[2023-06-05 05:15:46,750] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:15:46,771] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:15:46,771] [INFO] DQC Reference Directory: /var/lib/cwl/stg533ea595-a90f-41bf-a5a4-8a952ebe051a/dqc_reference
[2023-06-05 05:15:47,974] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:15:47,975] [INFO] Task started: Prodigal
[2023-06-05 05:15:47,976] [INFO] Running command: gunzip -c /var/lib/cwl/stg30671ef8-65d5-45d1-8d22-7e02dd39994e/GCA_004322005.1_ASM432200v1_genomic.fna.gz | prodigal -d GCA_004322005.1_ASM432200v1_genomic.fna/cds.fna -a GCA_004322005.1_ASM432200v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:15:58,886] [INFO] Task succeeded: Prodigal
[2023-06-05 05:15:58,887] [INFO] Task started: HMMsearch
[2023-06-05 05:15:58,887] [INFO] Running command: hmmsearch --tblout GCA_004322005.1_ASM432200v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg533ea595-a90f-41bf-a5a4-8a952ebe051a/dqc_reference/reference_markers.hmm GCA_004322005.1_ASM432200v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:15:59,159] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:15:59,160] [INFO] Found 6/6 markers.
[2023-06-05 05:15:59,194] [INFO] Query marker FASTA was written to GCA_004322005.1_ASM432200v1_genomic.fna/markers.fasta
[2023-06-05 05:15:59,195] [INFO] Task started: Blastn
[2023-06-05 05:15:59,195] [INFO] Running command: blastn -query GCA_004322005.1_ASM432200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg533ea595-a90f-41bf-a5a4-8a952ebe051a/dqc_reference/reference_markers.fasta -out GCA_004322005.1_ASM432200v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:16:00,237] [INFO] Task succeeded: Blastn
[2023-06-05 05:16:00,241] [INFO] Selected 14 target genomes.
[2023-06-05 05:16:00,242] [INFO] Target genome list was writen to GCA_004322005.1_ASM432200v1_genomic.fna/target_genomes.txt
[2023-06-05 05:16:00,244] [INFO] Task started: fastANI
[2023-06-05 05:16:00,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg30671ef8-65d5-45d1-8d22-7e02dd39994e/GCA_004322005.1_ASM432200v1_genomic.fna.gz --refList GCA_004322005.1_ASM432200v1_genomic.fna/target_genomes.txt --output GCA_004322005.1_ASM432200v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:16:12,144] [INFO] Task succeeded: fastANI
[2023-06-05 05:16:12,144] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg533ea595-a90f-41bf-a5a4-8a952ebe051a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:16:12,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg533ea595-a90f-41bf-a5a4-8a952ebe051a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:16:12,164] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 05:16:12,164] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 05:16:12,164] [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
Rhodanobacter denitrificans	strain=2APBS1	GCA_000230695.3	666685	666685	type	True	83.8207	789	1137	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	83.6573	721	1137	95	below_threshold
Rhodanobacter panaciterrae	strain=KCTC 22232	GCA_014651895.1	490572	490572	type	True	83.3521	690	1137	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	83.3254	676	1137	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	82.2099	609	1137	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	82.2017	625	1137	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	82.19	661	1137	95	below_threshold
Frateuria terrea	strain=CGMCC 1.7053	GCA_900115705.1	529704	529704	type	True	81.2123	597	1137	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	81.1643	582	1137	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	80.5776	586	1137	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	80.2657	543	1137	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	80.0687	481	1137	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	80.0422	556	1137	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.972	362	1137	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 05:16:12,166] [INFO] DFAST Taxonomy check result was written to GCA_004322005.1_ASM432200v1_genomic.fna/tc_result.tsv
[2023-06-05 05:16:12,167] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:16:12,167] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:16:12,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg533ea595-a90f-41bf-a5a4-8a952ebe051a/dqc_reference/checkm_data
[2023-06-05 05:16:12,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:16:12,210] [INFO] Task started: CheckM
[2023-06-05 05:16:12,210] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004322005.1_ASM432200v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004322005.1_ASM432200v1_genomic.fna/checkm_input GCA_004322005.1_ASM432200v1_genomic.fna/checkm_result
[2023-06-05 05:16:51,652] [INFO] Task succeeded: CheckM
[2023-06-05 05:16:51,653] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.27%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:16:51,675] [INFO] ===== Completeness check finished =====
[2023-06-05 05:16:51,676] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:16:51,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004322005.1_ASM432200v1_genomic.fna/markers.fasta)
[2023-06-05 05:16:51,676] [INFO] Task started: Blastn
[2023-06-05 05:16:51,677] [INFO] Running command: blastn -query GCA_004322005.1_ASM432200v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg533ea595-a90f-41bf-a5a4-8a952ebe051a/dqc_reference/reference_markers_gtdb.fasta -out GCA_004322005.1_ASM432200v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:16:53,669] [INFO] Task succeeded: Blastn
[2023-06-05 05:16:53,675] [INFO] Selected 21 target genomes.
