[2024-01-24 15:02:18,274] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:18,282] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:18,282] [INFO] DQC Reference Directory: /var/lib/cwl/stg2a03ae60-839b-47df-8b88-bad4c4d2d132/dqc_reference
[2024-01-24 15:02:20,858] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:20,860] [INFO] Task started: Prodigal
[2024-01-24 15:02:20,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg88a9290b-03b2-43e7-82a8-9a2082433291/GCF_018449475.1_ASM1844947v1_genomic.fna.gz | prodigal -d GCF_018449475.1_ASM1844947v1_genomic.fna/cds.fna -a GCF_018449475.1_ASM1844947v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:34,259] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:34,259] [INFO] Task started: HMMsearch
[2024-01-24 15:02:34,259] [INFO] Running command: hmmsearch --tblout GCF_018449475.1_ASM1844947v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2a03ae60-839b-47df-8b88-bad4c4d2d132/dqc_reference/reference_markers.hmm GCF_018449475.1_ASM1844947v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:34,556] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:34,558] [INFO] Found 6/6 markers.
[2024-01-24 15:02:34,596] [INFO] Query marker FASTA was written to GCF_018449475.1_ASM1844947v1_genomic.fna/markers.fasta
[2024-01-24 15:02:34,597] [INFO] Task started: Blastn
[2024-01-24 15:02:34,597] [INFO] Running command: blastn -query GCF_018449475.1_ASM1844947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a03ae60-839b-47df-8b88-bad4c4d2d132/dqc_reference/reference_markers.fasta -out GCF_018449475.1_ASM1844947v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:35,745] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:35,749] [INFO] Selected 11 target genomes.
[2024-01-24 15:02:35,749] [INFO] Target genome list was writen to GCF_018449475.1_ASM1844947v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:35,763] [INFO] Task started: fastANI
[2024-01-24 15:02:35,764] [INFO] Running command: fastANI --query /var/lib/cwl/stg88a9290b-03b2-43e7-82a8-9a2082433291/GCF_018449475.1_ASM1844947v1_genomic.fna.gz --refList GCF_018449475.1_ASM1844947v1_genomic.fna/target_genomes.txt --output GCF_018449475.1_ASM1844947v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:49,471] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:49,471] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2a03ae60-839b-47df-8b88-bad4c4d2d132/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:49,472] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2a03ae60-839b-47df-8b88-bad4c4d2d132/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:49,482] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:02:49,482] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:02:49,482] [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	84.642	984	1395	95	below_threshold
Ancylobacter rudongensis	strain=CGMCC 1.1761	GCA_900100155.1	177413	177413	type	True	84.5967	1000	1395	95	below_threshold
Ancylobacter dichloromethanicus	strain=VKM B-2484	GCA_018390645.1	518825	518825	type	True	84.5943	984	1395	95	below_threshold
Starkeya koreensis	strain=Jip08	GCA_023016525.1	266121	266121	type	True	84.5456	943	1395	95	below_threshold
Ancylobacter aquaticus	strain=DSM 101	GCA_004339465.1	100	100	type	True	83.9807	968	1395	95	below_threshold
Ancylobacter oerskovii	strain=CCM 7435	GCA_018390555.1	459519	459519	type	True	83.5231	945	1395	95	below_threshold
Ancylobacter defluvii	strain=VKM B-2789	GCA_018390605.1	1282440	1282440	type	True	83.4239	952	1395	95	below_threshold
Ancylobacter sonchi	strain=VKM B-3145	GCA_018390695.1	1937790	1937790	type	True	83.3788	994	1395	95	below_threshold
Xanthobacter oligotrophicus	strain=29k	GCA_008364685.1	2607286	2607286	type	True	78.7022	519	1395	95	below_threshold
Bradyrhizobium viridifuturi	strain=SEMIA 690	GCA_001238275.1	1654716	1654716	type	True	77.8739	417	1395	95	below_threshold
Bradyrhizobium oropedii	strain=Pear76	GCA_020889685.1	1571201	1571201	type	True	77.6382	405	1395	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:49,484] [INFO] DFAST Taxonomy check result was written to GCF_018449475.1_ASM1844947v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:49,485] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:49,485] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:49,485] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2a03ae60-839b-47df-8b88-bad4c4d2d132/dqc_reference/checkm_data
[2024-01-24 15:02:49,487] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:49,531] [INFO] Task started: CheckM
[2024-01-24 15:02:49,531] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018449475.1_ASM1844947v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018449475.1_ASM1844947v1_genomic.fna/checkm_input GCF_018449475.1_ASM1844947v1_genomic.fna/checkm_result
[2024-01-24 15:03:33,671] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:33,673] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:33,691] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:33,691] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:33,692] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018449475.1_ASM1844947v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:33,692] [INFO] Task started: Blastn
[2024-01-24 15:03:33,692] [INFO] Running command: blastn -query GCF_018449475.1_ASM1844947v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2a03ae60-839b-47df-8b88-bad4c4d2d132/dqc_reference/reference_markers_gtdb.fasta -out GCF_018449475.1_ASM1844947v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:36,042] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:36,045] [INFO] Selected 9 target genomes.
[2024-01-24 15:03:36,045] [INFO] Target genome list was writen to GCF_018449475.1_ASM1844947v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:36,054] [INFO] Task started: fastANI
[2024-01-24 15:03:36,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg88a9290b-03b2-43e7-82a8-9a2082433291/GCF_018449475.1_ASM1844947v1_genomic.fna.gz --refList GCF_018449475.1_ASM1844947v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018449475.1_ASM1844947v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:47,146] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:47,154] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:47,155] [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_018449475.1	s__Angulomicrobium sp018449475	100.0	1395	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009223885.1	s__Ancylobacter sp009223885	84.859	935	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003241485.1	s__Angulomicrobium novellum_A	84.6891	952	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092925.1	s__Starkeya novella	84.6454	983	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100155.1	s__Ancylobacter rudongensis	84.5821	1001	1395	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	84.5739	986	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Ancylobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007559435.1	s__Starkeya sp007559435	84.3951	934	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	98.55	98.55	0.95	0.95	2	-
GCF_017872635.1	s__Starkeya sp017872635	84.3207	959	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Starkeya	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014195655.1	s__Angulomicrobium tetraedrale	84.2972	993	1395	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Rhizobiales;f__Xanthobacteraceae;g__Angulomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:47,156] [INFO] GTDB search result was written to GCF_018449475.1_ASM1844947v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:47,157] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:47,160] [INFO] DFAST_QC result json was written to GCF_018449475.1_ASM1844947v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:47,161] [INFO] DFAST_QC completed!
[2024-01-24 15:03:47,161] [INFO] Total running time: 0h1m29s