[2024-01-24 14:54:56,628] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,630] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,630] [INFO] DQC Reference Directory: /var/lib/cwl/stg87d28729-e615-48e2-ab6d-918bd85c9fc4/dqc_reference
[2024-01-24 14:54:58,022] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:58,023] [INFO] Task started: Prodigal
[2024-01-24 14:54:58,023] [INFO] Running command: gunzip -c /var/lib/cwl/stgc49a00d2-5755-4e53-9926-a34ec82c52c8/GCF_012979535.1_ASM1297953v1_genomic.fna.gz | prodigal -d GCF_012979535.1_ASM1297953v1_genomic.fna/cds.fna -a GCF_012979535.1_ASM1297953v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:08,642] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:08,643] [INFO] Task started: HMMsearch
[2024-01-24 14:55:08,643] [INFO] Running command: hmmsearch --tblout GCF_012979535.1_ASM1297953v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg87d28729-e615-48e2-ab6d-918bd85c9fc4/dqc_reference/reference_markers.hmm GCF_012979535.1_ASM1297953v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:08,916] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:08,917] [INFO] Found 6/6 markers.
[2024-01-24 14:55:08,947] [INFO] Query marker FASTA was written to GCF_012979535.1_ASM1297953v1_genomic.fna/markers.fasta
[2024-01-24 14:55:08,948] [INFO] Task started: Blastn
[2024-01-24 14:55:08,948] [INFO] Running command: blastn -query GCF_012979535.1_ASM1297953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87d28729-e615-48e2-ab6d-918bd85c9fc4/dqc_reference/reference_markers.fasta -out GCF_012979535.1_ASM1297953v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:09,845] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:09,848] [INFO] Selected 26 target genomes.
[2024-01-24 14:55:09,849] [INFO] Target genome list was writen to GCF_012979535.1_ASM1297953v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:09,876] [INFO] Task started: fastANI
[2024-01-24 14:55:09,876] [INFO] Running command: fastANI --query /var/lib/cwl/stgc49a00d2-5755-4e53-9926-a34ec82c52c8/GCF_012979535.1_ASM1297953v1_genomic.fna.gz --refList GCF_012979535.1_ASM1297953v1_genomic.fna/target_genomes.txt --output GCF_012979535.1_ASM1297953v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:33,868] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:33,868] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg87d28729-e615-48e2-ab6d-918bd85c9fc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:33,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg87d28729-e615-48e2-ab6d-918bd85c9fc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:33,891] [INFO] Found 23 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:33,892] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:33,892] [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 lacunae	strain=CSW-10	GCA_012979535.1	2698828	2698828	type	True	100.0	992	992	95	conclusive
Sphingopyxis italica	strain=DSM 25229	GCA_011926545.1	1129133	1129133	type	True	78.6163	280	992	95	below_threshold
Sphingopyxis terrae subsp. terrae	strain=NBRC 15098	GCA_001598815.1	2448440	33052	type	True	78.5652	277	992	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=DSM 24316	GCA_002374275.1	429001	33052	type	True	78.5405	277	992	95	below_threshold
Sphingopyxis terrae subsp. ummariensis	strain=UI2	GCA_900177755.1	429001	33052	type	True	78.5155	280	992	95	below_threshold
Sphingopyxis macrogoltabida	strain=203	GCA_001314325.1	33050	33050	type	True	78.5154	297	992	95	below_threshold
Sphingopyxis indica	strain=DS15	GCA_900188185.1	436663	436663	type	True	78.4888	275	992	95	below_threshold
Sphingopyxis solisilvae	strain=R366	GCA_015475875.1	1886788	1886788	type	True	78.4747	274	992	95	below_threshold
Sphingopyxis panaciterrae	strain=DSM 27164	GCA_011762125.1	363841	363841	type	True	78.4565	284	992	95	below_threshold
Sphingopyxis soli	strain=BL03	GCA_018682675.1	592051	592051	type	True	78.4291	271	992	95	below_threshold
Sphingopyxis alaskensis	strain=RB2256	GCA_000013985.1	117207	117207	type	True	78.269	277	992	95	below_threshold
Sphingopyxis fribergensis	strain=Kp5.2	GCA_000803645.1	1515612	1515612	type	True	78.2618	272	992	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	78.2036	267	992	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	77.8198	209	992	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	77.7269	212	992	95	below_threshold
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	77.5952	206	992	95	below_threshold
Sphingobium xanthum	strain=NL9	GCA_019737615.1	1387165	1387165	type	True	77.5897	205	992	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	77.541	215	992	95	below_threshold
Sphingomonas oligoaromativorans	strain=DSM 102246	GCA_011762195.1	575322	575322	type	True	77.5374	175	992	95	below_threshold
Stakelama flava	strain=CBK3Z-3	GCA_019351405.1	2860338	2860338	type	True	77.4634	147	992	95	below_threshold
Sphingomonas changbaiensis	strain=NBRC 104936	GCA_000974765.1	529705	529705	type	True	77.2925	179	992	95	below_threshold
Croceibacterium ferulae	strain=SX2RGS8	GCA_003660445.1	1854641	1854641	type	True	77.1884	160	992	95	below_threshold
Sphingorhabdus lacus	strain=IMCC1753	GCA_009768975.1	392610	392610	type	True	76.9535	153	992	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:33,895] [INFO] DFAST Taxonomy check result was written to GCF_012979535.1_ASM1297953v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:33,896] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:33,896] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:33,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg87d28729-e615-48e2-ab6d-918bd85c9fc4/dqc_reference/checkm_data
