[2024-01-24 15:02:33,668] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:33,670] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:33,670] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3722a48-75e1-417f-9539-6b9518b9c77c/dqc_reference
[2024-01-24 15:02:34,967] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:34,968] [INFO] Task started: Prodigal
[2024-01-24 15:02:34,969] [INFO] Running command: gunzip -c /var/lib/cwl/stgfb9c343a-278f-4739-a04c-ad94501c67d2/GCF_006970865.1_ASM697086v1_genomic.fna.gz | prodigal -d GCF_006970865.1_ASM697086v1_genomic.fna/cds.fna -a GCF_006970865.1_ASM697086v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:49,927] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:49,928] [INFO] Task started: HMMsearch
[2024-01-24 15:02:49,928] [INFO] Running command: hmmsearch --tblout GCF_006970865.1_ASM697086v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3722a48-75e1-417f-9539-6b9518b9c77c/dqc_reference/reference_markers.hmm GCF_006970865.1_ASM697086v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:50,236] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:50,237] [INFO] Found 6/6 markers.
[2024-01-24 15:02:50,275] [INFO] Query marker FASTA was written to GCF_006970865.1_ASM697086v1_genomic.fna/markers.fasta
[2024-01-24 15:02:50,276] [INFO] Task started: Blastn
[2024-01-24 15:02:50,276] [INFO] Running command: blastn -query GCF_006970865.1_ASM697086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3722a48-75e1-417f-9539-6b9518b9c77c/dqc_reference/reference_markers.fasta -out GCF_006970865.1_ASM697086v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:51,296] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:51,299] [INFO] Selected 28 target genomes.
[2024-01-24 15:02:51,300] [INFO] Target genome list was writen to GCF_006970865.1_ASM697086v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:51,310] [INFO] Task started: fastANI
[2024-01-24 15:02:51,311] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb9c343a-278f-4739-a04c-ad94501c67d2/GCF_006970865.1_ASM697086v1_genomic.fna.gz --refList GCF_006970865.1_ASM697086v1_genomic.fna/target_genomes.txt --output GCF_006970865.1_ASM697086v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:20,577] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:20,578] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3722a48-75e1-417f-9539-6b9518b9c77c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:20,578] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3722a48-75e1-417f-9539-6b9518b9c77c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:20,600] [INFO] Found 28 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:03:20,600] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:03:20,601] [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
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	80.9859	626	1462	95	below_threshold
Variovorax paradoxus	strain=NBRC 15149	GCA_001591365.1	34073	34073	suspected-type	True	80.5547	709	1462	95	below_threshold
Polaromonas jejuensis	strain=NBRC 106434	GCA_001598235.1	457502	457502	type	True	80.4862	633	1462	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	80.4762	605	1462	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	80.436	628	1462	95	below_threshold
Acidovorax soli	strain=DSM 25157	GCA_900107605.1	592050	592050	type	True	80.2204	574	1462	95	below_threshold
Variovorax guangxiensis	strain=DSM 27352	GCA_003952165.1	1775474	1775474	type	True	80.2093	699	1462	95	below_threshold
Variovorax beijingensis	strain=502	GCA_003951285.1	2496117	2496117	type	True	80.1981	729	1462	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.187	596	1462	95	below_threshold
Pseudorhodoferax soli	strain=DSM 21634	GCA_003337555.1	545864	545864	type	True	80.1367	655	1462	95	below_threshold
Hydrogenophaga palleronii	strain=NBRC 102513	GCA_001571225.1	65655	65655	type	True	80.0671	574	1462	95	below_threshold
Curvibacter lanceolatus	strain=ATCC 14669	GCA_000381265.1	86182	86182	type	True	79.9493	607	1462	95	below_threshold
Curvibacter gracilis	strain=ATCC BAA-807	GCA_000518645.1	230310	230310	type	True	79.855	625	1462	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	79.846	573	1462	95	below_threshold
Acidovorax wautersii	strain=DSM 27981	GCA_900113035.1	1177982	1177982	type	True	79.8089	630	1462	95	below_threshold
Acidovorax kalamii	strain=KNDSW-TSA6	GCA_002245625.1	2004485	2004485	type	True	79.7909	609	1462	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	79.7567	593	1462	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	79.7494	656	1462	95	below_threshold
Acidovorax radicis	strain=N35	GCA_000204195.2	758826	758826	type	True	79.7196	590	1462	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	79.6588	500	1462	95	below_threshold
Hydrogenophaga flava	strain=NBRC 102514	GCA_001571145.1	65657	65657	type	True	79.6563	585	1462	95	below_threshold
Acidovorax facilis	strain=DSM 649	GCA_023913775.1	12917	12917	type	True	79.638	570	1462	95	below_threshold
Comamonas terrae	strain=NBRC 106524	GCA_001544075.1	673548	673548	type	True	79.6303	554	1462	95	below_threshold
