	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	83.874	720	1152	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	83.2786	726	1152	95	below_threshold
Dyella kyungheensis	strain=THG-B117	GCA_016905005.1	1242174	1242174	type	True	82.0432	722	1152	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	82.0353	724	1152	95	below_threshold
Dyella amyloliquefaciens	strain=DHC06	GCA_004296575.1	1770545	1770545	type	True	81.99	756	1152	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	81.7212	599	1152	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	81.2676	679	1152	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	78.6377	505	1152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:20,799] [INFO] DFAST Taxonomy check result was written to GCF_006352285.1_ASM635228v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:20,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:20,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:20,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfbc4ebfa-26e4-487b-b179-d0fd23287d8f/dqc_reference/checkm_data
[2024-01-24 11:35:20,801] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:20,843] [INFO] Task started: CheckM
[2024-01-24 11:35:20,843] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006352285.1_ASM635228v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006352285.1_ASM635228v1_genomic.fna/checkm_input GCF_006352285.1_ASM635228v1_genomic.fna/checkm_result
[2024-01-24 11:35:56,798] [INFO] Task succeeded: CheckM
[2024-01-24 11:35:56,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:35:56,819] [INFO] ===== Completeness check finished =====
[2024-01-24 11:35:56,820] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:35:56,820] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006352285.1_ASM635228v1_genomic.fna/markers.fasta)
[2024-01-24 11:35:56,821] [INFO] Task started: Blastn
[2024-01-24 11:35:56,821] [INFO] Running command: blastn -query GCF_006352285.1_ASM635228v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfbc4ebfa-26e4-487b-b179-d0fd23287d8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_006352285.1_ASM635228v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:59,024] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:59,029] [INFO] Selected 13 target genomes.
[2024-01-24 11:35:59,030] [INFO] Target genome list was writen to GCF_006352285.1_ASM635228v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:35:59,041] [INFO] Task started: fastANI
[2024-01-24 11:35:59,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg4618be1b-07a6-42ac-85f1-bc635b718b60/GCF_006352285.1_ASM635228v1_genomic.fna.gz --refList GCF_006352285.1_ASM635228v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006352285.1_ASM635228v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:12,411] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:12,425] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:12,426] [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_003148905.1	s__Fulvimonas soli	99.9865	1139	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_001182895.1	s__Frateuria_B defendens	86.7671	777	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428405.1	s__Frateuria_A sp001428405	86.3805	870	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848855.1	s__Rhodanobacter denitrificans_B	85.4066	733	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013362045.1	s__Frateuria_A sp013362045	85.1586	617	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013620825.1	s__Rhodanobacter sp001899565	84.869	774	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
GCF_012275375.1	s__Dyella sp012275375	84.4942	819	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	96.64	95.58	0.92	0.90	4	-
GCF_900112865.1	s__Dyella marensis	84.4432	823	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900115705.1	s__Frateuria_A terrea	84.1378	756	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002279065.1	s__Dyella_A sp002279065	84.105	761	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	100.00	100.00	0.99	0.99	2	-
GCA_018970895.1	s__Dyella_A sp018970895	83.9929	674	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001641285.1	s__Dyella_A thiooxydans	83.894	778	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Dyella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017837635.1	s__Frateuria_A sp017837635	83.8609	721	1152	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Frateuria_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:12,427] [INFO] GTDB search result was written to GCF_006352285.1_ASM635228v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:12,428] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:12,431] [INFO] DFAST_QC result json was written to GCF_006352285.1_ASM635228v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:12,431] [INFO] DFAST_QC completed!
[2024-01-24 11:36:12,432] [INFO] Total running time: 0h1m17s