[2024-01-24 13:25:58,093] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:58,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:58,101] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fae2f24-8993-4872-8a99-d4abf901a6ec/dqc_reference
[2024-01-24 13:26:00,374] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:26:00,376] [INFO] Task started: Prodigal
[2024-01-24 13:26:00,376] [INFO] Running command: gunzip -c /var/lib/cwl/stga883104c-53bf-4f40-9cb9-8df57df9950a/GCF_001591025.1_ASM159102v1_genomic.fna.gz | prodigal -d GCF_001591025.1_ASM159102v1_genomic.fna/cds.fna -a GCF_001591025.1_ASM159102v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:10,621] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:10,621] [INFO] Task started: HMMsearch
[2024-01-24 13:26:10,621] [INFO] Running command: hmmsearch --tblout GCF_001591025.1_ASM159102v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fae2f24-8993-4872-8a99-d4abf901a6ec/dqc_reference/reference_markers.hmm GCF_001591025.1_ASM159102v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:10,922] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:10,924] [INFO] Found 6/6 markers.
[2024-01-24 13:26:10,969] [INFO] Query marker FASTA was written to GCF_001591025.1_ASM159102v1_genomic.fna/markers.fasta
[2024-01-24 13:26:10,970] [INFO] Task started: Blastn
[2024-01-24 13:26:10,970] [INFO] Running command: blastn -query GCF_001591025.1_ASM159102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fae2f24-8993-4872-8a99-d4abf901a6ec/dqc_reference/reference_markers.fasta -out GCF_001591025.1_ASM159102v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:12,052] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:12,056] [INFO] Selected 19 target genomes.
[2024-01-24 13:26:12,057] [INFO] Target genome list was writen to GCF_001591025.1_ASM159102v1_genomic.fna/target_genomes.txt
[2024-01-24 13:26:12,071] [INFO] Task started: fastANI
[2024-01-24 13:26:12,072] [INFO] Running command: fastANI --query /var/lib/cwl/stga883104c-53bf-4f40-9cb9-8df57df9950a/GCF_001591025.1_ASM159102v1_genomic.fna.gz --refList GCF_001591025.1_ASM159102v1_genomic.fna/target_genomes.txt --output GCF_001591025.1_ASM159102v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:27,936] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:27,936] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fae2f24-8993-4872-8a99-d4abf901a6ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:27,937] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fae2f24-8993-4872-8a99-d4abf901a6ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:27,962] [INFO] Found 19 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:27,962] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:27,962] [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 soli	strain=NBRC 100801	GCA_001591025.1	266127	266127	type	True	100.0	1155	1156	95	conclusive
Sphingomonas naasensis	strain=DSM 100060	GCA_011762145.1	1344951	1344951	type	True	81.5548	716	1156	95	below_threshold
Sphingomonas naasensis	strain=KIS18-15	GCA_004792695.1	1344951	1344951	type	True	81.5279	715	1156	95	below_threshold
Sphingomonas leidyi	strain=DSM 4733	GCA_011761945.1	68569	68569	type	True	81.4003	703	1156	95	below_threshold
Sphingomonas kyeonggiensis	strain=DSM 101806	GCA_014196745.1	1268553	1268553	type	True	81.334	714	1156	95	below_threshold
Sphingomonas hengshuiensis	strain=WHSC-8	GCA_000935025.1	1609977	1609977	type	True	80.9863	708	1156	95	below_threshold
Sphingomonas gei	strain=ZFGT-11	GCA_004792685.1	1395960	1395960	type	True	80.8746	655	1156	95	below_threshold
Sphingomonas psychrotolerans	strain=Cra20	GCA_002796605.1	1327635	1327635	type	True	80.8522	662	1156	95	below_threshold
Sphingomonas pituitosa	strain=NBRC 102491	GCA_001598435.1	99597	99597	type	True	80.5392	551	1156	95	below_threshold
Sphingomonas trueperi	strain=DSM 7225	GCA_011927635.1	53317	53317	type	True	80.5307	573	1156	95	below_threshold
Sphingomonas koreensis	strain=JSS26	GCA_002797435.1	93064	93064	type	True	80.0789	546	1156	95	below_threshold
Sphingomonas koreensis	strain=KCTC 2882	GCA_003953035.1	93064	93064	type	True	80.0304	549	1156	95	below_threshold
Sphingomonas koreensis	strain=NBRC 16723	GCA_001598395.1	93064	93064	type	True	80.0091	553	1156	95	below_threshold
Sphingomonas xinjiangensis	strain=DSM 26736	GCA_014199255.1	643568	643568	type	True	79.7475	510	1156	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	79.736	558	1156	95	below_threshold
Sphingosinithalassobacter portus	strain=FM6	GCA_003171655.1	2676234	2676234	type	True	79.2087	495	1156	95	below_threshold
Sphingomonas baiyangensis	strain=L-1-4 w-11	GCA_005144715.1	2572576	2572576	type	True	79.1139	491	1156	95	below_threshold
Sphingomonas citri	strain=RRHST34	GCA_019429485.1	2862499	2862499	type	True	78.561	429	1156	95	below_threshold
