[2024-01-25 19:11:50,821] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:50,822] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:50,822] [INFO] DQC Reference Directory: /var/lib/cwl/stg2e7453f2-6a00-46fe-957e-a64dc48b0107/dqc_reference
[2024-01-25 19:11:52,007] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:52,008] [INFO] Task started: Prodigal
[2024-01-25 19:11:52,008] [INFO] Running command: gunzip -c /var/lib/cwl/stge9f02b90-2572-41c2-b7b7-5e7d6838016a/GCF_002288825.1_ASM228882v1_genomic.fna.gz | prodigal -d GCF_002288825.1_ASM228882v1_genomic.fna/cds.fna -a GCF_002288825.1_ASM228882v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:12:01,079] [INFO] Task succeeded: Prodigal
[2024-01-25 19:12:01,079] [INFO] Task started: HMMsearch
[2024-01-25 19:12:01,079] [INFO] Running command: hmmsearch --tblout GCF_002288825.1_ASM228882v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2e7453f2-6a00-46fe-957e-a64dc48b0107/dqc_reference/reference_markers.hmm GCF_002288825.1_ASM228882v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:12:01,335] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:12:01,337] [INFO] Found 6/6 markers.
[2024-01-25 19:12:01,368] [INFO] Query marker FASTA was written to GCF_002288825.1_ASM228882v1_genomic.fna/markers.fasta
[2024-01-25 19:12:01,368] [INFO] Task started: Blastn
[2024-01-25 19:12:01,368] [INFO] Running command: blastn -query GCF_002288825.1_ASM228882v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e7453f2-6a00-46fe-957e-a64dc48b0107/dqc_reference/reference_markers.fasta -out GCF_002288825.1_ASM228882v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:02,351] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:02,354] [INFO] Selected 19 target genomes.
[2024-01-25 19:12:02,354] [INFO] Target genome list was writen to GCF_002288825.1_ASM228882v1_genomic.fna/target_genomes.txt
[2024-01-25 19:12:02,363] [INFO] Task started: fastANI
[2024-01-25 19:12:02,363] [INFO] Running command: fastANI --query /var/lib/cwl/stge9f02b90-2572-41c2-b7b7-5e7d6838016a/GCF_002288825.1_ASM228882v1_genomic.fna.gz --refList GCF_002288825.1_ASM228882v1_genomic.fna/target_genomes.txt --output GCF_002288825.1_ASM228882v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:18,189] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:18,189] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2e7453f2-6a00-46fe-957e-a64dc48b0107/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:18,190] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2e7453f2-6a00-46fe-957e-a64dc48b0107/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:18,201] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:12:18,201] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:12:18,201] [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 lenta	strain=1PNM-20	GCA_002288825.1	1141887	1141887	type	True	100.0	1248	1249	95	conclusive
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	80.0782	567	1249	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	80.0104	595	1249	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	79.9951	607	1249	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	79.8198	621	1249	95	below_threshold
Sphingomonas yunnanensis	strain=YIM 3	GCA_019898765.1	310400	310400	type	True	79.6189	590	1249	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_009789535.1	1166323	1166323	type	True	79.5589	526	1249	95	below_threshold
Sphingomonas carotinifaciens	strain=DSM 27347	GCA_014197095.1	1166323	1166323	type	True	79.5321	528	1249	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	79.4816	567	1249	95	below_threshold
Sphingomonas hominis	strain=HHU CXW	GCA_013328205.1	2741495	2741495	type	True	79.4816	556	1249	95	below_threshold
Sphingomonas citricola	strain=RHCKR47	GCA_019429535.1	2862498	2862498	type	True	79.416	529	1249	95	below_threshold
Sphingomonas desiccabilis	strain=CP1D	GCA_004135605.1	429134	429134	type	True	79.3574	469	1249	95	below_threshold
Sphingomonas desiccabilis	strain=DSM 16792	GCA_014196135.1	429134	429134	type	True	79.2984	475	1249	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	79.2699	513	1249	95	below_threshold
Sphingomonas guangdongensis	strain=CGMCC 1.12672	GCA_900199185.1	1141890	1141890	type	True	79.2135	537	1249	95	below_threshold
Sphingomonas gellani	strain=S6-262	GCA_900110035.1	1166340	1166340	type	True	79.0297	469	1249	95	below_threshold
Sphingomonas aerophila	strain=DSM 100044	GCA_014199305.1	1344948	1344948	type	True	78.5745	417	1249	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	78.1836	440	1249	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	78.1187	448	1249	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:18,203] [INFO] DFAST Taxonomy check result was written to GCF_002288825.1_ASM228882v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:18,204] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:18,204] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:18,204] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2e7453f2-6a00-46fe-957e-a64dc48b0107/dqc_reference/checkm_data
