[2023-06-16 21:25:34,070] [INFO] DFAST_QC pipeline started.
[2023-06-16 21:25:34,073] [INFO] DFAST_QC version: 0.5.7
[2023-06-16 21:25:34,073] [INFO] DQC Reference Directory: /var/lib/cwl/stge10f6977-fcff-429d-ae03-1718dbaa038c/dqc_reference
[2023-06-16 21:25:35,586] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-16 21:25:35,587] [INFO] Task started: Prodigal
[2023-06-16 21:25:35,587] [INFO] Running command: gunzip -c /var/lib/cwl/stge1d4fd7a-a77e-4377-8c91-3524194e479c/GCA_028866435.1_ASM2886643v1_genomic.fna.gz | prodigal -d GCA_028866435.1_ASM2886643v1_genomic.fna/cds.fna -a GCA_028866435.1_ASM2886643v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-16 21:25:44,417] [INFO] Task succeeded: Prodigal
[2023-06-16 21:25:44,417] [INFO] Task started: HMMsearch
[2023-06-16 21:25:44,417] [INFO] Running command: hmmsearch --tblout GCA_028866435.1_ASM2886643v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge10f6977-fcff-429d-ae03-1718dbaa038c/dqc_reference/reference_markers.hmm GCA_028866435.1_ASM2886643v1_genomic.fna/protein.faa > /dev/null
[2023-06-16 21:25:44,606] [INFO] Task succeeded: HMMsearch
[2023-06-16 21:25:44,607] [WARNING] Found 5/6 markers. [/var/lib/cwl/stge1d4fd7a-a77e-4377-8c91-3524194e479c/GCA_028866435.1_ASM2886643v1_genomic.fna.gz]
[2023-06-16 21:25:44,634] [INFO] Query marker FASTA was written to GCA_028866435.1_ASM2886643v1_genomic.fna/markers.fasta
[2023-06-16 21:25:44,634] [INFO] Task started: Blastn
[2023-06-16 21:25:44,634] [INFO] Running command: blastn -query GCA_028866435.1_ASM2886643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge10f6977-fcff-429d-ae03-1718dbaa038c/dqc_reference/reference_markers.fasta -out GCA_028866435.1_ASM2886643v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:25:45,437] [INFO] Task succeeded: Blastn
[2023-06-16 21:25:45,440] [INFO] Selected 13 target genomes.
[2023-06-16 21:25:45,441] [INFO] Target genome list was writen to GCA_028866435.1_ASM2886643v1_genomic.fna/target_genomes.txt
[2023-06-16 21:25:45,442] [INFO] Task started: fastANI
[2023-06-16 21:25:45,442] [INFO] Running command: fastANI --query /var/lib/cwl/stge1d4fd7a-a77e-4377-8c91-3524194e479c/GCA_028866435.1_ASM2886643v1_genomic.fna.gz --refList GCA_028866435.1_ASM2886643v1_genomic.fna/target_genomes.txt --output GCA_028866435.1_ASM2886643v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-16 21:25:55,782] [INFO] Task succeeded: fastANI
[2023-06-16 21:25:55,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge10f6977-fcff-429d-ae03-1718dbaa038c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-16 21:25:55,783] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge10f6977-fcff-429d-ae03-1718dbaa038c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-16 21:25:55,794] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2023-06-16 21:25:55,794] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-16 21:25:55,795] [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	84.1207	663	960	95	below_threshold
Rhodanobacter thiooxydans	strain=LCS2	GCA_000264375.1	416169	416169	type	True	83.7883	655	960	95	below_threshold
Rhodanobacter spathiphylli	strain=B39	GCA_000264295.1	347483	347483	type	True	83.6872	637	960	95	below_threshold
Rhodanobacter panaciterrae	strain=KCTC 22232	GCA_014651895.1	490572	490572	type	True	82.9783	609	960	95	below_threshold
Fulvimonas soli	strain=DSM 14263	GCA_003148905.1	155197	155197	type	True	82.6417	605	960	95	below_threshold
Fulvimonas soli	strain=LMG 19981	GCA_006352285.1	155197	155197	type	True	82.5637	562	960	95	below_threshold
Rhodanobacter fulvus	strain=Jip2	GCA_000264315.1	219571	219571	type	True	82.0391	576	960	95	below_threshold
Frateuria flava	strain=MAH-13	GCA_017837635.1	2821489	2821489	type	True	81.2145	531	960	95	below_threshold
Dyella solisilvae	strain=DHG54	GCA_003351225.1	1920168	1920168	type	True	80.8214	537	960	95	below_threshold
Dyella acidiphila	strain=7MK23	GCA_014863405.1	2775866	2775866	type	True	80.2041	486	960	95	below_threshold
Dyella telluris	strain=G9	GCA_014297575.1	2763498	2763498	type	True	80.1143	532	960	95	below_threshold
Dyella japonica	strain=DSM 16301	GCA_001010355.1	231455	231455	type	True	80.085	441	960	95	below_threshold
Tahibacter caeni	strain=BUT-6	GCA_024609805.1	1453545	1453545	type	True	77.8025	324	960	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-16 21:25:55,797] [INFO] DFAST Taxonomy check result was written to GCA_028866435.1_ASM2886643v1_genomic.fna/tc_result.tsv
[2023-06-16 21:25:55,797] [INFO] ===== Taxonomy check completed =====
[2023-06-16 21:25:55,797] [INFO] ===== Start completeness check using CheckM =====
