[2024-01-24 13:50:09,945] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:50:09,947] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:50:09,948] [INFO] DQC Reference Directory: /var/lib/cwl/stg242fa0e5-f3a9-48bc-8c57-a0008182b62f/dqc_reference
[2024-01-24 13:50:11,200] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:50:11,201] [INFO] Task started: Prodigal
[2024-01-24 13:50:11,201] [INFO] Running command: gunzip -c /var/lib/cwl/stg60256175-672f-4ba6-b2f4-54e5a03633d6/GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/cds.fna -a GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:50:23,032] [INFO] Task succeeded: Prodigal
[2024-01-24 13:50:23,033] [INFO] Task started: HMMsearch
[2024-01-24 13:50:23,033] [INFO] Running command: hmmsearch --tblout GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg242fa0e5-f3a9-48bc-8c57-a0008182b62f/dqc_reference/reference_markers.hmm GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:50:23,285] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:50:23,287] [INFO] Found 6/6 markers.
[2024-01-24 13:50:23,322] [INFO] Query marker FASTA was written to GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:50:23,322] [INFO] Task started: Blastn
[2024-01-24 13:50:23,322] [INFO] Running command: blastn -query GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg242fa0e5-f3a9-48bc-8c57-a0008182b62f/dqc_reference/reference_markers.fasta -out GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:24,308] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:24,311] [INFO] Selected 22 target genomes.
[2024-01-24 13:50:24,311] [INFO] Target genome list was writen to GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:50:24,315] [INFO] Task started: fastANI
[2024-01-24 13:50:24,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg60256175-672f-4ba6-b2f4-54e5a03633d6/GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna.gz --refList GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:50:40,406] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:40,406] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg242fa0e5-f3a9-48bc-8c57-a0008182b62f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:50:40,406] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg242fa0e5-f3a9-48bc-8c57-a0008182b62f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:50:40,422] [INFO] Found 22 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:50:40,423] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:50:40,423] [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 gellani	strain=S6-262	GCA_900110035.1	1166340	1166340	type	True	100.0	1271	1273	95	conclusive
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	80.3558	612	1273	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	80.2243	560	1273	95	below_threshold
Sphingomonas abaci	strain=DSM 15867	GCA_014199625.1	237611	237611	type	True	80.2208	628	1273	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	80.1916	545	1273	95	below_threshold
Sphingomonas aerophila	strain=DSM 100044	GCA_014199305.1	1344948	1344948	type	True	80.1519	566	1273	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	80.0756	556	1273	95	below_threshold
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	80.0403	540	1273	95	below_threshold
Sphingomonas pseudosanguinis	strain=DSM 19512	GCA_014196255.1	413712	413712	type	True	80.022	574	1273	95	below_threshold
Sphingomonas aquatilis	strain=DSM 15581	GCA_014196115.1	93063	93063	type	True	80.0006	557	1273	95	below_threshold
Sphingomonas aquatilis	strain=NBRC 16722	GCA_007990915.1	93063	93063	type	True	79.9896	516	1273	95	below_threshold
Sphingomonas insulae	strain=DSM 21792	GCA_011762035.1	424800	424800	type	True	79.9802	530	1273	95	below_threshold
Sphingomonas melonis	strain=DAPP-PG 224	GCA_000379045.1	152682	152682	type	True	79.9649	573	1273	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	79.9474	505	1273	95	below_threshold
Sphingomonas paucimobilis	strain=FDAARGOS_908	GCA_016027095.1	13689	13689	type	True	79.7322	544	1273	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	79.7103	538	1273	95	below_threshold
Sphingomonas paucimobilis	strain=NBRC 13935	GCA_000739895.2	13689	13689	type	True	79.7011	535	1273	95	below_threshold
Sphingomonas dokdonensis	strain=DSM 21029	GCA_002197685.1	344880	344880	type	True	79.4639	469	1273	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.3691	576	1273	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	79.2398	596	1273	95	below_threshold
Sphingomonas lenta	strain=1PNM-20	GCA_002288825.1	1141887	1141887	type	True	78.9841	476	1273	95	below_threshold
Sphingomonas radiodurans	strain=S9-5	GCA_020866845.1	2890321	2890321	type	True	78.2899	401	1273	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:50:40,424] [INFO] DFAST Taxonomy check result was written to GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:50:40,425] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:50:40,425] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:50:40,425] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg242fa0e5-f3a9-48bc-8c57-a0008182b62f/dqc_reference/checkm_data
[2024-01-24 13:50:40,426] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:50:40,464] [INFO] Task started: CheckM
[2024-01-24 13:50:40,464] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/checkm_input GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:51:19,545] [INFO] Task succeeded: CheckM
[2024-01-24 13:51:19,547] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:51:19,566] [INFO] ===== Completeness check finished =====
[2024-01-24 13:51:19,567] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:51:19,567] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:51:19,567] [INFO] Task started: Blastn
[2024-01-24 13:51:19,568] [INFO] Running command: blastn -query GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg242fa0e5-f3a9-48bc-8c57-a0008182b62f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:51:21,436] [INFO] Task succeeded: Blastn
[2024-01-24 13:51:21,440] [INFO] Selected 20 target genomes.
[2024-01-24 13:51:21,441] [INFO] Target genome list was writen to GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:51:21,748] [INFO] Task started: fastANI
[2024-01-24 13:51:21,748] [INFO] Running command: fastANI --query /var/lib/cwl/stg60256175-672f-4ba6-b2f4-54e5a03633d6/GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna.gz --refList GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:51:37,011] [INFO] Task succeeded: fastANI
[2024-01-24 13:51:37,033] [INFO] Found 20 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:51:37,034] [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_900110035.1	s__Sphingomonas gellani	100.0	1272	1273	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_016107325.1	s__Sphingomonas sp016107325	80.2785	575	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199625.1	s__Sphingomonas abaci	80.2344	624	1273	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	80.2226	542	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002374855.1	s__Sphingomonas adhaesiva	80.221	539	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.76	99.56	0.89	0.87	3	-
GCF_014641735.1	s__Sphingomonas metalli	80.1764	561	1273	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	80.1585	625	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199305.1	s__Sphingomonas aerophila	80.1518	566	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014197105.1	s__Sphingomonas jinjuensis	80.1357	550	1273	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	80.0377	537	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_014196115.1	s__Sphingomonas aquatilis	80.0308	554	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.36	95.86	0.87	0.82	11	-
GCA_003075315.1	s__Sphingomonas sp003075315	79.9554	536	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.84	96.53	0.96	0.89	4	-
GCF_018139225.1	s__Sphingomonas sp018139225	79.9514	563	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000739895.2	s__Sphingomonas paucimobilis	79.7152	533	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.74	99.40	0.92	0.87	13	-
GCA_001897375.1	s__Sphingomonas sp001897375	79.5405	476	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_007995065.1	s__Sphingomonas ginsenosidivorax	79.4973	531	1273	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	79.4808	467	1273	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	79.2597	462	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001421355.1	s__Sphingomonas sp001421355	79.1722	484	1273	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.29	96.58	0.97	0.94	3	-
GCF_002288825.1	s__Sphingomonas lenta	78.994	475	1273	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 13:51:37,039] [INFO] GTDB search result was written to GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:51:37,042] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:51:37,048] [INFO] DFAST_QC result json was written to GCF_900110035.1_IMG-taxon_2654588200_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:51:37,049] [INFO] DFAST_QC completed!
[2024-01-24 13:51:37,049] [INFO] Total running time: 0h1m27s