[2023-06-17 10:14:19,637] [INFO] DFAST_QC pipeline started.
[2023-06-17 10:14:19,642] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 10:14:19,642] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf515b15-eeff-460f-9cc4-a76cdb216377/dqc_reference
[2023-06-17 10:14:21,043] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 10:14:21,044] [INFO] Task started: Prodigal
[2023-06-17 10:14:21,044] [INFO] Running command: gunzip -c /var/lib/cwl/stgf5a7e173-66fc-4b84-88cf-36b107082eef/GCA_003331695.1_ASM333169v1_genomic.fna.gz | prodigal -d GCA_003331695.1_ASM333169v1_genomic.fna/cds.fna -a GCA_003331695.1_ASM333169v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 10:14:31,771] [INFO] Task succeeded: Prodigal
[2023-06-17 10:14:31,771] [INFO] Task started: HMMsearch
[2023-06-17 10:14:31,771] [INFO] Running command: hmmsearch --tblout GCA_003331695.1_ASM333169v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf515b15-eeff-460f-9cc4-a76cdb216377/dqc_reference/reference_markers.hmm GCA_003331695.1_ASM333169v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 10:14:32,086] [INFO] Task succeeded: HMMsearch
[2023-06-17 10:14:32,088] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgf5a7e173-66fc-4b84-88cf-36b107082eef/GCA_003331695.1_ASM333169v1_genomic.fna.gz]
[2023-06-17 10:14:32,142] [INFO] Query marker FASTA was written to GCA_003331695.1_ASM333169v1_genomic.fna/markers.fasta
[2023-06-17 10:14:32,142] [INFO] Task started: Blastn
[2023-06-17 10:14:32,142] [INFO] Running command: blastn -query GCA_003331695.1_ASM333169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf515b15-eeff-460f-9cc4-a76cdb216377/dqc_reference/reference_markers.fasta -out GCA_003331695.1_ASM333169v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 10:14:33,043] [INFO] Task succeeded: Blastn
[2023-06-17 10:14:33,050] [INFO] Selected 7 target genomes.
[2023-06-17 10:14:33,051] [INFO] Target genome list was writen to GCA_003331695.1_ASM333169v1_genomic.fna/target_genomes.txt
[2023-06-17 10:14:33,051] [INFO] Task started: fastANI
[2023-06-17 10:14:33,052] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5a7e173-66fc-4b84-88cf-36b107082eef/GCA_003331695.1_ASM333169v1_genomic.fna.gz --refList GCA_003331695.1_ASM333169v1_genomic.fna/target_genomes.txt --output GCA_003331695.1_ASM333169v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 10:14:39,454] [INFO] Task succeeded: fastANI
[2023-06-17 10:14:39,454] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf515b15-eeff-460f-9cc4-a76cdb216377/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 10:14:39,454] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf515b15-eeff-460f-9cc4-a76cdb216377/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 10:14:39,462] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2023-06-17 10:14:39,463] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-17 10:14:39,463] [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
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	97.1586	993	1199	95	conclusive
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	97.154	989	1199	95	conclusive
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	90.7751	904	1199	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	90.7498	903	1199	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	90.7272	903	1199	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	88.7142	892	1199	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	88.5524	901	1199	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 10:14:39,465] [INFO] DFAST Taxonomy check result was written to GCA_003331695.1_ASM333169v1_genomic.fna/tc_result.tsv
[2023-06-17 10:14:39,465] [INFO] ===== Taxonomy check completed =====
[2023-06-17 10:14:39,466] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 10:14:39,466] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf515b15-eeff-460f-9cc4-a76cdb216377/dqc_reference/checkm_data
[2023-06-17 10:14:39,468] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 10:14:39,514] [INFO] Task started: CheckM
[2023-06-17 10:14:39,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_003331695.1_ASM333169v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_003331695.1_ASM333169v1_genomic.fna/checkm_input GCA_003331695.1_ASM333169v1_genomic.fna/checkm_result
[2023-06-17 10:15:14,782] [INFO] Task succeeded: CheckM
[2023-06-17 10:15:14,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 61.46%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-17 10:15:14,806] [INFO] ===== Completeness check finished =====
[2023-06-17 10:15:14,806] [INFO] ===== Start GTDB Search =====
[2023-06-17 10:15:14,806] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_003331695.1_ASM333169v1_genomic.fna/markers.fasta)
[2023-06-17 10:15:14,807] [INFO] Task started: Blastn
[2023-06-17 10:15:14,807] [INFO] Running command: blastn -query GCA_003331695.1_ASM333169v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf515b15-eeff-460f-9cc4-a76cdb216377/dqc_reference/reference_markers_gtdb.fasta -out GCA_003331695.1_ASM333169v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 10:15:16,334] [INFO] Task succeeded: Blastn
[2023-06-17 10:15:16,338] [INFO] Selected 10 target genomes.
[2023-06-17 10:15:16,338] [INFO] Target genome list was writen to GCA_003331695.1_ASM333169v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 10:15:16,344] [INFO] Task started: fastANI
[2023-06-17 10:15:16,344] [INFO] Running command: fastANI --query /var/lib/cwl/stgf5a7e173-66fc-4b84-88cf-36b107082eef/GCA_003331695.1_ASM333169v1_genomic.fna.gz --refList GCA_003331695.1_ASM333169v1_genomic.fna/target_genomes_gtdb.txt --output GCA_003331695.1_ASM333169v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 10:15:26,173] [INFO] Task succeeded: fastANI
[2023-06-17 10:15:26,189] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 10:15:26,190] [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_000219605.1	s__Pseudomonas_A stutzeri	97.1741	992	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.69	96.98	0.90	0.83	156	conclusive
GCF_003205815.1	s__Pseudomonas_A sp003205815	90.0675	922	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.18	96.58	0.91	0.87	27	-
GCF_003696315.1	s__Pseudomonas_A songnenensis	88.7142	892	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.36	98.32	0.94	0.90	4	-
GCA_007713455.1	s__Pseudomonas_A sp007713455	87.1421	931	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.0636	N/A	N/A	N/A	N/A	1	-
GCF_000495915.1	s__Pseudomonas_A chloritidismutans	87.0516	898	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.9847	97.37	97.19	0.88	0.85	8	-
GCF_013409135.1	s__Pseudomonas_A kunmingensis_A	87.015	919	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	97.08	97.66	97.10	0.91	0.87	14	-
GCF_000661915.1	s__Pseudomonas_A stutzeri_A	86.9449	901	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	99.44	99.44	0.92	0.92	2	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	86.6103	875	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.35	98.08	0.91	0.89	3	-
GCF_000307775.2	s__Pseudomonas_A stutzeri_B	85.9063	884	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.65	98.65	0.90	0.90	2	-
GCF_015070855.1	s__Pseudomonas_A lopnurensis	85.3755	824	1199	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
--------------------------------------------------------------------------------
[2023-06-17 10:15:26,192] [INFO] GTDB search result was written to GCA_003331695.1_ASM333169v1_genomic.fna/result_gtdb.tsv
[2023-06-17 10:15:26,192] [INFO] ===== GTDB Search completed =====
[2023-06-17 10:15:26,196] [INFO] DFAST_QC result json was written to GCA_003331695.1_ASM333169v1_genomic.fna/dqc_result.json
[2023-06-17 10:15:26,196] [INFO] DFAST_QC completed!
[2023-06-17 10:15:26,196] [INFO] Total running time: 0h1m7s