[2024-01-24 12:31:54,264] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:54,266] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:54,267] [INFO] DQC Reference Directory: /var/lib/cwl/stgbf037121-7cc5-4c19-acb9-89b9c407b8b1/dqc_reference
[2024-01-24 12:31:55,529] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:55,530] [INFO] Task started: Prodigal
[2024-01-24 12:31:55,530] [INFO] Running command: gunzip -c /var/lib/cwl/stge6a46ecd-a99a-4291-871f-05cd44e10193/GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/cds.fna -a GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:07,773] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:07,773] [INFO] Task started: HMMsearch
[2024-01-24 12:32:07,773] [INFO] Running command: hmmsearch --tblout GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbf037121-7cc5-4c19-acb9-89b9c407b8b1/dqc_reference/reference_markers.hmm GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:08,213] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:08,214] [INFO] Found 6/6 markers.
[2024-01-24 12:32:08,252] [INFO] Query marker FASTA was written to GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 12:32:08,253] [INFO] Task started: Blastn
[2024-01-24 12:32:08,253] [INFO] Running command: blastn -query GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf037121-7cc5-4c19-acb9-89b9c407b8b1/dqc_reference/reference_markers.fasta -out GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:09,158] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:09,162] [INFO] Selected 18 target genomes.
[2024-01-24 12:32:09,162] [INFO] Target genome list was writen to GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 12:32:09,169] [INFO] Task started: fastANI
[2024-01-24 12:32:09,169] [INFO] Running command: fastANI --query /var/lib/cwl/stge6a46ecd-a99a-4291-871f-05cd44e10193/GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna.gz --refList GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:24,931] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:24,932] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbf037121-7cc5-4c19-acb9-89b9c407b8b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:24,932] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbf037121-7cc5-4c19-acb9-89b9c407b8b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:24,946] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:32:24,947] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:24,947] [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
Sphingopyxis flava	strain=R11H	GCA_900168005.1	1507287	1507287	type	True	100.0	1324	1327	95	conclusive
Sphingopyxis panaciterrulae	strain=DSM 27163	GCA_014199295.1	462372	462372	type	True	83.3382	805	1327	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	82.4034	732	1327	95	below_threshold
Sphingopyxis granuli	strain=NBRC 100800	GCA_001591045.1	267128	267128	type	True	82.3778	696	1327	95	below_threshold
Sphingopyxis lindanitolerans	strain=WS5A3p	GCA_002993885.1	2054227	2054227	type	True	82.1275	725	1327	95	below_threshold
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	81.7509	745	1327	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	81.6117	666	1327	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	81.5556	758	1327	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	81.4914	683	1327	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=UI2	GCA_900177755.1	429001	33052	type	True	81.4528	692	1327	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=NBRC 15098	GCA_001598815.1	2448440	33052	type	True	81.423	695	1327	95	below_threshold
Sphingopyxis panaciterrae	strain=DSM 27164	GCA_011762125.1	363841	363841	type	True	81.3739	723	1327	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	80.9248	731	1327	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.1088	268	1327	95	below_threshold
Novosphingobium huizhouense	strain=c7	GCA_020179475.1	2866625	2866625	type	True	77.5946	278	1327	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	77.4267	283	1327	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.278	271	1327	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	77.1741	269	1327	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:24,950] [INFO] DFAST Taxonomy check result was written to GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 12:32:24,951] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:24,951] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:24,951] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbf037121-7cc5-4c19-acb9-89b9c407b8b1/dqc_reference/checkm_data
[2024-01-24 12:32:24,952] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:24,994] [INFO] Task started: CheckM
[2024-01-24 12:32:24,994] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/checkm_input GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 12:33:03,027] [INFO] Task succeeded: CheckM
[2024-01-24 12:33:03,028] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:33:03,047] [INFO] ===== Completeness check finished =====
[2024-01-24 12:33:03,048] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:33:03,048] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 12:33:03,048] [INFO] Task started: Blastn
[2024-01-24 12:33:03,049] [INFO] Running command: blastn -query GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgbf037121-7cc5-4c19-acb9-89b9c407b8b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:33:04,800] [INFO] Task succeeded: Blastn
[2024-01-24 12:33:04,811] [INFO] Selected 14 target genomes.
[2024-01-24 12:33:04,811] [INFO] Target genome list was writen to GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:33:04,823] [INFO] Task started: fastANI
[2024-01-24 12:33:04,824] [INFO] Running command: fastANI --query /var/lib/cwl/stge6a46ecd-a99a-4291-871f-05cd44e10193/GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna.gz --refList GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:18,105] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:18,119] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:18,119] [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_900168005.1	s__Sphingopyxis flava	100.0	1324	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001278035.1	s__Sphingopyxis sp001278035	91.6376	962	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002277025.1	s__Sphingopyxis sp002277025	85.7382	864	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199295.1	s__Sphingopyxis panaciterrulae	83.347	804	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188185.1	s__Sphingopyxis indica	82.4144	730	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001591045.1	s__Sphingopyxis granuli	82.3825	695	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	97.56	96.77	0.81	0.78	6	-
GCA_900078365.1	s__Sphingopyxis sp900078365	82.2857	770	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018682675.1	s__Sphingopyxis soli	81.6044	667	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001314325.1	s__Sphingopyxis macrogoltabida	81.5186	762	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.99	99.99	1.00	1.00	2	-
GCF_001990265.1	s__Sphingopyxis sp001990265	81.5145	663	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873485.1	s__Sphingopyxis sp014873485	81.3884	722	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762125.1	s__Sphingopyxis panaciterrae	81.3736	723	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016463645.1	s__Sphingopyxis sp016463645	81.2712	647	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017309275.1	s__Sphingopyxis sp017309275	81.118	673	1327	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:18,121] [INFO] GTDB search result was written to GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:18,121] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:18,127] [INFO] DFAST_QC result json was written to GCF_900168005.1_IMG-taxon_2706795030_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 12:33:18,128] [INFO] DFAST_QC completed!
[2024-01-24 12:33:18,128] [INFO] Total running time: 0h1m24s