[2024-01-24 12:23:03,969] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:23:03,971] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:23:03,971] [INFO] DQC Reference Directory: /var/lib/cwl/stgb192363a-1cac-461b-a6bb-f185b83117eb/dqc_reference
[2024-01-24 12:23:05,267] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:23:05,268] [INFO] Task started: Prodigal
[2024-01-24 12:23:05,268] [INFO] Running command: gunzip -c /var/lib/cwl/stg8b4a5cf9-6d63-443e-a3a9-fe32ec28ec12/GCF_003345355.1_ASM334535v1_genomic.fna.gz | prodigal -d GCF_003345355.1_ASM334535v1_genomic.fna/cds.fna -a GCF_003345355.1_ASM334535v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:23:16,463] [INFO] Task succeeded: Prodigal
[2024-01-24 12:23:16,464] [INFO] Task started: HMMsearch
[2024-01-24 12:23:16,464] [INFO] Running command: hmmsearch --tblout GCF_003345355.1_ASM334535v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb192363a-1cac-461b-a6bb-f185b83117eb/dqc_reference/reference_markers.hmm GCF_003345355.1_ASM334535v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:23:16,718] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:23:16,719] [INFO] Found 6/6 markers.
[2024-01-24 12:23:16,752] [INFO] Query marker FASTA was written to GCF_003345355.1_ASM334535v1_genomic.fna/markers.fasta
[2024-01-24 12:23:16,752] [INFO] Task started: Blastn
[2024-01-24 12:23:16,753] [INFO] Running command: blastn -query GCF_003345355.1_ASM334535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb192363a-1cac-461b-a6bb-f185b83117eb/dqc_reference/reference_markers.fasta -out GCF_003345355.1_ASM334535v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:23:17,796] [INFO] Task succeeded: Blastn
[2024-01-24 12:23:17,800] [INFO] Selected 23 target genomes.
[2024-01-24 12:23:17,801] [INFO] Target genome list was writen to GCF_003345355.1_ASM334535v1_genomic.fna/target_genomes.txt
[2024-01-24 12:23:17,811] [INFO] Task started: fastANI
[2024-01-24 12:23:17,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b4a5cf9-6d63-443e-a3a9-fe32ec28ec12/GCF_003345355.1_ASM334535v1_genomic.fna.gz --refList GCF_003345355.1_ASM334535v1_genomic.fna/target_genomes.txt --output GCF_003345355.1_ASM334535v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:23:36,724] [INFO] Task succeeded: fastANI
[2024-01-24 12:23:36,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb192363a-1cac-461b-a6bb-f185b83117eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:23:36,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb192363a-1cac-461b-a6bb-f185b83117eb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:23:36,755] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:23:36,755] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:23:36,755] [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 aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	100.0	1209	1209	95	conclusive
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	80.5009	577	1209	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	80.3559	571	1209	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	80.2399	599	1209	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	80.1725	607	1209	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	80.1503	588	1209	95	below_threshold
Sphingomonas insulae	strain=DSM 21792	GCA_011762035.1	424800	424800	type	True	80.0013	552	1209	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	79.9921	559	1209	95	below_threshold
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	79.9836	561	1209	95	below_threshold
Sphingomonas gellani	strain=S6-262	GCA_900110035.1	1166340	1166340	type	True	79.8882	516	1209	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.7407	602	1209	95	below_threshold
Sphingomonas palmae	strain=JS21-1	GCA_900109565.1	1855283	1855283	type	True	79.7263	506	1209	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.7156	595	1209	95	below_threshold
Sphingomonas hylomeconis	strain=CCTCC AB 2013304	GCA_025370105.1	1395958	1395958	type	True	79.6732	569	1209	95	below_threshold
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	79.6686	527	1209	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.5622	580	1209	95	below_threshold
Sphingomonas jeddahensis	strain=G39	GCA_001981525.1	1915074	1915074	type	True	79.5317	489	1209	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	79.5154	509	1209	95	below_threshold
Sphingomonas panacis	strain=DCY99	GCA_001717955.1	1560345	1560345	type	True	79.3795	536	1209	95	below_threshold
Sphingomonas aurantiaca	strain=MA101b	GCA_003050705.1	185949	185949	type	True	79.3443	509	1209	95	below_threshold
Sphingomonas glacialis	strain=CGMCC 1.8957	GCA_014653575.1	658225	658225	type	True	79.213	547	1209	95	below_threshold
Sphingomonas mali	strain=NBRC 15500	GCA_001598415.1	40682	40682	type	True	78.98	486	1209	95	below_threshold
Sphingomonas chungangi	strain=CGMCC 1.13654	GCA_013778325.1	2683589	2683589	type	True	78.6775	437	1209	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:23:36,757] [INFO] DFAST Taxonomy check result was written to GCF_003345355.1_ASM334535v1_genomic.fna/tc_result.tsv
