[2024-01-24 13:33:40,977] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:33:40,979] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:33:40,979] [INFO] DQC Reference Directory: /var/lib/cwl/stg46bbef30-cfec-4cac-a15f-04fc98ceca26/dqc_reference
[2024-01-24 13:33:42,434] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:33:42,435] [INFO] Task started: Prodigal
[2024-01-24 13:33:42,435] [INFO] Running command: gunzip -c /var/lib/cwl/stg4692daf0-2625-41f2-a929-57626a0c64d6/GCF_021391395.1_ASM2139139v1_genomic.fna.gz | prodigal -d GCF_021391395.1_ASM2139139v1_genomic.fna/cds.fna -a GCF_021391395.1_ASM2139139v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:33:55,192] [INFO] Task succeeded: Prodigal
[2024-01-24 13:33:55,193] [INFO] Task started: HMMsearch
[2024-01-24 13:33:55,193] [INFO] Running command: hmmsearch --tblout GCF_021391395.1_ASM2139139v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg46bbef30-cfec-4cac-a15f-04fc98ceca26/dqc_reference/reference_markers.hmm GCF_021391395.1_ASM2139139v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:33:55,481] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:33:55,483] [INFO] Found 6/6 markers.
[2024-01-24 13:33:55,526] [INFO] Query marker FASTA was written to GCF_021391395.1_ASM2139139v1_genomic.fna/markers.fasta
[2024-01-24 13:33:55,526] [INFO] Task started: Blastn
[2024-01-24 13:33:55,526] [INFO] Running command: blastn -query GCF_021391395.1_ASM2139139v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46bbef30-cfec-4cac-a15f-04fc98ceca26/dqc_reference/reference_markers.fasta -out GCF_021391395.1_ASM2139139v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:56,530] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:56,534] [INFO] Selected 27 target genomes.
[2024-01-24 13:33:56,534] [INFO] Target genome list was writen to GCF_021391395.1_ASM2139139v1_genomic.fna/target_genomes.txt
[2024-01-24 13:33:56,543] [INFO] Task started: fastANI
[2024-01-24 13:33:56,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg4692daf0-2625-41f2-a929-57626a0c64d6/GCF_021391395.1_ASM2139139v1_genomic.fna.gz --refList GCF_021391395.1_ASM2139139v1_genomic.fna/target_genomes.txt --output GCF_021391395.1_ASM2139139v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:34:19,777] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:19,778] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg46bbef30-cfec-4cac-a15f-04fc98ceca26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:34:19,778] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg46bbef30-cfec-4cac-a15f-04fc98ceca26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:34:19,803] [INFO] Found 27 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:34:19,804] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:34:19,804] [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	81.2576	785	1462	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	81.1904	786	1462	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	80.7474	587	1462	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	80.7217	588	1462	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	80.7072	696	1462	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	80.6648	670	1462	95	below_threshold
Sphingomonas gilva	strain=ZDH117	GCA_003515075.1	2305907	2305907	type	True	80.5447	633	1462	95	below_threshold
Sphingomonas azotifigens	strain=NBRC 15497	GCA_002091475.1	330920	330920	type	True	80.5272	664	1462	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	80.5101	664	1462	95	below_threshold
Sphingomonas guangdongensis	strain=CGMCC 1.12672	GCA_900199185.1	1141890	1141890	type	True	80.4752	626	1462	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	80.4477	650	1462	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	80.3586	660	1462	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	80.1212	555	1462	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	80.0507	590	1462	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	79.9517	736	1462	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	79.8959	605	1462	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	79.8829	584	1462	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	79.8298	563	1462	95	below_threshold
Sphingomonas pruni	strain=NBRC 15498	GCA_001598455.1	40683	40683	type	True	79.7474	612	1462	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	79.6809	546	1462	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.6584	599	1462	95	below_threshold
Sphingomonas lenta	strain=1PNM-20	GCA_002288825.1	1141887	1141887	type	True	79.5542	562	1462	95	below_threshold
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	79.5094	675	1462	95	below_threshold
Sphingomonas hominis	strain=HHU CXW	GCA_013328205.1	2741495	2741495	type	True	79.4726	554	1462	95	below_threshold
Sphingomonas panni	strain=DSM 15761	GCA_022664435.1	237612	237612	type	True	79.4425	535	1462	95	below_threshold
Sphingosinithalassobacter tenebrarum	strain=zrk23	GCA_011057975.1	2711215	2711215	type	True	79.3108	516	1462	95	below_threshold
Sphingomonas alpina	strain=DSM 22537	GCA_025370095.1	653931	653931	type	True	79.0761	613	1462	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:34:19,806] [INFO] DFAST Taxonomy check result was written to GCF_021391395.1_ASM2139139v1_genomic.fna/tc_result.tsv
