[2024-01-24 13:43:26,795] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:43:26,797] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:43:26,797] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf8d7f5b-37b6-4d72-bdc9-4ae8c7fd756d/dqc_reference
[2024-01-24 13:43:28,012] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:43:28,013] [INFO] Task started: Prodigal
[2024-01-24 13:43:28,014] [INFO] Running command: gunzip -c /var/lib/cwl/stg01000e46-0ddd-4804-9d55-41e423d26928/GCF_008710155.1_ASM871015v1_genomic.fna.gz | prodigal -d GCF_008710155.1_ASM871015v1_genomic.fna/cds.fna -a GCF_008710155.1_ASM871015v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:42,851] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:42,851] [INFO] Task started: HMMsearch
[2024-01-24 13:43:42,851] [INFO] Running command: hmmsearch --tblout GCF_008710155.1_ASM871015v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf8d7f5b-37b6-4d72-bdc9-4ae8c7fd756d/dqc_reference/reference_markers.hmm GCF_008710155.1_ASM871015v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:43,094] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:43,095] [INFO] Found 6/6 markers.
[2024-01-24 13:43:43,137] [INFO] Query marker FASTA was written to GCF_008710155.1_ASM871015v1_genomic.fna/markers.fasta
[2024-01-24 13:43:43,138] [INFO] Task started: Blastn
[2024-01-24 13:43:43,138] [INFO] Running command: blastn -query GCF_008710155.1_ASM871015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf8d7f5b-37b6-4d72-bdc9-4ae8c7fd756d/dqc_reference/reference_markers.fasta -out GCF_008710155.1_ASM871015v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:43,944] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:43,947] [INFO] Selected 16 target genomes.
[2024-01-24 13:43:43,947] [INFO] Target genome list was writen to GCF_008710155.1_ASM871015v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:43,954] [INFO] Task started: fastANI
[2024-01-24 13:43:43,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg01000e46-0ddd-4804-9d55-41e423d26928/GCF_008710155.1_ASM871015v1_genomic.fna.gz --refList GCF_008710155.1_ASM871015v1_genomic.fna/target_genomes.txt --output GCF_008710155.1_ASM871015v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:59,151] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:59,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf8d7f5b-37b6-4d72-bdc9-4ae8c7fd756d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:59,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf8d7f5b-37b6-4d72-bdc9-4ae8c7fd756d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:59,165] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:43:59,165] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:59,165] [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 limneticum	strain=DSM 25076	GCA_008710155.1	1007511	1007511	type	True	100.0	1643	1646	95	conclusive
Sphingobium cupriresistens	strain=CCTCC AB 2011146	GCA_004152865.1	1132417	1132417	type	True	86.3828	944	1646	95	below_threshold
Sphingobium psychrophilum	strain=AR-3-1	GCA_012927105.1	2728834	2728834	type	True	86.0991	1015	1646	95	below_threshold
Sphingobium yanoikuyae	strain=ATCC 51230	GCA_000315525.1	13690	13690	suspected-type	True	85.1395	979	1646	95	below_threshold
Sphingobium scionense	strain=DSM 19371	GCA_014197035.1	1404341	1404341	type	True	84.2372	996	1646	95	below_threshold
Sphingobium terrigena	strain=EO9	GCA_003591655.1	2304063	2304063	type	True	83.9884	921	1646	95	below_threshold
Sphingobium amiense	strain=NBRC 102518	GCA_001591305.1	135719	135719	type	True	83.0608	771	1646	95	below_threshold
Sphingobium amiense	strain=DSM 16289	GCA_003967075.1	135719	135719	type	True	83.0322	801	1646	95	below_threshold
Sphingobium abikonense	strain=NBRC 16140	GCA_001598335.1	86193	86193	type	True	83.0306	768	1646	95	below_threshold
Sphingobium lactosutens	strain=DS20	GCA_000445105.1	522773	522773	type	True	82.9746	837	1646	95	below_threshold
Sphingobium chungbukense	strain=DJ77	GCA_001005725.1	56193	56193	type	True	82.6419	789	1646	95	below_threshold
Sphingobium estronivorans	strain=AXB	GCA_008692605.1	1577690	1577690	type	True	82.4135	729	1646	95	below_threshold
Sphingomonas changnyeongensis	strain=C33	GCA_009913435.1	2698679	2698679	type	True	78.0187	385	1646	95	below_threshold
Sphingomonas aracearum	strain=WZY 27	GCA_003345355.1	2283317	2283317	type	True	78.0091	368	1646	95	below_threshold
Sphingomonas morindae	strain=NBD5	GCA_023822065.1	1541170	1541170	type	True	77.2811	385	1646	95	below_threshold
Sphingomonas profundi	strain=LMO-1	GCA_009739515.1	2681549	2681549	type	True	77.1969	405	1646	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:59,167] [INFO] DFAST Taxonomy check result was written to GCF_008710155.1_ASM871015v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:59,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:59,167] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:59,168] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf8d7f5b-37b6-4d72-bdc9-4ae8c7fd756d/dqc_reference/checkm_data
[2024-01-24 13:43:59,169] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:59,215] [INFO] Task started: CheckM
[2024-01-24 13:43:59,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008710155.1_ASM871015v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008710155.1_ASM871015v1_genomic.fna/checkm_input GCF_008710155.1_ASM871015v1_genomic.fna/checkm_result
[2024-01-24 13:44:42,437] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:42,439] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:42,465] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:42,465] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:42,465] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008710155.1_ASM871015v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:42,466] [INFO] Task started: Blastn
[2024-01-24 13:44:42,466] [INFO] Running command: blastn -query GCF_008710155.1_ASM871015v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf8d7f5b-37b6-4d72-bdc9-4ae8c7fd756d/dqc_reference/reference_markers_gtdb.fasta -out GCF_008710155.1_ASM871015v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:43,768] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:43,771] [INFO] Selected 10 target genomes.
[2024-01-24 13:44:43,772] [INFO] Target genome list was writen to GCF_008710155.1_ASM871015v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:43,785] [INFO] Task started: fastANI
[2024-01-24 13:44:43,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg01000e46-0ddd-4804-9d55-41e423d26928/GCF_008710155.1_ASM871015v1_genomic.fna.gz --refList GCF_008710155.1_ASM871015v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008710155.1_ASM871015v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:55,912] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:55,921] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:55,921] [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_008710155.1	s__Sphingobium limneticum	100.0	1643	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.69	97.69	0.91	0.88	5	conclusive
GCF_001421665.1	s__Sphingobium sp001421665	89.1285	1072	1646	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	88.8447	1112	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900111125.1	s__Sphingobium sp900111125	86.4917	1029	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004152865.1	s__Sphingobium cupriresistens	86.3824	944	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	98.64	98.49	0.81	0.81	3	-
GCF_900013425.1	s__Sphingobium sp900013425	86.2254	1032	1646	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Sphingomonadales;f__Sphingomonadaceae;g__Sphingobium	95.0	99.99	99.97	0.99	0.99	6	-
GCF_900109095.1	s__Sphingobium sp900109095	86.1051	1033	1646	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	85.8134	944	1646	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	85.5016	980	1646	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	83.9036	765	1646	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 13:44:55,922] [INFO] GTDB search result was written to GCF_008710155.1_ASM871015v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:55,923] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:55,926] [INFO] DFAST_QC result json was written to GCF_008710155.1_ASM871015v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:55,926] [INFO] DFAST_QC completed!
[2024-01-24 13:44:55,926] [INFO] Total running time: 0h1m29s