[2023-06-05 05:16:53,675] [INFO] Target genome list was writen to GCA_004322005.1_ASM432200v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:16:53,772] [INFO] Task started: fastANI
[2023-06-05 05:16:53,773] [INFO] Running command: fastANI --query /var/lib/cwl/stg30671ef8-65d5-45d1-8d22-7e02dd39994e/GCA_004322005.1_ASM432200v1_genomic.fna.gz --refList GCA_004322005.1_ASM432200v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004322005.1_ASM432200v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:17:11,016] [INFO] Task succeeded: fastANI
[2023-06-05 05:17:11,034] [INFO] Found 21 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 05:17:11,034] [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
GCA_004322005.1	s__Rhodanobacter sp004322005	100.0	1128	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_018599185.1	s__Rhodanobacter sp018599185	84.2701	772	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001617365.1	s__Rhodanobacter sp001617365	84.2555	721	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.98	99.98	0.98	0.97	3	-
GCF_001428385.1	s__Rhodanobacter sp001428385	84.1641	736	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003069545.1	s__Rhodanobacter thiooxydans_A	84.0671	711	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.26	98.26	0.94	0.94	2	-
GCF_000230695.2	s__Rhodanobacter denitrificans	83.8204	789	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.49	98.47	0.91	0.89	4	-
GCF_003335105.1	s__Rhodanobacter denitrificans_A	83.7506	756	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000427505.1	s__Rhodanobacter sp000427505	83.6254	737	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.93	99.93	0.96	0.96	2	-
GCF_008329435.1	s__Rhodanobacter sp008329435	83.5886	701	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001125.1	s__Rhodanobacter sp002001125	83.5854	675	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016889805.1	s__Rhodanobacter sp001427365	83.3575	686	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.107	97.01	96.97	0.88	0.88	3	-
GCF_014651895.1	s__Rhodanobacter panaciterrae	83.3298	691	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001175.1	s__Rhodanobacter sp002001175	83.0569	693	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142825.1	s__Rhodanobacter sp900142825	83.0207	747	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002413455.1	s__Rhodanobacter sp002413455	82.9629	631	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001898415.1	s__Rhodanobacter sp001898415	82.9113	674	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.06	98.37	0.88	0.82	4	-
GCF_002001165.1	s__Rhodanobacter sp002001165	82.9008	664	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009766065.1	s__Rhodanobacter sp009766065	82.56	678	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003148905.1	s__Fulvimonas soli	82.2168	658	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Fulvimonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_013620825.1	s__Rhodanobacter sp001899565	82.0462	670	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.48	98.45	0.90	0.89	4	-
GCF_014205795.1	s__Rhodanobacter sp014205795	81.9578	664	1137	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 05:17:11,037] [INFO] GTDB search result was written to GCA_004322005.1_ASM432200v1_genomic.fna/result_gtdb.tsv
[2023-06-05 05:17:11,037] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:17:11,041] [INFO] DFAST_QC result json was written to GCA_004322005.1_ASM432200v1_genomic.fna/dqc_result.json
[2023-06-05 05:17:11,042] [INFO] DFAST_QC completed!
[2023-06-05 05:17:11,042] [INFO] Total running time: 0h1m24s