Acidovorax delafieldii	strain=DSM 64	GCA_007993815.1	47920	47920	type	True	79.4905	604	1462	95	below_threshold
Acidovorax citrulli	strain=DSM 17060	GCA_900100305.1	80869	80869	type	True	79.4791	570	1462	95	below_threshold
Rhodoferax lacus	strain=IMCC26218	GCA_003415675.1	2184758	2184758	type	True	79.199	466	1462	95	below_threshold
Extensimonas perlucida	strain=HX2-24	GCA_007655255.1	2590786	2590786	type	True	79.1744	453	1462	95	below_threshold
Rhodoferax ferrireducens	strain=DSM 15236	GCA_000013605.1	192843	192843	type	True	78.8406	453	1462	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:20,603] [INFO] DFAST Taxonomy check result was written to GCF_006970865.1_ASM697086v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:20,603] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:20,604] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:20,604] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3722a48-75e1-417f-9539-6b9518b9c77c/dqc_reference/checkm_data
[2024-01-24 15:03:20,605] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:20,652] [INFO] Task started: CheckM
[2024-01-24 15:03:20,652] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006970865.1_ASM697086v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006970865.1_ASM697086v1_genomic.fna/checkm_input GCF_006970865.1_ASM697086v1_genomic.fna/checkm_result
[2024-01-24 15:04:11,981] [INFO] Task succeeded: CheckM
[2024-01-24 15:04:11,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:04:12,004] [INFO] ===== Completeness check finished =====
[2024-01-24 15:04:12,005] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:04:12,005] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006970865.1_ASM697086v1_genomic.fna/markers.fasta)
[2024-01-24 15:04:12,006] [INFO] Task started: Blastn
[2024-01-24 15:04:12,006] [INFO] Running command: blastn -query GCF_006970865.1_ASM697086v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3722a48-75e1-417f-9539-6b9518b9c77c/dqc_reference/reference_markers_gtdb.fasta -out GCF_006970865.1_ASM697086v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:04:13,760] [INFO] Task succeeded: Blastn
[2024-01-24 15:04:13,765] [INFO] Selected 14 target genomes.
[2024-01-24 15:04:13,765] [INFO] Target genome list was writen to GCF_006970865.1_ASM697086v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:04:13,778] [INFO] Task started: fastANI
[2024-01-24 15:04:13,778] [INFO] Running command: fastANI --query /var/lib/cwl/stgfb9c343a-278f-4739-a04c-ad94501c67d2/GCF_006970865.1_ASM697086v1_genomic.fna.gz --refList GCF_006970865.1_ASM697086v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006970865.1_ASM697086v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:04:26,445] [INFO] Task succeeded: fastANI
[2024-01-24 15:04:26,456] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:04:26,456] [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_006970865.1	s__Rhodoferax_A sediminis	100.0	1460	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002002705.1	s__Rhodoferax_A sp002002705	94.7854	1096	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004322085.1	s__Rhodoferax_A sp004322085	85.4602	703	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004323695.1	s__Rhodoferax_A sp004323695	84.8149	778	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_A	95.0	99.22	98.48	0.92	0.91	3	-
GCA_005503335.1	s__SCMQ01 sp005503335	81.3442	667	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__SCMQ01	95.0	99.99	99.99	1.00	1.00	3	-
GCA_018241985.1	s__Rhodoferax_A sp018241985	81.0385	405	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Rhodoferax_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014170375.1	s__Variovorax sp014170375	80.5672	662	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016721925.1	s__JAABQG01 sp016721925	80.2888	595	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	98.62	98.32	0.93	0.90	9	-
GCA_001770955.1	s__Giesbergeria sp001770955	79.9554	494	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Giesbergeria	95.0	97.11	95.02	0.83	0.80	5	-
GCF_007833165.1	s__Ramlibacter sp007833165	79.6744	611	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014879655.1	s__JAABQG01 sp014879655	79.514	505	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__JAABQG01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107745.1	s__Variovorax sp900107745	79.5034	621	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Variovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018780625.1	s__Polaromonas sp018780625	79.4963	457	1462	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Polaromonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:04:26,458] [INFO] GTDB search result was written to GCF_006970865.1_ASM697086v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:04:26,458] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:04:26,463] [INFO] DFAST_QC result json was written to GCF_006970865.1_ASM697086v1_genomic.fna/dqc_result.json
[2024-01-24 15:04:26,463] [INFO] DFAST_QC completed!
[2024-01-24 15:04:26,463] [INFO] Total running time: 0h1m53s