[2024-01-24 10:47:10,114] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:10,120] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:10,120] [INFO] DQC Reference Directory: /var/lib/cwl/stga062c5a0-8301-4acf-b825-c41c2a58d804/dqc_reference
[2024-01-24 10:47:12,069] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,070] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,071] [INFO] Running command: gunzip -c /var/lib/cwl/stg7508c194-083c-4ceb-93a3-0fb0e4bc7485/GCF_003634965.1_ASM363496v1_genomic.fna.gz | prodigal -d GCF_003634965.1_ASM363496v1_genomic.fna/cds.fna -a GCF_003634965.1_ASM363496v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:21,935] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:21,936] [INFO] Task started: HMMsearch
[2024-01-24 10:47:21,936] [INFO] Running command: hmmsearch --tblout GCF_003634965.1_ASM363496v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga062c5a0-8301-4acf-b825-c41c2a58d804/dqc_reference/reference_markers.hmm GCF_003634965.1_ASM363496v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:22,247] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:22,248] [INFO] Found 6/6 markers.
[2024-01-24 10:47:22,282] [INFO] Query marker FASTA was written to GCF_003634965.1_ASM363496v1_genomic.fna/markers.fasta
[2024-01-24 10:47:22,282] [INFO] Task started: Blastn
[2024-01-24 10:47:22,282] [INFO] Running command: blastn -query GCF_003634965.1_ASM363496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga062c5a0-8301-4acf-b825-c41c2a58d804/dqc_reference/reference_markers.fasta -out GCF_003634965.1_ASM363496v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:23,339] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:23,344] [INFO] Selected 12 target genomes.
[2024-01-24 10:47:23,344] [INFO] Target genome list was writen to GCF_003634965.1_ASM363496v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:23,668] [INFO] Task started: fastANI
[2024-01-24 10:47:23,668] [INFO] Running command: fastANI --query /var/lib/cwl/stg7508c194-083c-4ceb-93a3-0fb0e4bc7485/GCF_003634965.1_ASM363496v1_genomic.fna.gz --refList GCF_003634965.1_ASM363496v1_genomic.fna/target_genomes.txt --output GCF_003634965.1_ASM363496v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:35,368] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:35,368] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga062c5a0-8301-4acf-b825-c41c2a58d804/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:35,368] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga062c5a0-8301-4acf-b825-c41c2a58d804/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:35,379] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:47:35,379] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:35,379] [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
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	100.0	1173	1174	95	conclusive
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	86.9909	829	1174	95	below_threshold
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	82.4006	708	1174	95	below_threshold
Dechloromonas hortensis	strain=MA-1	GCA_009469765.1	337779	337779	type	True	82.3334	685	1174	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	80.0738	459	1174	95	below_threshold
Azospira oryzae	strain=DSM 21223	GCA_004217225.1	146939	146939	type	True	79.2424	490	1174	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	79.1566	405	1174	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.4192	432	1174	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.574	289	1174	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_024925465.1	1310165	1310165	type	True	77.5623	296	1174	95	below_threshold
Cupriavidus numazuensis	strain=LMG 26411	GCA_905397435.1	221992	221992	type	True	77.106	285	1174	95	below_threshold
Burkholderia perseverans	strain=INN12	GCA_022870505.1	2615214	2615214	type	True	76.9233	356	1174	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:35,381] [INFO] DFAST Taxonomy check result was written to GCF_003634965.1_ASM363496v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:35,381] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:35,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:35,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga062c5a0-8301-4acf-b825-c41c2a58d804/dqc_reference/checkm_data
[2024-01-24 10:47:35,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:35,435] [INFO] Task started: CheckM
[2024-01-24 10:47:35,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003634965.1_ASM363496v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003634965.1_ASM363496v1_genomic.fna/checkm_input GCF_003634965.1_ASM363496v1_genomic.fna/checkm_result
[2024-01-24 10:48:09,328] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:09,329] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:09,372] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:09,372] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:09,372] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003634965.1_ASM363496v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:09,373] [INFO] Task started: Blastn
[2024-01-24 10:48:09,373] [INFO] Running command: blastn -query GCF_003634965.1_ASM363496v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga062c5a0-8301-4acf-b825-c41c2a58d804/dqc_reference/reference_markers_gtdb.fasta -out GCF_003634965.1_ASM363496v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:11,375] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:11,378] [INFO] Selected 9 target genomes.
[2024-01-24 10:48:11,378] [INFO] Target genome list was writen to GCF_003634965.1_ASM363496v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:12,016] [INFO] Task started: fastANI
[2024-01-24 10:48:12,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg7508c194-083c-4ceb-93a3-0fb0e4bc7485/GCF_003634965.1_ASM363496v1_genomic.fna.gz --refList GCF_003634965.1_ASM363496v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003634965.1_ASM363496v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:20,217] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:20,230] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:20,231] [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_003634965.1	s__Azonexus fungiphilus	100.0	1173	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.36	98.36	0.85	0.85	2	conclusive
GCF_000429605.1	s__Azonexus hydrophilus	86.9908	829	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.24	97.24	0.86	0.86	2	-
GCA_017848965.1	s__Azonexus aromaticus_B	86.9117	875	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002470165.1	s__Azonexus sp002470165	86.673	546	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002425245.1	s__Azonexus sp002425245	86.2331	687	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001956855.1	s__Azonexus hydrophilus_A	85.8143	879	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008933675.1	s__Azonexus sp008933675	84.1845	700	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009469615.1	s__Azonexus sp009469615	83.7539	639	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002840765.1	s__Azonexus sp002840765	83.0837	701	1174	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:20,232] [INFO] GTDB search result was written to GCF_003634965.1_ASM363496v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:20,234] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:20,237] [INFO] DFAST_QC result json was written to GCF_003634965.1_ASM363496v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:20,237] [INFO] DFAST_QC completed!
[2024-01-24 10:48:20,237] [INFO] Total running time: 0h1m10s