[2024-01-24 13:40:34,848] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:34,850] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:34,851] [INFO] DQC Reference Directory: /var/lib/cwl/stg06af64fb-2aa8-4f30-b57d-8657c71e8206/dqc_reference
[2024-01-24 13:40:36,389] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:36,390] [INFO] Task started: Prodigal
[2024-01-24 13:40:36,390] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd839d46-2773-4a66-991c-5e44a1622c83/GCF_024349785.1_ASM2434978v1_genomic.fna.gz | prodigal -d GCF_024349785.1_ASM2434978v1_genomic.fna/cds.fna -a GCF_024349785.1_ASM2434978v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:52,714] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:52,715] [INFO] Task started: HMMsearch
[2024-01-24 13:40:52,715] [INFO] Running command: hmmsearch --tblout GCF_024349785.1_ASM2434978v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg06af64fb-2aa8-4f30-b57d-8657c71e8206/dqc_reference/reference_markers.hmm GCF_024349785.1_ASM2434978v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:53,126] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:53,127] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgbd839d46-2773-4a66-991c-5e44a1622c83/GCF_024349785.1_ASM2434978v1_genomic.fna.gz]
[2024-01-24 13:40:53,195] [INFO] Query marker FASTA was written to GCF_024349785.1_ASM2434978v1_genomic.fna/markers.fasta
[2024-01-24 13:40:53,195] [INFO] Task started: Blastn
[2024-01-24 13:40:53,195] [INFO] Running command: blastn -query GCF_024349785.1_ASM2434978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06af64fb-2aa8-4f30-b57d-8657c71e8206/dqc_reference/reference_markers.fasta -out GCF_024349785.1_ASM2434978v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:54,164] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:54,167] [INFO] Selected 16 target genomes.
[2024-01-24 13:40:54,167] [INFO] Target genome list was writen to GCF_024349785.1_ASM2434978v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:54,178] [INFO] Task started: fastANI
[2024-01-24 13:40:54,178] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd839d46-2773-4a66-991c-5e44a1622c83/GCF_024349785.1_ASM2434978v1_genomic.fna.gz --refList GCF_024349785.1_ASM2434978v1_genomic.fna/target_genomes.txt --output GCF_024349785.1_ASM2434978v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:10,715] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:10,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg06af64fb-2aa8-4f30-b57d-8657c71e8206/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:10,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg06af64fb-2aa8-4f30-b57d-8657c71e8206/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:10,729] [INFO] Found 16 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:10,729] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:10,730] [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 cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	90.9215	1042	1733	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	89.0359	1131	1733	95	below_threshold
Sphingobium limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	86.9737	1081	1733	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	84.3315	827	1733	95	below_threshold
Sphingobium xenophagum	strain=NBRC 107872	GCA_000367345.1	121428	121428	type	True	84.3128	877	1733	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	84.248	952	1733	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	84.1673	896	1733	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	84.0771	800	1733	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	83.75	926	1733	95	below_threshold
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	83.1688	845	1733	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	82.738	826	1733	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	82.5176	733	1733	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.2271	412	1733	95	below_threshold
Sphingomonas cavernae	strain=K2R01-6	GCA_003590775.1	2320861	2320861	type	True	78.2193	393	1733	95	below_threshold
Sphingomonas flavalba	strain=ZLT-5	GCA_004796535.1	2559804	2559804	type	True	78.0814	395	1733	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.7574	438	1733	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:10,735] [INFO] DFAST Taxonomy check result was written to GCF_024349785.1_ASM2434978v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:10,736] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:10,736] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:10,736] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg06af64fb-2aa8-4f30-b57d-8657c71e8206/dqc_reference/checkm_data
[2024-01-24 13:41:10,738] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:10,797] [INFO] Task started: CheckM
[2024-01-24 13:41:10,798] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024349785.1_ASM2434978v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024349785.1_ASM2434978v1_genomic.fna/checkm_input GCF_024349785.1_ASM2434978v1_genomic.fna/checkm_result
[2024-01-24 13:41:58,784] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:58,786] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:58,808] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:58,808] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:58,808] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024349785.1_ASM2434978v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:58,809] [INFO] Task started: Blastn
[2024-01-24 13:41:58,809] [INFO] Running command: blastn -query GCF_024349785.1_ASM2434978v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg06af64fb-2aa8-4f30-b57d-8657c71e8206/dqc_reference/reference_markers_gtdb.fasta -out GCF_024349785.1_ASM2434978v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:00,403] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:00,407] [INFO] Selected 12 target genomes.
[2024-01-24 13:42:00,407] [INFO] Target genome list was writen to GCF_024349785.1_ASM2434978v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:00,437] [INFO] Task started: fastANI
[2024-01-24 13:42:00,437] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd839d46-2773-4a66-991c-5e44a1622c83/GCF_024349785.1_ASM2434978v1_genomic.fna.gz --refList GCF_024349785.1_ASM2434978v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024349785.1_ASM2434978v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:14,123] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:14,135] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:14,136] [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
GCA_013822485.1	s__Sphingobium sp013822485	98.1001	1087	1733	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_004152865.1	s__Sphingobium cupriresistens	90.9311	1041	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	98.49	0.81	0.81	3	-
GCF_012927105.1	s__Sphingobium psychrophilum	89.0433	1129	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900013425.1	s__Sphingobium sp900013425	88.5985	1111	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.97	0.99	0.99	6	-
GCF_008710155.1	s__Sphingobium limneticum	86.992	1079	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.69	97.69	0.91	0.88	5	-
GCF_001421665.1	s__Sphingobium sp001421665	86.5095	1040	1733	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	86.4994	1045	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009720145.1	s__Sphingobium sp009720145	85.8717	984	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900109095.1	s__Sphingobium sp900109095	85.3576	1023	1733	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	85.2444	1016	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000382885.1	s__Sphingobium japonicum_C	84.4267	743	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016000085.1	s__Sphingobium sp016000085	83.7486	731	1733	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.94	98.94	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:14,137] [INFO] GTDB search result was written to GCF_024349785.1_ASM2434978v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:14,138] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:14,141] [INFO] DFAST_QC result json was written to GCF_024349785.1_ASM2434978v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:14,142] [INFO] DFAST_QC completed!
[2024-01-24 13:42:14,142] [INFO] Total running time: 0h1m39s