[2024-01-24 13:45:46,578] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:46,587] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:46,587] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc8a06e1-b9c8-4d5d-a5b0-94441777992b/dqc_reference
[2024-01-24 13:45:47,895] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:47,896] [INFO] Task started: Prodigal
[2024-01-24 13:45:47,896] [INFO] Running command: gunzip -c /var/lib/cwl/stg157f6143-bb07-4804-a992-d1b1254ad6d9/GCF_014199305.1_ASM1419930v1_genomic.fna.gz | prodigal -d GCF_014199305.1_ASM1419930v1_genomic.fna/cds.fna -a GCF_014199305.1_ASM1419930v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:00,094] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:00,095] [INFO] Task started: HMMsearch
[2024-01-24 13:46:00,095] [INFO] Running command: hmmsearch --tblout GCF_014199305.1_ASM1419930v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc8a06e1-b9c8-4d5d-a5b0-94441777992b/dqc_reference/reference_markers.hmm GCF_014199305.1_ASM1419930v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:00,469] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:00,470] [INFO] Found 6/6 markers.
[2024-01-24 13:46:00,510] [INFO] Query marker FASTA was written to GCF_014199305.1_ASM1419930v1_genomic.fna/markers.fasta
[2024-01-24 13:46:00,510] [INFO] Task started: Blastn
[2024-01-24 13:46:00,510] [INFO] Running command: blastn -query GCF_014199305.1_ASM1419930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc8a06e1-b9c8-4d5d-a5b0-94441777992b/dqc_reference/reference_markers.fasta -out GCF_014199305.1_ASM1419930v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:01,551] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:01,559] [INFO] Selected 18 target genomes.
[2024-01-24 13:46:01,560] [INFO] Target genome list was writen to GCF_014199305.1_ASM1419930v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:01,570] [INFO] Task started: fastANI
[2024-01-24 13:46:01,571] [INFO] Running command: fastANI --query /var/lib/cwl/stg157f6143-bb07-4804-a992-d1b1254ad6d9/GCF_014199305.1_ASM1419930v1_genomic.fna.gz --refList GCF_014199305.1_ASM1419930v1_genomic.fna/target_genomes.txt --output GCF_014199305.1_ASM1419930v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:15,326] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:15,326] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc8a06e1-b9c8-4d5d-a5b0-94441777992b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:15,326] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc8a06e1-b9c8-4d5d-a5b0-94441777992b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:15,342] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:15,342] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:15,342] [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 aerophila	strain=DSM 100044	GCA_014199305.1	1344948	1344948	type	True	100.0	1317	1318	95	conclusive
Sphingomonas gellani	strain=S6-262	GCA_900110035.1	1166340	1166340	type	True	80.0845	563	1318	95	below_threshold
Sphingomonas rubra	strain=CGMCC 1.9113	GCA_900115745.1	634430	634430	type	True	79.297	436	1318	95	below_threshold
Sphingomonas metalli	strain=CGMCC 1.15330	GCA_014641735.1	1779358	1779358	type	True	79.1997	467	1318	95	below_threshold
Sphingomonas jinjuensis	strain=YC6723	GCA_014197105.1	535907	535907	type	True	79.0844	474	1318	95	below_threshold
Sphingomonas adhaesiva	strain=NBRC 15099	GCA_001592345.1	28212	28212	type	True	79.0448	368	1318	95	below_threshold
Sphingomonas insulae	strain=KCTC 12872	GCA_010450875.1	424800	424800	type	True	78.9663	452	1318	95	below_threshold
Sphingomonas insulae	strain=DSM 21792	GCA_011762035.1	424800	424800	type	True	78.9617	446	1318	95	below_threshold
Sphingomonas parapaucimobilis	strain=NBRC 15100	GCA_000787715.1	28213	28213	type	True	78.9218	425	1318	95	below_threshold
Sphingomonas taxi	strain=ATCC 55669	GCA_000764535.1	1549858	1549858	type	True	78.7633	494	1318	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.7469	441	1318	95	below_threshold
Sphingomonas endophytica	strain=DSM 101535	GCA_014199415.1	869719	869719	type	True	78.6518	413	1318	95	below_threshold
Sphingomonas folli	strain=RHCKR7	GCA_019429525.1	2862497	2862497	type	True	78.6048	479	1318	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.6047	469	1318	95	below_threshold
Sphingomonas phyllosphaerae	strain=FA2	GCA_000427645.1	257003	257003	type	True	78.5313	426	1318	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.5124	457	1318	95	below_threshold
Sphingomonas lenta	strain=1PNM-20	GCA_002288825.1	1141887	1141887	type	True	78.4419	430	1318	95	below_threshold