[2023-06-16 21:25:55,798] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge10f6977-fcff-429d-ae03-1718dbaa038c/dqc_reference/checkm_data
[2023-06-16 21:25:55,799] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-16 21:25:55,829] [INFO] Task started: CheckM
[2023-06-16 21:25:55,829] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028866435.1_ASM2886643v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028866435.1_ASM2886643v1_genomic.fna/checkm_input GCA_028866435.1_ASM2886643v1_genomic.fna/checkm_result
[2023-06-16 21:26:28,606] [INFO] Task succeeded: CheckM
[2023-06-16 21:26:28,607] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.23%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-16 21:26:28,624] [INFO] ===== Completeness check finished =====
[2023-06-16 21:26:28,624] [INFO] ===== Start GTDB Search =====
[2023-06-16 21:26:28,624] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028866435.1_ASM2886643v1_genomic.fna/markers.fasta)
[2023-06-16 21:26:28,625] [INFO] Task started: Blastn
[2023-06-16 21:26:28,625] [INFO] Running command: blastn -query GCA_028866435.1_ASM2886643v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge10f6977-fcff-429d-ae03-1718dbaa038c/dqc_reference/reference_markers_gtdb.fasta -out GCA_028866435.1_ASM2886643v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-16 21:26:30,054] [INFO] Task succeeded: Blastn
[2023-06-16 21:26:30,058] [INFO] Selected 18 target genomes.
[2023-06-16 21:26:30,058] [INFO] Target genome list was writen to GCA_028866435.1_ASM2886643v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-16 21:26:30,072] [INFO] Task started: fastANI
[2023-06-16 21:26:30,072] [INFO] Running command: fastANI --query /var/lib/cwl/stge1d4fd7a-a77e-4377-8c91-3524194e479c/GCA_028866435.1_ASM2886643v1_genomic.fna.gz --refList GCA_028866435.1_ASM2886643v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028866435.1_ASM2886643v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-16 21:26:45,358] [INFO] Task succeeded: fastANI
[2023-06-16 21:26:45,373] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-16 21:26:45,374] [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_018599185.1	s__Rhodanobacter sp018599185	84.5817	665	960	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	84.2805	653	960	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	84.1941	677	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230695.2	s__Rhodanobacter denitrificans	84.1438	661	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.49	98.47	0.91	0.89	4	-
GCF_003069545.1	s__Rhodanobacter thiooxydans_A	84.0833	661	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	98.26	98.26	0.94	0.94	2	-
GCF_003335105.1	s__Rhodanobacter denitrificans_A	83.9625	676	960	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	83.8523	650	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.107	97.01	96.97	0.88	0.88	3	-
GCF_000264375.1	s__Rhodanobacter thiooxydans	83.7739	656	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.24	99.24	0.91	0.91	2	-
GCA_001898415.1	s__Rhodanobacter sp001898415	83.4579	635	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	99.06	98.37	0.88	0.82	4	-
GCF_004799035.1	s__Rhodanobacter lindaniclasticus	83.4413	653	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329435.1	s__Rhodanobacter sp008329435	83.2022	643	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004322005.1	s__Rhodanobacter sp004322005	83.1552	624	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428405.1	s__Frateuria_A sp001428405	82.7511	629	960	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_002001175.1	s__Rhodanobacter sp002001175	82.6948	606	960	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	82.4976	656	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001165.1	s__Rhodanobacter sp002001165	82.3778	604	960	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	82.3256	590	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002001045.1	s__Rhodanobacter sp002001045	82.2226	640	960	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Xanthomonadales;f__Rhodanobacteraceae;g__Rhodanobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-16 21:26:45,375] [INFO] GTDB search result was written to GCA_028866435.1_ASM2886643v1_genomic.fna/result_gtdb.tsv
[2023-06-16 21:26:45,376] [INFO] ===== GTDB Search completed =====
[2023-06-16 21:26:45,380] [INFO] DFAST_QC result json was written to GCA_028866435.1_ASM2886643v1_genomic.fna/dqc_result.json
[2023-06-16 21:26:45,380] [INFO] DFAST_QC completed!
[2023-06-16 21:26:45,380] [INFO] Total running time: 0h1m11s