[2024-01-24 12:45:10,266] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:45:10,268] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:45:10,268] [INFO] DQC Reference Directory: /var/lib/cwl/stgb9947c96-636a-4e7d-bf95-6669b1102261/dqc_reference
[2024-01-24 12:45:13,083] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:45:13,084] [INFO] Task started: Prodigal
[2024-01-24 12:45:13,084] [INFO] Running command: gunzip -c /var/lib/cwl/stgb851db93-0dc3-4224-b34a-6cce68e6bf2a/GCF_014197035.1_ASM1419703v1_genomic.fna.gz | prodigal -d GCF_014197035.1_ASM1419703v1_genomic.fna/cds.fna -a GCF_014197035.1_ASM1419703v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:45:30,905] [INFO] Task succeeded: Prodigal
[2024-01-24 12:45:30,905] [INFO] Task started: HMMsearch
[2024-01-24 12:45:30,906] [INFO] Running command: hmmsearch --tblout GCF_014197035.1_ASM1419703v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb9947c96-636a-4e7d-bf95-6669b1102261/dqc_reference/reference_markers.hmm GCF_014197035.1_ASM1419703v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:45:31,230] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:45:31,232] [INFO] Found 6/6 markers.
[2024-01-24 12:45:31,286] [INFO] Query marker FASTA was written to GCF_014197035.1_ASM1419703v1_genomic.fna/markers.fasta
[2024-01-24 12:45:31,286] [INFO] Task started: Blastn
[2024-01-24 12:45:31,286] [INFO] Running command: blastn -query GCF_014197035.1_ASM1419703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9947c96-636a-4e7d-bf95-6669b1102261/dqc_reference/reference_markers.fasta -out GCF_014197035.1_ASM1419703v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:45:32,186] [INFO] Task succeeded: Blastn
[2024-01-24 12:45:32,190] [INFO] Selected 15 target genomes.
[2024-01-24 12:45:32,190] [INFO] Target genome list was writen to GCF_014197035.1_ASM1419703v1_genomic.fna/target_genomes.txt
[2024-01-24 12:45:32,196] [INFO] Task started: fastANI
[2024-01-24 12:45:32,196] [INFO] Running command: fastANI --query /var/lib/cwl/stgb851db93-0dc3-4224-b34a-6cce68e6bf2a/GCF_014197035.1_ASM1419703v1_genomic.fna.gz --refList GCF_014197035.1_ASM1419703v1_genomic.fna/target_genomes.txt --output GCF_014197035.1_ASM1419703v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:45:48,037] [INFO] Task succeeded: fastANI
[2024-01-24 12:45:48,038] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb9947c96-636a-4e7d-bf95-6669b1102261/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:45:48,039] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb9947c96-636a-4e7d-bf95-6669b1102261/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:45:48,052] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:45:48,052] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:45:48,052] [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
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	100.0	1926	1936	95	conclusive
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	93.4054	1355	1936	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	84.2891	987	1936	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	83.8442	898	1936	95	below_threshold
Sphingobium fuliginis	strain=DSM 18781	GCA_004152845.1	336203	336203	type	True	83.2305	864	1936	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	83.1934	862	1936	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	83.0454	941	1936	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	82.8396	751	1936	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	82.8076	837	1936	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	82.4956	921	1936	95	below_threshold
Sphingobium wenxiniae	strain=JZ-1	GCA_014205735.1	595605	595605	type	True	82.3548	711	1936	95	below_threshold
Sphingobium sufflavum	strain=HL-25	GCA_021403115.1	1129547	1129547	type	True	79.0371	532	1936	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.6367	414	1936	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.1369	429	1936	95	below_threshold
Novosphingobium umbonatum	strain=FSY-9	GCA_004005905.1	1908524	1908524	type	True	77.4445	282	1936	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:45:48,054] [INFO] DFAST Taxonomy check result was written to GCF_014197035.1_ASM1419703v1_genomic.fna/tc_result.tsv
[2024-01-24 12:45:48,054] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:45:48,055] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:45:48,055] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb9947c96-636a-4e7d-bf95-6669b1102261/dqc_reference/checkm_data
[2024-01-24 12:45:48,056] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:45:48,111] [INFO] Task started: CheckM
[2024-01-24 12:45:48,111] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014197035.1_ASM1419703v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014197035.1_ASM1419703v1_genomic.fna/checkm_input GCF_014197035.1_ASM1419703v1_genomic.fna/checkm_result
[2024-01-24 12:46:39,566] [INFO] Task succeeded: CheckM
[2024-01-24 12:46:39,568] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:46:39,591] [INFO] ===== Completeness check finished =====
[2024-01-24 12:46:39,591] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:46:39,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014197035.1_ASM1419703v1_genomic.fna/markers.fasta)
[2024-01-24 12:46:39,592] [INFO] Task started: Blastn
[2024-01-24 12:46:39,592] [INFO] Running command: blastn -query GCF_014197035.1_ASM1419703v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb9947c96-636a-4e7d-bf95-6669b1102261/dqc_reference/reference_markers_gtdb.fasta -out GCF_014197035.1_ASM1419703v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:40,989] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:40,993] [INFO] Selected 16 target genomes.
[2024-01-24 12:46:40,993] [INFO] Target genome list was writen to GCF_014197035.1_ASM1419703v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:46:41,009] [INFO] Task started: fastANI
[2024-01-24 12:46:41,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgb851db93-0dc3-4224-b34a-6cce68e6bf2a/GCF_014197035.1_ASM1419703v1_genomic.fna.gz --refList GCF_014197035.1_ASM1419703v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014197035.1_ASM1419703v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:46:59,893] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:59,909] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:46:59,909] [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_014197035.1	s__Sphingobium scionense	100.0	1927	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000315525.1	s__Sphingobium yanoikuyae	93.381	1357	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCF_000281715.1	s__Sphingobium sp000281715	89.9795	1150	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008710155.1	s__Sphingobium limneticum	84.2875	987	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.69	97.69	0.91	0.88	5	-
GCF_013393185.1	s__Sphingobium lactosutens_A	84.2435	982	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001650725.1	s__Sphingobium sp001650725	84.2196	996	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.12	99.12	0.95	0.95	2	-
GCF_900111125.1	s__Sphingobium sp900111125	84.1565	1036	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014203965.1	s__Sphingobium sp014203965	84.0937	928	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900109095.1	s__Sphingobium sp900109095	84.0354	962	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013822485.1	s__Sphingobium sp013822485	83.5041	689	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003591655.1	s__Sphingobium sp003591655	82.49	921	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013375535.1	s__Sphingobium sp013375535	82.4631	866	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000367345.1	s__Sphingobium xenophagum	82.4538	778	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.29	96.67	0.79	0.71	22	-
GCF_014873695.1	s__Sphingobium sp014873695	82.3348	801	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001713415.1	s__Sphingobium sp001713415	82.2535	859	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	95.59	95.59	0.75	0.75	2	-
GCF_013375555.1	s__Sphingobium sp013375555	82.0848	795	1936	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:46:59,910] [INFO] GTDB search result was written to GCF_014197035.1_ASM1419703v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:46:59,911] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:46:59,915] [INFO] DFAST_QC result json was written to GCF_014197035.1_ASM1419703v1_genomic.fna/dqc_result.json
[2024-01-24 12:46:59,915] [INFO] DFAST_QC completed!
[2024-01-24 12:46:59,915] [INFO] Total running time: 0h1m50s