[2024-01-25 19:33:35,856] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:33:35,858] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:33:35,858] [INFO] DQC Reference Directory: /var/lib/cwl/stgbdb44003-bcaa-4209-8b05-0408be8d39cc/dqc_reference
[2024-01-25 19:33:36,955] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:33:36,956] [INFO] Task started: Prodigal
[2024-01-25 19:33:36,956] [INFO] Running command: gunzip -c /var/lib/cwl/stga912658b-488a-439b-b063-df78232b9b77/GCF_014195655.1_ASM1419565v1_genomic.fna.gz | prodigal -d GCF_014195655.1_ASM1419565v1_genomic.fna/cds.fna -a GCF_014195655.1_ASM1419565v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:33:50,243] [INFO] Task succeeded: Prodigal
[2024-01-25 19:33:50,243] [INFO] Task started: HMMsearch
[2024-01-25 19:33:50,244] [INFO] Running command: hmmsearch --tblout GCF_014195655.1_ASM1419565v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbdb44003-bcaa-4209-8b05-0408be8d39cc/dqc_reference/reference_markers.hmm GCF_014195655.1_ASM1419565v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:33:50,490] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:33:50,491] [INFO] Found 6/6 markers.
[2024-01-25 19:33:50,531] [INFO] Query marker FASTA was written to GCF_014195655.1_ASM1419565v1_genomic.fna/markers.fasta
[2024-01-25 19:33:50,531] [INFO] Task started: Blastn
[2024-01-25 19:33:50,531] [INFO] Running command: blastn -query GCF_014195655.1_ASM1419565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdb44003-bcaa-4209-8b05-0408be8d39cc/dqc_reference/reference_markers.fasta -out GCF_014195655.1_ASM1419565v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:51,502] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:51,505] [INFO] Selected 11 target genomes.
[2024-01-25 19:33:51,505] [INFO] Target genome list was writen to GCF_014195655.1_ASM1419565v1_genomic.fna/target_genomes.txt
[2024-01-25 19:33:51,508] [INFO] Task started: fastANI
[2024-01-25 19:33:51,508] [INFO] Running command: fastANI --query /var/lib/cwl/stga912658b-488a-439b-b063-df78232b9b77/GCF_014195655.1_ASM1419565v1_genomic.fna.gz --refList GCF_014195655.1_ASM1419565v1_genomic.fna/target_genomes.txt --output GCF_014195655.1_ASM1419565v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:34:03,750] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:03,751] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbdb44003-bcaa-4209-8b05-0408be8d39cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:34:03,751] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbdb44003-bcaa-4209-8b05-0408be8d39cc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:34:03,759] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:34:03,759] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:34:03,760] [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
Starkeya novella	strain=DSM 506	GCA_000092925.1	921	921	type	True	84.4824	1008	1662	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	84.4509	941	1662	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	84.0633	937	1662	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	84.0456	969	1662	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	83.4916	1033	1662	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	83.4904	974	1662	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	83.4617	991	1662	95	below_threshold
Ancylobacter defluvii	strain=VKM B-2789	GCA_018390605.1	1282440	1282440	type	True	83.2073	1002	1662	95	below_threshold
Methylobacterium oryzihabitans	strain=TER-1	GCA_004004555.2	2499852	2499852	type	True	77.1939	477	1662	95	below_threshold
Salinarimonas soli	strain=BN140002	GCA_008386575.1	1638099	1638099	type	True	77.1714	348	1662	95	below_threshold
Methylobacterium crusticola	strain=KCTC 52305	GCA_022179145.1	1697972	1697972	type	True	76.8321	460	1662	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:34:03,761] [INFO] DFAST Taxonomy check result was written to GCF_014195655.1_ASM1419565v1_genomic.fna/tc_result.tsv
[2024-01-25 19:34:03,761] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:34:03,761] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:34:03,762] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbdb44003-bcaa-4209-8b05-0408be8d39cc/dqc_reference/checkm_data
[2024-01-25 19:34:03,762] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:34:03,809] [INFO] Task started: CheckM
[2024-01-25 19:34:03,810] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014195655.1_ASM1419565v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014195655.1_ASM1419565v1_genomic.fna/checkm_input GCF_014195655.1_ASM1419565v1_genomic.fna/checkm_result
[2024-01-25 19:34:51,811] [INFO] Task succeeded: CheckM
[2024-01-25 19:34:51,812] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:34:51,828] [INFO] ===== Completeness check finished =====
[2024-01-25 19:34:51,829] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:34:51,830] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014195655.1_ASM1419565v1_genomic.fna/markers.fasta)
[2024-01-25 19:34:51,830] [INFO] Task started: Blastn
[2024-01-25 19:34:51,830] [INFO] Running command: blastn -query GCF_014195655.1_ASM1419565v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbdb44003-bcaa-4209-8b05-0408be8d39cc/dqc_reference/reference_markers_gtdb.fasta -out GCF_014195655.1_ASM1419565v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:53,836] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:53,839] [INFO] Selected 10 target genomes.
[2024-01-25 19:34:53,839] [INFO] Target genome list was writen to GCF_014195655.1_ASM1419565v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:34:53,844] [INFO] Task started: fastANI
[2024-01-25 19:34:53,844] [INFO] Running command: fastANI --query /var/lib/cwl/stga912658b-488a-439b-b063-df78232b9b77/GCF_014195655.1_ASM1419565v1_genomic.fna.gz --refList GCF_014195655.1_ASM1419565v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014195655.1_ASM1419565v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:04,996] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:05,003] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:35:05,003] [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_014195655.1	s__Angulomicrobium tetraedrale	100.0	1661	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003241485.1	s__Angulomicrobium novellum_A	85.412	1012	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009223885.1	s__Ancylobacter sp009223885	84.6372	959	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092925.1	s__Starkeya novella	84.4956	1006	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018449475.1	s__Angulomicrobium sp018449475	84.2137	1003	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017872635.1	s__Starkeya sp017872635	84.1934	963	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_007559435.1	s__Starkeya sp007559435	84.1087	950	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCF_900100155.1	s__Ancylobacter rudongensis	84.045	940	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	96.36	96.36	0.88	0.88	2	-
GCF_018390645.1	s__Ancylobacter dichloromethanicus	84.0307	971	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339465.1	s__Ancylobacter aquaticus	83.509	972	1662	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:05,004] [INFO] GTDB search result was written to GCF_014195655.1_ASM1419565v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:05,005] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:05,007] [INFO] DFAST_QC result json was written to GCF_014195655.1_ASM1419565v1_genomic.fna/dqc_result.json
[2024-01-25 19:35:05,007] [INFO] DFAST_QC completed!
[2024-01-25 19:35:05,007] [INFO] Total running time: 0h1m29s