Sphingomonas radiodurans	strain=S9-5	GCA_020866845.1	2890321	2890321	type	True	78.0484	338	1318	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:15,344] [INFO] DFAST Taxonomy check result was written to GCF_014199305.1_ASM1419930v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:15,345] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:15,345] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:15,345] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc8a06e1-b9c8-4d5d-a5b0-94441777992b/dqc_reference/checkm_data
[2024-01-24 13:46:15,346] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:15,400] [INFO] Task started: CheckM
[2024-01-24 13:46:15,400] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014199305.1_ASM1419930v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014199305.1_ASM1419930v1_genomic.fna/checkm_input GCF_014199305.1_ASM1419930v1_genomic.fna/checkm_result
[2024-01-24 13:46:55,511] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:55,512] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:55,534] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:55,534] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:55,535] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014199305.1_ASM1419930v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:55,535] [INFO] Task started: Blastn
[2024-01-24 13:46:55,536] [INFO] Running command: blastn -query GCF_014199305.1_ASM1419930v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc8a06e1-b9c8-4d5d-a5b0-94441777992b/dqc_reference/reference_markers_gtdb.fasta -out GCF_014199305.1_ASM1419930v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:57,284] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:57,290] [INFO] Selected 19 target genomes.
[2024-01-24 13:46:57,290] [INFO] Target genome list was writen to GCF_014199305.1_ASM1419930v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:57,322] [INFO] Task started: fastANI
[2024-01-24 13:46:57,322] [INFO] Running command: fastANI --query /var/lib/cwl/stg157f6143-bb07-4804-a992-d1b1254ad6d9/GCF_014199305.1_ASM1419930v1_genomic.fna.gz --refList GCF_014199305.1_ASM1419930v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014199305.1_ASM1419930v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:10,945] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:10,969] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:10,969] [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_014199305.1	s__Sphingomonas aerophila	100.0	1317	1318	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_900110035.1	s__Sphingomonas gellani	80.045	567	1318	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	79.333	437	1318	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003951315.1	s__Sphingomonas sp003951315	79.2581	502	1318	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	79.2247	465	1318	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	79.085	474	1318	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	79.0684	491	1318	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	79.0585	511	1318	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	78.9667	241	1318	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016820445.1	s__Sphingomonas sp016820445	78.9667	434	1318	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	97.21	97.21	0.90	0.90	2	-
GCF_010450875.1	s__Sphingomonas insulae	78.9473	454	1318	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.99	99.99	0.99	0.99	2	-
GCF_001476905.1	s__Sphingomonas sanguinis_B	78.935	403	1318	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	96.13	96.11	0.83	0.82	3	-
GCF_003355005.1	s__Sphingomonas sp003355005	78.9332	482	1318	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	78.9122	432	1318	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	99.76	99.56	0.89	0.87	3	-
GCF_903644135.1	s__Sphingomonas sp903644135	78.8662	293	1318	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001477495.1	s__Sphingomonas yabuuchiae_A	78.7035	412	1318	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	78.5025	457	1318	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002288825.1	s__Sphingomonas lenta	78.4605	428	1318	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	78.3692	384	1318	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 13:47:10,971] [INFO] GTDB search result was written to GCF_014199305.1_ASM1419930v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:10,972] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:10,976] [INFO] DFAST_QC result json was written to GCF_014199305.1_ASM1419930v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:10,977] [INFO] DFAST_QC completed!
[2024-01-24 13:47:10,977] [INFO] Total running time: 0h1m24s