Sphingomonas corticis	strain=36D10-4-7	GCA_012035195.1	2722791	2722791	type	True	78.2363	433	1156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:27,965] [INFO] DFAST Taxonomy check result was written to GCF_001591025.1_ASM159102v1_genomic.fna/tc_result.tsv
[2024-01-24 13:26:27,966] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:27,966] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:27,966] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fae2f24-8993-4872-8a99-d4abf901a6ec/dqc_reference/checkm_data
[2024-01-24 13:26:27,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:28,005] [INFO] Task started: CheckM
[2024-01-24 13:26:28,006] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001591025.1_ASM159102v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001591025.1_ASM159102v1_genomic.fna/checkm_input GCF_001591025.1_ASM159102v1_genomic.fna/checkm_result
[2024-01-24 13:27:02,004] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:02,007] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:02,031] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:02,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:02,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001591025.1_ASM159102v1_genomic.fna/markers.fasta)
[2024-01-24 13:27:02,033] [INFO] Task started: Blastn
[2024-01-24 13:27:02,033] [INFO] Running command: blastn -query GCF_001591025.1_ASM159102v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fae2f24-8993-4872-8a99-d4abf901a6ec/dqc_reference/reference_markers_gtdb.fasta -out GCF_001591025.1_ASM159102v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:03,866] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:03,871] [INFO] Selected 19 target genomes.
[2024-01-24 13:27:03,871] [INFO] Target genome list was writen to GCF_001591025.1_ASM159102v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:03,906] [INFO] Task started: fastANI
[2024-01-24 13:27:03,907] [INFO] Running command: fastANI --query /var/lib/cwl/stga883104c-53bf-4f40-9cb9-8df57df9950a/GCF_001591025.1_ASM159102v1_genomic.fna.gz --refList GCF_001591025.1_ASM159102v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001591025.1_ASM159102v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:21,637] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:21,664] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:21,664] [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_001591025.1	s__Sphingomonas soli	100.0	1155	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_004173185.1	s__Sphingomonas sp004173185	83.8032	808	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449795.1	s__Sphingomonas sp018449795	81.7652	662	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004792695.1	s__Sphingomonas naasensis	81.544	713	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013416555.1	s__Sphingomonas sp013416555	81.4616	728	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096895.1	s__Sphingomonas sp003096895	81.4357	716	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761945.1	s__Sphingomonas leidyi	81.4231	700	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.87	98.83	0.90	0.87	3	-
GCA_017418975.1	s__Sphingomonas sp017418975	81.4204	717	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002127225.1	s__Sphingomonas sp002127225	81.3986	715	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428865.1	s__Sphingomonas sp001428865	81.3873	681	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014489075.1	s__Sphingomonas sp014489075	81.376	705	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012927115.1	s__Sphingomonas sp012927115	81.3661	706	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014196745.1	s__Sphingomonas kyeonggiensis	81.3092	717	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000712135.1	s__Sphingomonas sp000712135	81.2701	675	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002002925.1	s__Sphingomonas sp002002925	81.226	675	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000935025.1	s__Sphingomonas hengshuiensis	80.9808	709	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002797435.1	s__Sphingomonas koreensis	80.0766	547	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	98.13	98.00	0.88	0.86	72	-
GCA_017745215.1	s__Sphingomonas sp017745215	80.0184	637	1156	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199255.1	s__Sphingomonas xinjiangensis	79.759	508	1156	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 13:27:21,666] [INFO] GTDB search result was written to GCF_001591025.1_ASM159102v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:21,667] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:21,672] [INFO] DFAST_QC result json was written to GCF_001591025.1_ASM159102v1_genomic.fna/dqc_result.json
[2024-01-24 13:27:21,672] [INFO] DFAST_QC completed!
[2024-01-24 13:27:21,672] [INFO] Total running time: 0h1m24s