[2024-01-24 14:55:33,899] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:33,932] [INFO] Task started: CheckM
[2024-01-24 14:55:33,933] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012979535.1_ASM1297953v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012979535.1_ASM1297953v1_genomic.fna/checkm_input GCF_012979535.1_ASM1297953v1_genomic.fna/checkm_result
[2024-01-24 14:56:08,327] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:08,329] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:08,354] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:08,354] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:08,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012979535.1_ASM1297953v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:08,355] [INFO] Task started: Blastn
[2024-01-24 14:56:08,356] [INFO] Running command: blastn -query GCF_012979535.1_ASM1297953v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg87d28729-e615-48e2-ab6d-918bd85c9fc4/dqc_reference/reference_markers_gtdb.fasta -out GCF_012979535.1_ASM1297953v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:09,807] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:09,812] [INFO] Selected 26 target genomes.
[2024-01-24 14:56:09,812] [INFO] Target genome list was writen to GCF_012979535.1_ASM1297953v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:09,833] [INFO] Task started: fastANI
[2024-01-24 14:56:09,834] [INFO] Running command: fastANI --query /var/lib/cwl/stgc49a00d2-5755-4e53-9926-a34ec82c52c8/GCF_012979535.1_ASM1297953v1_genomic.fna.gz --refList GCF_012979535.1_ASM1297953v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012979535.1_ASM1297953v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:27,229] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:27,256] [INFO] Found 26 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:27,257] [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_012979535.1	s__Sphingopyxis lacunae	100.0	992	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001990265.1	s__Sphingopyxis sp001990265	78.66	302	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598815.1	s__Sphingopyxis terrae	78.5661	278	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	96.70	95.58	0.84	0.76	19	-
GCF_900188185.1	s__Sphingopyxis indica	78.5033	274	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842935.1	s__Sphingopyxis sp002842935	78.4467	217	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003609835.1	s__Sphingopyxis sp003609835	78.3919	276	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078365.1	s__Sphingopyxis sp900078365	78.3901	285	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001984035.1	s__Sphingopyxis sp001984035	78.3643	297	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001468285.1	s__Sphingopyxis sp001468285	78.315	312	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.98	99.98	0.98	0.98	2	-
GCF_000315525.1	s__Sphingobium yanoikuyae	78.2073	266	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCF_002205635.1	s__Sphingopyxis witflariensis	78.1758	281	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004795895.1	s__Sphingopyxis sp004795895	78.1231	280	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002454115.1	s__Sphingopyxis sp002454115	78.0324	278	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.98	99.98	0.96	0.96	2	-
GCA_005518185.1	s__Chakrabartia godavariana	78.0143	211	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Chakrabartia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375555.1	s__Sphingobium sp013375555	77.9657	238	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016704835.1	s__Sphingopyxis sp016704835	77.9567	261	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002198665.1	s__Novosphingobium sp002198665	77.9206	207	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018823905.1	s__Sphingopyxis sp018823905	77.9194	258	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingopyxis	95.0	99.80	99.78	0.95	0.94	3	-
GCF_014196745.1	s__Sphingomonas kyeonggiensis	77.5557	214	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011762195.1	s__Sphingomonas_N oligoaromativorans	77.5489	175	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_N	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018603885.1	s__Sphingobium sp018603885	77.5463	216	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440635.1	s__Novosphingobium sp002440635	77.5429	202	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Novosphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839675.1	s__Chakrabartia sp903839675	77.5073	160	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Chakrabartia	95.0	100.00	100.00	0.99	0.99	3	-
GCA_017418975.1	s__Sphingomonas sp017418975	77.4439	207	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903958285.1	s__Chakrabartia sp903958285	77.3105	135	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Chakrabartia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000974765.1	s__Sphingomonas_B changbaiensis	77.308	178	992	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:27,258] [INFO] GTDB search result was written to GCF_012979535.1_ASM1297953v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:27,259] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:27,263] [INFO] DFAST_QC result json was written to GCF_012979535.1_ASM1297953v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:27,264] [INFO] DFAST_QC completed!
[2024-01-24 14:56:27,264] [INFO] Total running time: 0h1m31s