[2024-01-24 12:13:40,343] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:40,347] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:40,347] [INFO] DQC Reference Directory: /var/lib/cwl/stg921a2eda-0fae-4df9-88f0-af6b48c83a94/dqc_reference
[2024-01-24 12:13:41,588] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:41,588] [INFO] Task started: Prodigal
[2024-01-24 12:13:41,589] [INFO] Running command: gunzip -c /var/lib/cwl/stg13a8b57c-b7f5-496c-9f6d-e061220a4ebd/GCF_004208535.1_ASM420853v1_genomic.fna.gz | prodigal -d GCF_004208535.1_ASM420853v1_genomic.fna/cds.fna -a GCF_004208535.1_ASM420853v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:56,984] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:56,984] [INFO] Task started: HMMsearch
[2024-01-24 12:13:56,984] [INFO] Running command: hmmsearch --tblout GCF_004208535.1_ASM420853v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg921a2eda-0fae-4df9-88f0-af6b48c83a94/dqc_reference/reference_markers.hmm GCF_004208535.1_ASM420853v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:57,317] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:57,318] [INFO] Found 6/6 markers.
[2024-01-24 12:13:57,362] [INFO] Query marker FASTA was written to GCF_004208535.1_ASM420853v1_genomic.fna/markers.fasta
[2024-01-24 12:13:57,363] [INFO] Task started: Blastn
[2024-01-24 12:13:57,363] [INFO] Running command: blastn -query GCF_004208535.1_ASM420853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg921a2eda-0fae-4df9-88f0-af6b48c83a94/dqc_reference/reference_markers.fasta -out GCF_004208535.1_ASM420853v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:58,288] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:58,291] [INFO] Selected 17 target genomes.
[2024-01-24 12:13:58,291] [INFO] Target genome list was writen to GCF_004208535.1_ASM420853v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:58,299] [INFO] Task started: fastANI
[2024-01-24 12:13:58,299] [INFO] Running command: fastANI --query /var/lib/cwl/stg13a8b57c-b7f5-496c-9f6d-e061220a4ebd/GCF_004208535.1_ASM420853v1_genomic.fna.gz --refList GCF_004208535.1_ASM420853v1_genomic.fna/target_genomes.txt --output GCF_004208535.1_ASM420853v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:15,073] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:15,073] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg921a2eda-0fae-4df9-88f0-af6b48c83a94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:15,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg921a2eda-0fae-4df9-88f0-af6b48c83a94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:15,086] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:15,086] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:15,087] [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
Sphingomonas populi	strain=3-7	GCA_004208535.1	2484750	2484750	type	True	100.0	1634	1646	95	conclusive
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	91.2306	1145	1646	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	81.3017	678	1646	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	80.5825	626	1646	95	below_threshold
Sphingomonas aurantiaca	strain=MA101b	GCA_003050705.1	185949	185949	type	True	80.1516	591	1646	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_014490665.1	653931	653931	type	True	79.9651	578	1646	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	79.9139	584	1646	95	below_threshold
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	79.6754	602	1646	95	below_threshold
Sphingomonas panacisoli	strain=HKS19	GCA_007859635.1	1813879	1813879	type	True	79.6247	504	1646	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.5328	594	1646	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.4976	603	1646	95	below_threshold
Sphingomonas aliaeris	strain=DH-S5	GCA_016743815.1	2759526	2759526	type	True	79.4841	538	1646	95	below_threshold
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	79.4561	566	1646	95	below_threshold
Sphingomonas pruni	strain=NBRC 15498	GCA_001598455.1	40683	40683	type	True	79.3818	513	1646	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	79.2997	561	1646	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.253	596	1646	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	79.2503	499	1646	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:14:15,091] [INFO] DFAST Taxonomy check result was written to GCF_004208535.1_ASM420853v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:15,092] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:15,092] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:15,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg921a2eda-0fae-4df9-88f0-af6b48c83a94/dqc_reference/checkm_data
[2024-01-24 12:14:15,093] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:15,150] [INFO] Task started: CheckM
[2024-01-24 12:14:15,150] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004208535.1_ASM420853v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004208535.1_ASM420853v1_genomic.fna/checkm_input GCF_004208535.1_ASM420853v1_genomic.fna/checkm_result
[2024-01-24 12:15:02,996] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:02,998] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:03,022] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:03,023] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:03,023] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004208535.1_ASM420853v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:03,024] [INFO] Task started: Blastn
[2024-01-24 12:15:03,024] [INFO] Running command: blastn -query GCF_004208535.1_ASM420853v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg921a2eda-0fae-4df9-88f0-af6b48c83a94/dqc_reference/reference_markers_gtdb.fasta -out GCF_004208535.1_ASM420853v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:04,681] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:04,684] [INFO] Selected 13 target genomes.
[2024-01-24 12:15:04,685] [INFO] Target genome list was writen to GCF_004208535.1_ASM420853v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:04,699] [INFO] Task started: fastANI
[2024-01-24 12:15:04,699] [INFO] Running command: fastANI --query /var/lib/cwl/stg13a8b57c-b7f5-496c-9f6d-e061220a4ebd/GCF_004208535.1_ASM420853v1_genomic.fna.gz --refList GCF_004208535.1_ASM420853v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004208535.1_ASM420853v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:15:20,537] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:20,549] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:15:20,550] [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_004208535.1	s__Sphingomonas populi	100.0	1633	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001717955.1	s__Sphingomonas panacis	91.236	1145	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103265.1	s__Sphingomonas sp900103265	88.9354	1037	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000241485.1	s__Sphingomonas sp000241485	81.4518	715	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439055.1	s__Sphingomonas glacialis_A	81.4045	751	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014653575.1	s__Sphingomonas glacialis	81.3005	678	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.17	97.17	0.81	0.81	2	-
GCA_903884945.1	s__Sphingomonas sp903884945	79.9108	642	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000803065.1	s__Sphingomonas sp000803065	79.7638	579	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014171475.1	s__Sphingomonas alpina_A	79.7402	596	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795835.1	s__Sphingomonas sp004795835	79.4818	565	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598415.1	s__Sphingomonas mali	79.429	567	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598455.1	s__Sphingomonas pruni	79.3944	512	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004173185.1	s__Sphingomonas sp004173185	78.5757	474	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:15:20,551] [INFO] GTDB search result was written to GCF_004208535.1_ASM420853v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:15:20,552] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:15:20,556] [INFO] DFAST_QC result json was written to GCF_004208535.1_ASM420853v1_genomic.fna/dqc_result.json
[2024-01-24 12:15:20,556] [INFO] DFAST_QC completed!
[2024-01-24 12:15:20,556] [INFO] Total running time: 0h1m40s