[2024-01-24 12:23:36,758] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:23:36,758] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:23:36,758] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb192363a-1cac-461b-a6bb-f185b83117eb/dqc_reference/checkm_data
[2024-01-24 12:23:36,759] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:23:36,794] [INFO] Task started: CheckM
[2024-01-24 12:23:36,795] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003345355.1_ASM334535v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003345355.1_ASM334535v1_genomic.fna/checkm_input GCF_003345355.1_ASM334535v1_genomic.fna/checkm_result
[2024-01-24 12:24:14,187] [INFO] Task succeeded: CheckM
[2024-01-24 12:24:14,188] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:24:14,207] [INFO] ===== Completeness check finished =====
[2024-01-24 12:24:14,208] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:24:14,208] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003345355.1_ASM334535v1_genomic.fna/markers.fasta)
[2024-01-24 12:24:14,208] [INFO] Task started: Blastn
[2024-01-24 12:24:14,209] [INFO] Running command: blastn -query GCF_003345355.1_ASM334535v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb192363a-1cac-461b-a6bb-f185b83117eb/dqc_reference/reference_markers_gtdb.fasta -out GCF_003345355.1_ASM334535v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:24:16,206] [INFO] Task succeeded: Blastn
[2024-01-24 12:24:16,210] [INFO] Selected 25 target genomes.
[2024-01-24 12:24:16,210] [INFO] Target genome list was writen to GCF_003345355.1_ASM334535v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:24:16,228] [INFO] Task started: fastANI
[2024-01-24 12:24:16,229] [INFO] Running command: fastANI --query /var/lib/cwl/stg8b4a5cf9-6d63-443e-a3a9-fe32ec28ec12/GCF_003345355.1_ASM334535v1_genomic.fna.gz --refList GCF_003345355.1_ASM334535v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003345355.1_ASM334535v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:24:36,522] [INFO] Task succeeded: fastANI
[2024-01-24 12:24:36,545] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:24:36,545] [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_003345355.1	s__Sphingomonas sp003345355	100.0	1209	1209	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_014641735.1	s__Sphingomonas metalli	80.508	576	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196115.1	s__Sphingomonas aquatilis	80.2207	601	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.36	95.86	0.87	0.82	11	-
GCF_013344685.1	s__Sphingomonas sp013344685	80.1561	538	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001897375.1	s__Sphingomonas sp001897375	80.1132	525	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_014197105.1	s__Sphingomonas jinjuensis	79.9996	557	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010450875.1	s__Sphingomonas insulae	79.9832	560	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_900110035.1	s__Sphingomonas gellani	79.8655	519	1209	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	79.838	527	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_007995065.1	s__Sphingomonas ginsenosidivorax	79.7195	560	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004345855.1	s__Sphingomonas sp004345855	79.7141	606	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423845.1	s__Sphingomonas sp001423845	79.7074	582	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109565.1	s__Sphingomonas palmae	79.6863	509	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017418975.1	s__Sphingomonas sp017418975	79.6852	569	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002197685.1	s__Sphingomonas dokdonensis	79.6672	527	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014194975.1	s__Sphingomonas sp014194975	79.6605	601	1209	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	79.6235	508	1209	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	79.5709	596	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
GCA_019112965.1	s__Sphingomonas excrementigallinarum	79.5198	489	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421995.1	s__Sphingomonas sp001421995	79.5107	502	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204495.1	s__Sphingomonas kyeonggiensis_A	79.4034	564	1209	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	79.2786	559	1209	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	79.226	545	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.17	97.17	0.81	0.81	2	-
GCF_000803065.1	s__Sphingomonas sp000803065	78.7495	514	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778325.1	s__Sphingomonas_N chungangi	78.6866	437	1209	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:24:36,547] [INFO] GTDB search result was written to GCF_003345355.1_ASM334535v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:24:36,548] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:24:36,553] [INFO] DFAST_QC result json was written to GCF_003345355.1_ASM334535v1_genomic.fna/dqc_result.json
[2024-01-24 12:24:36,553] [INFO] DFAST_QC completed!
[2024-01-24 12:24:36,553] [INFO] Total running time: 0h1m33s