[2024-01-25 20:13:35,402] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:35,403] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:35,403] [INFO] DQC Reference Directory: /var/lib/cwl/stge2e84bf7-8bb0-480b-8580-18f00028fe88/dqc_reference
[2024-01-25 20:13:36,565] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:36,565] [INFO] Task started: Prodigal
[2024-01-25 20:13:36,566] [INFO] Running command: gunzip -c /var/lib/cwl/stg9a62a8c8-fc61-4024-bd0a-e07af6df23ce/GCF_001598335.1_ASM159833v1_genomic.fna.gz | prodigal -d GCF_001598335.1_ASM159833v1_genomic.fna/cds.fna -a GCF_001598335.1_ASM159833v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:46,641] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:46,642] [INFO] Task started: HMMsearch
[2024-01-25 20:13:46,642] [INFO] Running command: hmmsearch --tblout GCF_001598335.1_ASM159833v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge2e84bf7-8bb0-480b-8580-18f00028fe88/dqc_reference/reference_markers.hmm GCF_001598335.1_ASM159833v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:46,853] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:46,854] [INFO] Found 6/6 markers.
[2024-01-25 20:13:46,885] [INFO] Query marker FASTA was written to GCF_001598335.1_ASM159833v1_genomic.fna/markers.fasta
[2024-01-25 20:13:46,885] [INFO] Task started: Blastn
[2024-01-25 20:13:46,886] [INFO] Running command: blastn -query GCF_001598335.1_ASM159833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2e84bf7-8bb0-480b-8580-18f00028fe88/dqc_reference/reference_markers.fasta -out GCF_001598335.1_ASM159833v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:47,608] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:47,611] [INFO] Selected 17 target genomes.
[2024-01-25 20:13:47,611] [INFO] Target genome list was writen to GCF_001598335.1_ASM159833v1_genomic.fna/target_genomes.txt
[2024-01-25 20:13:47,624] [INFO] Task started: fastANI
[2024-01-25 20:13:47,624] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a62a8c8-fc61-4024-bd0a-e07af6df23ce/GCF_001598335.1_ASM159833v1_genomic.fna.gz --refList GCF_001598335.1_ASM159833v1_genomic.fna/target_genomes.txt --output GCF_001598335.1_ASM159833v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:14:02,456] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:02,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge2e84bf7-8bb0-480b-8580-18f00028fe88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:14:02,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge2e84bf7-8bb0-480b-8580-18f00028fe88/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:14:02,468] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 20:14:02,468] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 20:14:02,468] [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 abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	100.0	1224	1228	95	inconclusive
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	95.3976	973	1228	95	inconclusive
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	82.9416	767	1228	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	82.8998	791	1228	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	82.6589	778	1228	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	82.4403	697	1228	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	82.4359	682	1228	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	82.1788	714	1228	95	below_threshold
Sphingobium fuliginis	strain=CCM 7327	GCA_014636045.1	336203	336203	type	True	82.0367	683	1228	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	81.9034	655	1228	95	below_threshold
Sphingobium chlorophenolicum	strain=NBRC 16172	GCA_000722875.1	46429	46429	type	True	81.809	608	1228	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	81.7108	653	1228	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	81.6387	636	1228	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.0275	343	1228	95	below_threshold
Sphingomonas suaedae	strain=XS-10	GCA_007833215.1	2599297	2599297	type	True	77.9974	359	1228	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	77.6678	310	1228	95	below_threshold
Sphingosinicella ginsenosidimutans	strain=BS-11	GCA_007995055.1	1176539	1176539	type	True	77.3614	254	1228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:14:02,470] [INFO] DFAST Taxonomy check result was written to GCF_001598335.1_ASM159833v1_genomic.fna/tc_result.tsv
[2024-01-25 20:14:02,470] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:14:02,471] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:14:02,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge2e84bf7-8bb0-480b-8580-18f00028fe88/dqc_reference/checkm_data
[2024-01-25 20:14:02,472] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:14:02,519] [INFO] Task started: CheckM
[2024-01-25 20:14:02,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001598335.1_ASM159833v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001598335.1_ASM159833v1_genomic.fna/checkm_input GCF_001598335.1_ASM159833v1_genomic.fna/checkm_result
[2024-01-25 20:14:34,496] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:34,497] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:34,512] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:34,512] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:34,513] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001598335.1_ASM159833v1_genomic.fna/markers.fasta)
[2024-01-25 20:14:34,513] [INFO] Task started: Blastn
[2024-01-25 20:14:34,513] [INFO] Running command: blastn -query GCF_001598335.1_ASM159833v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge2e84bf7-8bb0-480b-8580-18f00028fe88/dqc_reference/reference_markers_gtdb.fasta -out GCF_001598335.1_ASM159833v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:35,809] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:35,812] [INFO] Selected 13 target genomes.
[2024-01-25 20:14:35,812] [INFO] Target genome list was writen to GCF_001598335.1_ASM159833v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:35,819] [INFO] Task started: fastANI
[2024-01-25 20:14:35,820] [INFO] Running command: fastANI --query /var/lib/cwl/stg9a62a8c8-fc61-4024-bd0a-e07af6df23ce/GCF_001598335.1_ASM159833v1_genomic.fna.gz --refList GCF_001598335.1_ASM159833v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001598335.1_ASM159833v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:48,904] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:48,913] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:48,913] [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_001598335.1	s__Sphingobium abikonense	100.0	1224	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	conclusive
GCF_000445105.1	s__Sphingobium lactosutens	95.3976	973	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	conclusive
GCF_000153545.1	s__Sphingobium sp000153545	90.0492	992	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	97.72	97.49	0.82	0.71	9	-
GCA_002457415.1	s__Sphingobium sp002457415	86.296	780	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000508185.1	s__Sphingobium sp000508185	84.5333	811	1228	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	83.6561	792	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.12	99.12	0.95	0.95	2	-
GCF_009720145.1	s__Sphingobium sp009720145	83.4003	765	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013393185.1	s__Sphingobium lactosutens_A	83.2241	811	1228	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	82.9037	790	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.69	97.69	0.91	0.88	5	-
GCF_900109095.1	s__Sphingobium sp900109095	82.8196	805	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013911745.1	s__Sphingobium sp013911745	82.7306	543	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000315525.1	s__Sphingobium yanoikuyae	82.6438	780	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	96.25	95.31	0.82	0.72	34	-
GCF_003967075.1	s__Sphingobium amiense	82.4408	696	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:48,915] [INFO] GTDB search result was written to GCF_001598335.1_ASM159833v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:48,916] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:48,919] [INFO] DFAST_QC result json was written to GCF_001598335.1_ASM159833v1_genomic.fna/dqc_result.json
[2024-01-25 20:14:48,919] [INFO] DFAST_QC completed!
[2024-01-25 20:14:48,919] [INFO] Total running time: 0h1m14s