[2024-01-24 13:34:19,806] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:34:19,806] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:34:19,807] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg46bbef30-cfec-4cac-a15f-04fc98ceca26/dqc_reference/checkm_data
[2024-01-24 13:34:19,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:34:19,849] [INFO] Task started: CheckM
[2024-01-24 13:34:19,849] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021391395.1_ASM2139139v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021391395.1_ASM2139139v1_genomic.fna/checkm_input GCF_021391395.1_ASM2139139v1_genomic.fna/checkm_result
[2024-01-24 13:35:00,110] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:00,111] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:35:00,132] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:00,133] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:00,133] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021391395.1_ASM2139139v1_genomic.fna/markers.fasta)
[2024-01-24 13:35:00,134] [INFO] Task started: Blastn
[2024-01-24 13:35:00,134] [INFO] Running command: blastn -query GCF_021391395.1_ASM2139139v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg46bbef30-cfec-4cac-a15f-04fc98ceca26/dqc_reference/reference_markers_gtdb.fasta -out GCF_021391395.1_ASM2139139v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:02,164] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:02,169] [INFO] Selected 27 target genomes.
[2024-01-24 13:35:02,169] [INFO] Target genome list was writen to GCF_021391395.1_ASM2139139v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:02,232] [INFO] Task started: fastANI
[2024-01-24 13:35:02,233] [INFO] Running command: fastANI --query /var/lib/cwl/stg4692daf0-2625-41f2-a929-57626a0c64d6/GCF_021391395.1_ASM2139139v1_genomic.fna.gz --refList GCF_021391395.1_ASM2139139v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021391395.1_ASM2139139v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:35:25,522] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:25,548] [INFO] Found 27 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:35:25,549] [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
GCA_017744835.1	s__Sphingomonas sp017744835	81.5619	736	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792695.1	s__Sphingomonas naasensis	81.1862	786	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_017418975.1	s__Sphingomonas sp017418975	81.0833	714	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017745215.1	s__Sphingomonas sp017745215	81.0103	683	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004341505.2	s__Sphingomonas sp004341505	80.8542	596	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_004135605.1	s__Sphingomonas desiccabilis	80.7146	588	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011927635.1	s__Sphingomonas trueperi	80.7089	697	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.33	98.84	0.92	0.91	3	-
GCF_012650175.1	s__Sphingomonas sp012650175	80.6106	672	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428865.1	s__Sphingomonas sp001428865	80.5776	755	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598435.1	s__Sphingomonas pituitosa	80.5661	663	1462	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	80.5287	762	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003515075.1	s__Sphingomonas gilva	80.5207	636	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199185.1	s__Sphingomonas guangdongensis	80.4961	624	1462	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	80.4881	566	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409985.1	s__Sphingomonas melonis_A	80.4728	662	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193845.1	s__Sphingomonas sp014193845	80.4637	672	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
GCF_014194975.1	s__Sphingomonas sp014194975	80.424	695	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013416555.1	s__Sphingomonas sp013416555	80.3931	717	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014641735.1	s__Sphingomonas metalli	80.083	588	1462	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	80.0608	585	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012035195.1	s__Sphingomonas sp012035195	79.8885	607	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001557215.1	s__Sphingomonas sp001557215	79.8169	543	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.89	99.89	0.91	0.91	2	-
GCF_002288825.1	s__Sphingomonas lenta	79.5656	561	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927115.1	s__Sphingomonas sp012927115	79.5532	672	1462	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	79.5277	673	1462	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902498785.1	s__Sphingomonas sp902498785	79.5115	549	1462	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	79.3168	515	1462	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 13:35:25,550] [INFO] GTDB search result was written to GCF_021391395.1_ASM2139139v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:35:25,551] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:35:25,556] [INFO] DFAST_QC result json was written to GCF_021391395.1_ASM2139139v1_genomic.fna/dqc_result.json
[2024-01-24 13:35:25,556] [INFO] DFAST_QC completed!
[2024-01-24 13:35:25,556] [INFO] Total running time: 0h1m45s