[2024-01-24 15:18:47,939] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:47,941] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:47,941] [INFO] DQC Reference Directory: /var/lib/cwl/stg463f0219-ce19-4f2b-9397-3e7db15832b0/dqc_reference
[2024-01-24 15:18:51,761] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:51,762] [INFO] Task started: Prodigal
[2024-01-24 15:18:51,763] [INFO] Running command: gunzip -c /var/lib/cwl/stga29b489a-a625-4803-89cd-4acc7986dd56/GCF_022012295.1_ASM2201229v1_genomic.fna.gz | prodigal -d GCF_022012295.1_ASM2201229v1_genomic.fna/cds.fna -a GCF_022012295.1_ASM2201229v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:19:04,034] [INFO] Task succeeded: Prodigal
[2024-01-24 15:19:04,034] [INFO] Task started: HMMsearch
[2024-01-24 15:19:04,035] [INFO] Running command: hmmsearch --tblout GCF_022012295.1_ASM2201229v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg463f0219-ce19-4f2b-9397-3e7db15832b0/dqc_reference/reference_markers.hmm GCF_022012295.1_ASM2201229v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:19:04,349] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:19:04,350] [INFO] Found 6/6 markers.
[2024-01-24 15:19:04,394] [INFO] Query marker FASTA was written to GCF_022012295.1_ASM2201229v1_genomic.fna/markers.fasta
[2024-01-24 15:19:04,394] [INFO] Task started: Blastn
[2024-01-24 15:19:04,394] [INFO] Running command: blastn -query GCF_022012295.1_ASM2201229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg463f0219-ce19-4f2b-9397-3e7db15832b0/dqc_reference/reference_markers.fasta -out GCF_022012295.1_ASM2201229v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:05,421] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:05,424] [INFO] Selected 13 target genomes.
[2024-01-24 15:19:05,425] [INFO] Target genome list was writen to GCF_022012295.1_ASM2201229v1_genomic.fna/target_genomes.txt
[2024-01-24 15:19:05,528] [INFO] Task started: fastANI
[2024-01-24 15:19:05,528] [INFO] Running command: fastANI --query /var/lib/cwl/stga29b489a-a625-4803-89cd-4acc7986dd56/GCF_022012295.1_ASM2201229v1_genomic.fna.gz --refList GCF_022012295.1_ASM2201229v1_genomic.fna/target_genomes.txt --output GCF_022012295.1_ASM2201229v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:19:16,157] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:16,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg463f0219-ce19-4f2b-9397-3e7db15832b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:19:16,159] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg463f0219-ce19-4f2b-9397-3e7db15832b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:19:16,176] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:19:16,177] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:19:16,177] [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
Dechloromonas denitrificans	strain=ATCC BAA-841	GCA_001551835.1	281362	281362	type	True	83.2458	815	1357	95	below_threshold
Dechloromonas hortensis	strain=MA-1	GCA_009469765.1	337779	337779	type	True	83.2417	818	1357	95	below_threshold
Azonexus fungiphilus	strain=DSM 23841	GCA_003634965.1	146940	146940	type	True	83.0105	684	1357	95	below_threshold
Azonexus hydrophilus	strain=DSM 23864	GCA_000429605.1	418702	418702	type	True	82.709	648	1357	95	below_threshold
Rhodocyclus purpureus	strain=DSM 168	GCA_016653115.1	1067	1067	type	True	79.2878	399	1357	95	below_threshold
Sulfurisoma sediminicola	strain=BSN1	GCA_003865015.1	1381557	1381557	type	True	78.682	357	1357	95	below_threshold
Rhodocyclus gracilis	strain=DSM 110	GCA_009617575.1	2929842	2929842	type	True	78.4501	324	1357	95	below_threshold
Aromatoleum toluolicum	strain=T	GCA_012911005.2	90060	90060	type	True	78.172	404	1357	95	below_threshold
Aromatoleum toluclasticum	strain=MF63	GCA_000378245.1	92003	92003	type	True	78.0872	392	1357	95	below_threshold
Chromobacterium alticapitis	strain=MWU14-2602	GCA_002924365.1	2073169	2073169	type	True	77.3053	210	1357	95	below_threshold
Ralstonia pseudosolanacearum	strain=LMG 9673	GCA_919586305.1	1310165	1310165	type	True	77.284	267	1357	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	77.0112	261	1357	95	below_threshold
Massilia pinisoli	strain=JCM 31316	GCA_024753285.1	1772194	1772194	type	True	76.815	254	1357	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:19:16,215] [INFO] DFAST Taxonomy check result was written to GCF_022012295.1_ASM2201229v1_genomic.fna/tc_result.tsv