[2024-01-25 19:12:18,205] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:18,242] [INFO] Task started: CheckM
[2024-01-25 19:12:18,243] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002288825.1_ASM228882v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002288825.1_ASM228882v1_genomic.fna/checkm_input GCF_002288825.1_ASM228882v1_genomic.fna/checkm_result
[2024-01-25 19:12:46,398] [INFO] Task succeeded: CheckM
[2024-01-25 19:12:46,399] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:12:46,425] [INFO] ===== Completeness check finished =====
[2024-01-25 19:12:46,426] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:12:46,426] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002288825.1_ASM228882v1_genomic.fna/markers.fasta)
[2024-01-25 19:12:46,426] [INFO] Task started: Blastn
[2024-01-25 19:12:46,426] [INFO] Running command: blastn -query GCF_002288825.1_ASM228882v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2e7453f2-6a00-46fe-957e-a64dc48b0107/dqc_reference/reference_markers_gtdb.fasta -out GCF_002288825.1_ASM228882v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:48,400] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:48,406] [INFO] Selected 25 target genomes.
[2024-01-25 19:12:48,406] [INFO] Target genome list was writen to GCF_002288825.1_ASM228882v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:12:48,432] [INFO] Task started: fastANI
[2024-01-25 19:12:48,432] [INFO] Running command: fastANI --query /var/lib/cwl/stge9f02b90-2572-41c2-b7b7-5e7d6838016a/GCF_002288825.1_ASM228882v1_genomic.fna.gz --refList GCF_002288825.1_ASM228882v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002288825.1_ASM228882v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:09,112] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:09,128] [INFO] Found 25 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:13:09,128] [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_002288825.1	s__Sphingomonas lenta	100.0	1248	1249	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	80.0766	567	1249	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	80.0027	607	1249	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	79.9118	625	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903643065.1	s__Sphingomonas sp903643065	79.842	285	1249	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	79.6536	608	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.90	98.90	0.87	0.87	2	-
GCF_004345855.1	s__Sphingomonas sp004345855	79.6041	637	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000764535.1	s__Sphingomonas taxi	79.5567	567	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.55	97.55	0.88	0.88	2	-
GCF_014197105.1	s__Sphingomonas jinjuensis	79.5037	565	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013328205.1	s__Sphingomonas hominis	79.4991	554	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016107325.1	s__Sphingomonas sp016107325	79.4411	558	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_903643035.1	s__Sphingomonas sp903643035	79.4312	331	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002292295.1	s__Sphingomonas sp002292295	79.3955	574	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135605.1	s__Sphingomonas desiccabilis	79.335	472	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCA_001897375.1	s__Sphingomonas sp001897375	79.3119	533	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.01	98.04	0.97	0.96	3	-
GCF_004341505.2	s__Sphingomonas sp004341505	79.2941	476	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	95.45	95.45	0.78	0.78	2	-
GCF_014196115.1	s__Sphingomonas aquatilis	79.2717	547	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.36	95.86	0.87	0.82	11	-
GCF_010450875.1	s__Sphingomonas insulae	79.0907	513	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCA_003243195.1	s__Sphingomonas taxi_B	79.0842	509	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110035.1	s__Sphingomonas gellani	79.0199	470	1249	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	78.8193	500	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016427505.1	s__Sphingomonas sp016427505	78.6553	451	1249	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	78.5931	415	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792685.1	s__Sphingomonas gei	78.1963	438	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002796605.1	s__Sphingomonas sp002796605	78.1009	451	1249	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:13:09,135] [INFO] GTDB search result was written to GCF_002288825.1_ASM228882v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:09,136] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:09,144] [INFO] DFAST_QC result json was written to GCF_002288825.1_ASM228882v1_genomic.fna/dqc_result.json
[2024-01-25 19:13:09,144] [INFO] DFAST_QC completed!
[2024-01-25 19:13:09,144] [INFO] Total running time: 0h1m18s