[2024-01-24 11:13:04,351] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:13:04,355] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:13:04,355] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcd6f580-a819-4df5-8ea2-699989341046/dqc_reference
[2024-01-24 11:13:05,596] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:13:05,597] [INFO] Task started: Prodigal
[2024-01-24 11:13:05,597] [INFO] Running command: gunzip -c /var/lib/cwl/stg0a289c9d-d50c-4066-a31e-ff07deb52516/GCF_003696365.1_ASM369636v1_genomic.fna.gz | prodigal -d GCF_003696365.1_ASM369636v1_genomic.fna/cds.fna -a GCF_003696365.1_ASM369636v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:19,713] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:19,714] [INFO] Task started: HMMsearch
[2024-01-24 11:13:19,714] [INFO] Running command: hmmsearch --tblout GCF_003696365.1_ASM369636v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcd6f580-a819-4df5-8ea2-699989341046/dqc_reference/reference_markers.hmm GCF_003696365.1_ASM369636v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:20,053] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:20,054] [INFO] Found 6/6 markers.
[2024-01-24 11:13:20,096] [INFO] Query marker FASTA was written to GCF_003696365.1_ASM369636v1_genomic.fna/markers.fasta
[2024-01-24 11:13:20,096] [INFO] Task started: Blastn
[2024-01-24 11:13:20,097] [INFO] Running command: blastn -query GCF_003696365.1_ASM369636v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcd6f580-a819-4df5-8ea2-699989341046/dqc_reference/reference_markers.fasta -out GCF_003696365.1_ASM369636v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:20,949] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:20,953] [INFO] Selected 12 target genomes.
[2024-01-24 11:13:20,954] [INFO] Target genome list was writen to GCF_003696365.1_ASM369636v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:20,960] [INFO] Task started: fastANI
[2024-01-24 11:13:20,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a289c9d-d50c-4066-a31e-ff07deb52516/GCF_003696365.1_ASM369636v1_genomic.fna.gz --refList GCF_003696365.1_ASM369636v1_genomic.fna/target_genomes.txt --output GCF_003696365.1_ASM369636v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:31,792] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:31,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcd6f580-a819-4df5-8ea2-699989341046/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:31,794] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcd6f580-a819-4df5-8ea2-699989341046/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:31,807] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:13:31,807] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:13:31,807] [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
[Pseudomonas] zhaodongensis	strain=NEAU-ST5-21	GCA_003696365.1	1176257	1176257	suspected-type	True	100.0	1544	1545	95	conclusive
[Pseudomonas] zhaodongensis	strain=DSM 27559T	GCA_024448735.1	1176257	1176257	suspected-type	True	99.9886	1532	1545	95	conclusive
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_900129835.1	271420	271420	suspected-type	True	82.2175	986	1545	95	below_threshold
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_024328335.1	271420	271420	suspected-type	True	82.1745	985	1545	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	80.844	799	1545	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	80.8281	817	1545	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	80.8182	810	1545	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	80.7926	806	1545	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	80.7358	813	1545	95	below_threshold
[Pseudomonas] nosocomialis	strain=A31/70	GCA_005876855.1	1056496	1056496	type	True	80.2109	735	1545	95	below_threshold
Pseudomonas kuykendallii	strain=NRRL B-59562	GCA_900106975.1	1007099	1007099	type	True	79.0643	506	1545	95	below_threshold
Pseudomonas mangrovi	strain=TC11	GCA_003052585.1	2161748	2161748	type	True	78.9437	462	1545	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:31,809] [INFO] DFAST Taxonomy check result was written to GCF_003696365.1_ASM369636v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:31,809] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:31,809] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:31,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcd6f580-a819-4df5-8ea2-699989341046/dqc_reference/checkm_data
[2024-01-24 11:13:31,811] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:31,854] [INFO] Task started: CheckM
[2024-01-24 11:13:31,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003696365.1_ASM369636v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003696365.1_ASM369636v1_genomic.fna/checkm_input GCF_003696365.1_ASM369636v1_genomic.fna/checkm_result
[2024-01-24 11:14:15,198] [INFO] Task succeeded: CheckM
[2024-01-24 11:14:15,200] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:14:15,219] [INFO] ===== Completeness check finished =====
[2024-01-24 11:14:15,219] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:14:15,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003696365.1_ASM369636v1_genomic.fna/markers.fasta)
[2024-01-24 11:14:15,220] [INFO] Task started: Blastn
[2024-01-24 11:14:15,220] [INFO] Running command: blastn -query GCF_003696365.1_ASM369636v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcd6f580-a819-4df5-8ea2-699989341046/dqc_reference/reference_markers_gtdb.fasta -out GCF_003696365.1_ASM369636v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:14:16,734] [INFO] Task succeeded: Blastn
[2024-01-24 11:14:16,739] [INFO] Selected 17 target genomes.
[2024-01-24 11:14:16,739] [INFO] Target genome list was writen to GCF_003696365.1_ASM369636v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:14:16,752] [INFO] Task started: fastANI
[2024-01-24 11:14:16,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg0a289c9d-d50c-4066-a31e-ff07deb52516/GCF_003696365.1_ASM369636v1_genomic.fna.gz --refList GCF_003696365.1_ASM369636v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003696365.1_ASM369636v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:14:33,715] [INFO] Task succeeded: fastANI
[2024-01-24 11:14:33,731] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:14:33,731] [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_003696365.1	s__Pseudomonas_A zhaodongensis	100.0	1544	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002476945.1	s__Pseudomonas_A stutzeri_Q	85.645	1302	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004010935.1	s__Pseudomonas_A sp004010935	82.5549	1069	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	96.94	95.82	0.92	0.89	15	-
GCA_002452485.1	s__Pseudomonas_A stutzeri_P	82.4447	983	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129835.1	s__Pseudomonas_A xanthomarina	82.2251	985	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002890895.1	s__Pseudomonas_A stutzeri_AB	82.1556	1034	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.17	97.01	0.91	0.85	18	-
GCF_000590475.1	s__Pseudomonas_A stutzeri_D	82.1263	1007	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018138085.1	s__Pseudomonas_A stutzeri_AI	82.0876	1053	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.15	96.92	0.90	0.86	5	-
GCF_000952685.1	s__Pseudomonas_A stutzeri_E	82.0387	1073	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003325755.1	s__Pseudomonas_A sp003325755	82.0113	1001	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002387205.1	s__Pseudomonas_A stutzeri_N	81.8929	945	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.23	98.23	0.88	0.88	2	-
GCF_009789555.1	s__Pseudomonas_A stutzeri_R	81.8085	940	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	99.81	99.81	0.96	0.96	2	-
GCA_003527165.1	s__Pseudomonas_A sp003527165	81.8085	563	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339675.1	s__Pseudomonas_A stutzeri_O	81.7029	956	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005876855.1	s__Pseudomonas_R nosocomialis	80.191	738	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	98.98	98.95	0.91	0.90	3	-
GCA_900766265.1	s__Pseudomonas_R sp900766265	79.9982	684	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013522725.1	s__Pseudomonas_R azotifigens_A	79.78	689	1545	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_R	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:14:33,733] [INFO] GTDB search result was written to GCF_003696365.1_ASM369636v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:14:33,734] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:14:33,737] [INFO] DFAST_QC result json was written to GCF_003696365.1_ASM369636v1_genomic.fna/dqc_result.json
[2024-01-24 11:14:33,737] [INFO] DFAST_QC completed!
[2024-01-24 11:14:33,737] [INFO] Total running time: 0h1m29s