[2024-01-24 11:22:49,004] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:22:49,006] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:22:49,006] [INFO] DQC Reference Directory: /var/lib/cwl/stgde0d163e-2cc1-432d-a8df-426a5dcfd01f/dqc_reference
[2024-01-24 11:22:50,246] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:22:50,247] [INFO] Task started: Prodigal
[2024-01-24 11:22:50,247] [INFO] Running command: gunzip -c /var/lib/cwl/stg6481af57-c66d-4981-b6fa-36cfbf97093d/GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna.gz | prodigal -d GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/cds.fna -a GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:23:01,353] [INFO] Task succeeded: Prodigal
[2024-01-24 11:23:01,353] [INFO] Task started: HMMsearch
[2024-01-24 11:23:01,354] [INFO] Running command: hmmsearch --tblout GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgde0d163e-2cc1-432d-a8df-426a5dcfd01f/dqc_reference/reference_markers.hmm GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:23:01,625] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:23:01,627] [INFO] Found 6/6 markers.
[2024-01-24 11:23:01,657] [INFO] Query marker FASTA was written to GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/markers.fasta
[2024-01-24 11:23:01,657] [INFO] Task started: Blastn
[2024-01-24 11:23:01,657] [INFO] Running command: blastn -query GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde0d163e-2cc1-432d-a8df-426a5dcfd01f/dqc_reference/reference_markers.fasta -out GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:02,644] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:02,647] [INFO] Selected 17 target genomes.
[2024-01-24 11:23:02,647] [INFO] Target genome list was writen to GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/target_genomes.txt
[2024-01-24 11:23:02,654] [INFO] Task started: fastANI
[2024-01-24 11:23:02,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg6481af57-c66d-4981-b6fa-36cfbf97093d/GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna.gz --refList GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/target_genomes.txt --output GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:23:16,467] [INFO] Task succeeded: fastANI
[2024-01-24 11:23:16,468] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgde0d163e-2cc1-432d-a8df-426a5dcfd01f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:23:16,468] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgde0d163e-2cc1-432d-a8df-426a5dcfd01f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:23:16,487] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:23:16,487] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:23:16,487] [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 saudiphocaensis	strain=20_BN	GCA_000756775.2	1499686	1499686	type	True	100.0	1224	1224	95	conclusive
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	83.7	901	1224	95	below_threshold
Stutzerimonas frequens	strain=FDAARGOS_877	GCA_016028515.1	2968969	2968969	type	True	82.036	801	1224	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	81.9958	803	1224	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_024448335.1	2968969	2968969	type	True	81.9943	785	1224	95	below_threshold
Pseudomonas songnenensis	strain=DSM 27560T	GCA_024448495.1	1176259	1176259	type	True	81.9702	788	1224	95	below_threshold
Pseudomonas songnenensis	strain=NEAU-ST5-5	GCA_003696315.1	1176259	1176259	type	True	81.9084	786	1224	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	81.8772	793	1224	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	81.8705	771	1224	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	81.8456	812	1224	95	below_threshold
Stutzerimonas stutzeri	strain=FDAARGOS_875	GCA_016028655.1	316	316	type	True	81.8207	818	1224	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	81.8025	776	1224	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	81.7927	782	1224	95	below_threshold
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_024328335.1	271420	271420	suspected-type	True	80.701	722	1224	95	below_threshold
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_900129835.1	271420	271420	suspected-type	True	80.6726	728	1224	95	below_threshold
[Pseudomonas] zhaodongensis	strain=DSM 27559T	GCA_024448735.1	1176257	1176257	suspected-type	True	80.3132	703	1224	95	below_threshold
Azotobacter beijerinckii	strain=DSM 378	GCA_900110885.1	170623	170623	type	True	79.8329	509	1224	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:23:16,489] [INFO] DFAST Taxonomy check result was written to GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/tc_result.tsv
[2024-01-24 11:23:16,490] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:23:16,490] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:23:16,490] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgde0d163e-2cc1-432d-a8df-426a5dcfd01f/dqc_reference/checkm_data
[2024-01-24 11:23:16,491] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:23:16,528] [INFO] Task started: CheckM
[2024-01-24 11:23:16,529] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/checkm_input GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/checkm_result
[2024-01-24 11:23:51,984] [INFO] Task succeeded: CheckM
[2024-01-24 11:23:51,985] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:23:52,005] [INFO] ===== Completeness check finished =====
[2024-01-24 11:23:52,006] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:23:52,006] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/markers.fasta)
[2024-01-24 11:23:52,007] [INFO] Task started: Blastn
[2024-01-24 11:23:52,007] [INFO] Running command: blastn -query GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/markers.fasta -db /var/lib/cwl/stgde0d163e-2cc1-432d-a8df-426a5dcfd01f/dqc_reference/reference_markers_gtdb.fasta -out GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:23:53,877] [INFO] Task succeeded: Blastn
[2024-01-24 11:23:53,882] [INFO] Selected 9 target genomes.
[2024-01-24 11:23:53,882] [INFO] Target genome list was writen to GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:23:53,912] [INFO] Task started: fastANI
[2024-01-24 11:23:53,913] [INFO] Running command: fastANI --query /var/lib/cwl/stg6481af57-c66d-4981-b6fa-36cfbf97093d/GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna.gz --refList GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/target_genomes_gtdb.txt --output GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:24:03,341] [INFO] Task succeeded: fastANI
[2024-01-24 11:24:03,353] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:24:03,354] [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_000756775.1	s__Pseudomonas_A saudiphocaensis	100.0	1224	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.10	98.10	0.92	0.90	3	conclusive
GCA_002345575.1	s__Pseudomonas_A stutzeri_S	88.2369	1047	1224	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_013522825.1	s__Pseudomonas_A stutzeri_AK	85.9759	968	1224	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_002331645.1	s__Pseudomonas_A stutzeri_T	84.8343	909	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.46	98.46	0.92	0.92	2	-
GCF_003696285.1	s__Pseudomonas_A nitrititolerans	83.7118	899	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.45	96.83	0.90	0.83	53	-
GCF_002890915.1	s__Pseudomonas_A stutzeri_AF	82.675	809	1224	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_015070855.1	s__Pseudomonas_A lopnurensis	82.4521	793	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	98.76	98.41	0.83	0.83	4	-
GCF_004331835.1	s__Pseudomonas_A sp004331835	81.9312	828	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.93	97.83	0.93	0.91	3	-
GCF_018138085.1	s__Pseudomonas_A stutzeri_AI	81.4811	832	1224	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.15	96.92	0.90	0.86	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:24:03,355] [INFO] GTDB search result was written to GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:24:03,356] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:24:03,359] [INFO] DFAST_QC result json was written to GCF_000756775.1_PRJEB6478_assembly_1_genomic.fna/dqc_result.json
[2024-01-24 11:24:03,360] [INFO] DFAST_QC completed!
[2024-01-24 11:24:03,360] [INFO] Total running time: 0h1m14s