[2024-01-24 15:19:16,215] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:19:16,216] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:19:16,216] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg463f0219-ce19-4f2b-9397-3e7db15832b0/dqc_reference/checkm_data
[2024-01-24 15:19:16,218] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:19:16,266] [INFO] Task started: CheckM
[2024-01-24 15:19:16,266] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_022012295.1_ASM2201229v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_022012295.1_ASM2201229v1_genomic.fna/checkm_input GCF_022012295.1_ASM2201229v1_genomic.fna/checkm_result
[2024-01-24 15:19:53,523] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:53,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:53,548] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:53,548] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:53,549] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_022012295.1_ASM2201229v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:53,549] [INFO] Task started: Blastn
[2024-01-24 15:19:53,549] [INFO] Running command: blastn -query GCF_022012295.1_ASM2201229v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg463f0219-ce19-4f2b-9397-3e7db15832b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_022012295.1_ASM2201229v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:55,496] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:55,500] [INFO] Selected 18 target genomes.
[2024-01-24 15:19:55,500] [INFO] Target genome list was writen to GCF_022012295.1_ASM2201229v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:55,518] [INFO] Task started: fastANI
[2024-01-24 15:19:55,518] [INFO] Running command: fastANI --query /var/lib/cwl/stga29b489a-a625-4803-89cd-4acc7986dd56/GCF_022012295.1_ASM2201229v1_genomic.fna.gz --refList GCF_022012295.1_ASM2201229v1_genomic.fna/target_genomes_gtdb.txt --output GCF_022012295.1_ASM2201229v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:20:10,138] [INFO] Task succeeded: fastANI
[2024-01-24 15:20:10,153] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:20:10,154] [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_008711155.1	s__Azonexus sp008711155	85.7231	855	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	97.59	97.59	0.92	0.92	2	-
GCA_016790885.1	s__Azonexus sp016790885	85.0421	492	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000519045.1	s__Azonexus agitatus	84.7925	815	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	98.62	98.62	0.86	0.86	2	-
GCF_009469585.1	s__Azonexus sp009469585	84.4347	759	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017983615.1	s__Azonexus sp017983615	84.1539	686	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903922075.1	s__Azonexus sp903922075	83.813	593	1357	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	83.729	718	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018828385.1	s__Azonexus sp018828385	83.2116	785	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	100.00	100.00	1.00	1.00	4	-
GCA_008933675.1	s__Azonexus sp008933675	83.0771	686	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002440665.1	s__Azonexus sp002440665	83.012	656	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842345.1	s__Azonexus sp002842345	82.7792	722	1357	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	82.7732	439	1357	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	82.7116	546	1357	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	82.6536	785	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016791065.1	s__Azonexus sp016791065	82.4801	588	1357	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	82.4439	680	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002842145.1	s__Azonexus sp002842145	82.3912	700	1357	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Rhodocyclaceae;g__Azonexus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017848965.1	s__Azonexus aromaticus_B	82.3143	689	1357	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 15:20:10,155] [INFO] GTDB search result was written to GCF_022012295.1_ASM2201229v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:20:10,156] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:20:10,159] [INFO] DFAST_QC result json was written to GCF_022012295.1_ASM2201229v1_genomic.fna/dqc_result.json
[2024-01-24 15:20:10,160] [INFO] DFAST_QC completed!
[2024-01-24 15:20:10,160] [INFO] Total running time: 0h1m22s