[2024-01-24 15:09:55,460] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:09:55,463] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:09:55,464] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c866d7e-d761-450d-99f6-e7e41b3f5ede/dqc_reference
[2024-01-24 15:09:58,167] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:09:58,173] [INFO] Task started: Prodigal
[2024-01-24 15:09:58,173] [INFO] Running command: gunzip -c /var/lib/cwl/stgc93424a1-139a-4865-81a8-9c67d0de59a2/GCF_003967075.1_ASM396707v1_genomic.fna.gz | prodigal -d GCF_003967075.1_ASM396707v1_genomic.fna/cds.fna -a GCF_003967075.1_ASM396707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:12,729] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:12,729] [INFO] Task started: HMMsearch
[2024-01-24 15:10:12,729] [INFO] Running command: hmmsearch --tblout GCF_003967075.1_ASM396707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c866d7e-d761-450d-99f6-e7e41b3f5ede/dqc_reference/reference_markers.hmm GCF_003967075.1_ASM396707v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:13,097] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:13,098] [INFO] Found 6/6 markers.
[2024-01-24 15:10:13,153] [INFO] Query marker FASTA was written to GCF_003967075.1_ASM396707v1_genomic.fna/markers.fasta
[2024-01-24 15:10:13,154] [INFO] Task started: Blastn
[2024-01-24 15:10:13,155] [INFO] Running command: blastn -query GCF_003967075.1_ASM396707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c866d7e-d761-450d-99f6-e7e41b3f5ede/dqc_reference/reference_markers.fasta -out GCF_003967075.1_ASM396707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:14,285] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:14,289] [INFO] Selected 17 target genomes.
[2024-01-24 15:10:14,290] [INFO] Target genome list was writen to GCF_003967075.1_ASM396707v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:14,298] [INFO] Task started: fastANI
[2024-01-24 15:10:14,298] [INFO] Running command: fastANI --query /var/lib/cwl/stgc93424a1-139a-4865-81a8-9c67d0de59a2/GCF_003967075.1_ASM396707v1_genomic.fna.gz --refList GCF_003967075.1_ASM396707v1_genomic.fna/target_genomes.txt --output GCF_003967075.1_ASM396707v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:10:31,608] [INFO] Task succeeded: fastANI
[2024-01-24 15:10:31,609] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c866d7e-d761-450d-99f6-e7e41b3f5ede/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:10:31,610] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c866d7e-d761-450d-99f6-e7e41b3f5ede/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:10:31,624] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:10:31,625] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:10:31,625] [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 amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	100.0	1580	1588	95	conclusive
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	99.9195	1448	1588	95	conclusive
Sphingobium cloacae	strain=JCM 10874	GCA_002355855.1	120107	120107	type	True	84.6322	782	1588	95	below_threshold
Sphingobium cloacae	strain=NBRC 102517	GCA_001591285.1	120107	120107	type	True	84.5293	734	1588	95	below_threshold
Sphingobium indicum	strain=B90A	GCA_000264945.2	332055	332055	type	True	83.5158	708	1588	95	below_threshold
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	83.3878	760	1588	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	83.2094	782	1588	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	83.1894	785	1588	95	below_threshold
Sphingobium ummariense	strain=RL-3	GCA_000447205.1	420994	420994	type	True	83.0652	726	1588	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	83.0078	771	1588	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	82.7068	779	1588	95	below_threshold
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	82.4579	699	1588	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	82.1875	728	1588	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.5271	359	1588	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.2409	372	1588	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.2035	369	1588	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.9862	425	1588	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:10:31,627] [INFO] DFAST Taxonomy check result was written to GCF_003967075.1_ASM396707v1_genomic.fna/tc_result.tsv
[2024-01-24 15:10:31,627] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:10:31,627] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:10:31,627] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c866d7e-d761-450d-99f6-e7e41b3f5ede/dqc_reference/checkm_data
[2024-01-24 15:10:31,628] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:10:31,673] [INFO] Task started: CheckM
[2024-01-24 15:10:31,674] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003967075.1_ASM396707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003967075.1_ASM396707v1_genomic.fna/checkm_input GCF_003967075.1_ASM396707v1_genomic.fna/checkm_result
[2024-01-24 15:11:16,910] [INFO] Task succeeded: CheckM
[2024-01-24 15:11:16,911] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:11:16,932] [INFO] ===== Completeness check finished =====
[2024-01-24 15:11:16,933] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:11:16,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003967075.1_ASM396707v1_genomic.fna/markers.fasta)
[2024-01-24 15:11:16,933] [INFO] Task started: Blastn
[2024-01-24 15:11:16,933] [INFO] Running command: blastn -query GCF_003967075.1_ASM396707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c866d7e-d761-450d-99f6-e7e41b3f5ede/dqc_reference/reference_markers_gtdb.fasta -out GCF_003967075.1_ASM396707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:11:19,066] [INFO] Task succeeded: Blastn
[2024-01-24 15:11:19,069] [INFO] Selected 12 target genomes.
[2024-01-24 15:11:19,069] [INFO] Target genome list was writen to GCF_003967075.1_ASM396707v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:11:19,078] [INFO] Task started: fastANI
[2024-01-24 15:11:19,078] [INFO] Running command: fastANI --query /var/lib/cwl/stgc93424a1-139a-4865-81a8-9c67d0de59a2/GCF_003967075.1_ASM396707v1_genomic.fna.gz --refList GCF_003967075.1_ASM396707v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003967075.1_ASM396707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:11:32,597] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:32,616] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:11:32,616] [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_003967075.1	s__Sphingobium amiense	100.0	1577	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCA_003248505.1	s__Sphingobium sp003248505	85.4517	738	1588	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	85.2411	567	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001556865.1	s__Sphingobium sp001556865	84.6814	741	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720145.1	s__Sphingobium sp009720145	84.1633	779	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002457415.1	s__Sphingobium sp002457415	83.8729	638	1588	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	83.8253	766	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.12	99.12	0.95	0.95	2	-
GCF_008710155.1	s__Sphingobium limneticum	83.1957	784	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.69	97.69	0.91	0.88	5	-
GCF_000445105.1	s__Sphingobium lactosutens	83.0356	771	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	-
GCF_000508185.1	s__Sphingobium sp000508185	82.9935	724	1588	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	82.7072	763	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001598335.1	s__Sphingobium abikonense	82.4688	698	1588	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.3976	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:11:32,618] [INFO] GTDB search result was written to GCF_003967075.1_ASM396707v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:11:32,619] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:11:32,624] [INFO] DFAST_QC result json was written to GCF_003967075.1_ASM396707v1_genomic.fna/dqc_result.json
[2024-01-24 15:11:32,624] [INFO] DFAST_QC completed!
[2024-01-24 15:11:32,624] [INFO] Total running time: 0h1m37s