[2024-01-24 13:32:41,674] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:41,677] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:41,677] [INFO] DQC Reference Directory: /var/lib/cwl/stg7eff25ec-bed6-44fe-8729-1d2b07f28084/dqc_reference
[2024-01-24 13:32:43,021] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:43,022] [INFO] Task started: Prodigal
[2024-01-24 13:32:43,023] [INFO] Running command: gunzip -c /var/lib/cwl/stg3318e130-4e66-49db-ad59-dc38783696ed/GCF_003550065.1_ASM355006v1_genomic.fna.gz | prodigal -d GCF_003550065.1_ASM355006v1_genomic.fna/cds.fna -a GCF_003550065.1_ASM355006v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:57,545] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:57,545] [INFO] Task started: HMMsearch
[2024-01-24 13:32:57,545] [INFO] Running command: hmmsearch --tblout GCF_003550065.1_ASM355006v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7eff25ec-bed6-44fe-8729-1d2b07f28084/dqc_reference/reference_markers.hmm GCF_003550065.1_ASM355006v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:57,911] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:57,913] [INFO] Found 6/6 markers.
[2024-01-24 13:32:57,964] [INFO] Query marker FASTA was written to GCF_003550065.1_ASM355006v1_genomic.fna/markers.fasta
[2024-01-24 13:32:57,964] [INFO] Task started: Blastn
[2024-01-24 13:32:57,964] [INFO] Running command: blastn -query GCF_003550065.1_ASM355006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7eff25ec-bed6-44fe-8729-1d2b07f28084/dqc_reference/reference_markers.fasta -out GCF_003550065.1_ASM355006v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:59,019] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:59,022] [INFO] Selected 24 target genomes.
[2024-01-24 13:32:59,022] [INFO] Target genome list was writen to GCF_003550065.1_ASM355006v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:59,031] [INFO] Task started: fastANI
[2024-01-24 13:32:59,031] [INFO] Running command: fastANI --query /var/lib/cwl/stg3318e130-4e66-49db-ad59-dc38783696ed/GCF_003550065.1_ASM355006v1_genomic.fna.gz --refList GCF_003550065.1_ASM355006v1_genomic.fna/target_genomes.txt --output GCF_003550065.1_ASM355006v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:18,872] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:18,873] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7eff25ec-bed6-44fe-8729-1d2b07f28084/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:18,874] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7eff25ec-bed6-44fe-8729-1d2b07f28084/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:18,896] [INFO] Found 24 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:33:18,896] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:33:18,897] [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 naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	80.0271	634	1503	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	80.0033	644	1503	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.8806	583	1503	95	below_threshold
Sphingomonas pruni	strain=NBRC 15498	GCA_001598455.1	40683	40683	type	True	79.6215	526	1503	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	79.5961	591	1503	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	79.5808	478	1503	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	79.5725	526	1503	95	below_threshold
Sphingomonas aerolata	strain=NW12	GCA_003046295.1	185951	185951	type	True	79.5719	537	1503	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	79.5034	496	1503	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	79.4706	585	1503	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	79.4682	513	1503	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	79.4211	498	1503	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	79.411	542	1503	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.3563	556	1503	95	below_threshold
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	79.2845	598	1503	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.261	542	1503	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.2573	568	1503	95	below_threshold
Sphingomonas panacisoli	strain=HKS19	GCA_007859635.1	1813879	1813879	type	True	79.2545	534	1503	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	79.2168	496	1503	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	79.1635	538	1503	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	79.1445	535	1503	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_014197095.1	1166323	1166323	type	True	79.1316	491	1503	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	79.0059	476	1503	95	below_threshold
Sphingomonas soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	79.0006	495	1503	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:18,899] [INFO] DFAST Taxonomy check result was written to GCF_003550065.1_ASM355006v1_genomic.fna/tc_result.tsv
[2024-01-24 13:33:18,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:18,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:18,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7eff25ec-bed6-44fe-8729-1d2b07f28084/dqc_reference/checkm_data
[2024-01-24 13:33:18,903] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:18,950] [INFO] Task started: CheckM
[2024-01-24 13:33:18,951] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003550065.1_ASM355006v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003550065.1_ASM355006v1_genomic.fna/checkm_input GCF_003550065.1_ASM355006v1_genomic.fna/checkm_result
[2024-01-24 13:34:02,225] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:02,226] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:02,248] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:02,248] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:02,249] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003550065.1_ASM355006v1_genomic.fna/markers.fasta)
[2024-01-24 13:34:02,249] [INFO] Task started: Blastn
[2024-01-24 13:34:02,249] [INFO] Running command: blastn -query GCF_003550065.1_ASM355006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7eff25ec-bed6-44fe-8729-1d2b07f28084/dqc_reference/reference_markers_gtdb.fasta -out GCF_003550065.1_ASM355006v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:04,168] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:04,172] [INFO] Selected 19 target genomes.
[2024-01-24 13:34:04,172] [INFO] Target genome list was writen to GCF_003550065.1_ASM355006v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:04,219] [INFO] Task started: fastANI
[2024-01-24 13:34:04,219] [INFO] Running command: fastANI --query /var/lib/cwl/stg3318e130-4e66-49db-ad59-dc38783696ed/GCF_003550065.1_ASM355006v1_genomic.fna.gz --refList GCF_003550065.1_ASM355006v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003550065.1_ASM355006v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:21,072] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:21,092] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:21,092] [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_003550065.1	s__Sphingomonas caeni	100.0	1503	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_006438735.1	s__Sphingomonas koreensis_A	81.5745	634	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.05	96.05	0.80	0.80	2	-
GCA_001897375.1	s__Sphingomonas sp001897375	80.3093	571	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_013344685.1	s__Sphingomonas sp013344685	80.2985	586	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204695.1	s__Sphingomonas sp001897045	80.2844	616	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.82	96.97	0.94	0.83	6	-
GCF_004792695.1	s__Sphingomonas naasensis	80.0082	642	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_006439055.1	s__Sphingomonas glacialis_A	79.9333	609	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017304635.1	s__Sphingomonas sp017304635	79.8262	551	1503	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	79.6814	580	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115745.1	s__Sphingomonas rubra	79.6021	476	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018122655.1	s__Sphingomonas sp018122655	79.557	530	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001555965.1	s__Sphingomonas sp001555965	79.556	498	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	97.92	0.88	0.78	8	-
GCA_017304615.1	s__Sphingomonas sp017304615	79.5488	519	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014334115.1	s__Sphingomonas sp014334115	79.5089	505	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489075.1	s__Sphingomonas sp014489075	79.5054	625	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007859635.1	s__Sphingomonas panacisoli	79.2764	532	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011057975.1	s__Sphingomonas sp011057975	79.1442	535	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004796535.1	s__Sphingomonas_L sp004796535	78.988	440	1503	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927115.1	s__Sphingomonas sp012927115	78.9605	570	1503	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 13:34:21,094] [INFO] GTDB search result was written to GCF_003550065.1_ASM355006v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:21,094] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:21,098] [INFO] DFAST_QC result json was written to GCF_003550065.1_ASM355006v1_genomic.fna/dqc_result.json
[2024-01-24 13:34:21,098] [INFO] DFAST_QC completed!
[2024-01-24 13:34:21,098] [INFO] Total running time: 0h1m39s