[2024-01-24 13:09:29,211] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:29,213] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:29,213] [INFO] DQC Reference Directory: /var/lib/cwl/stg0390b6a3-ee61-4075-8f28-8af74cb976e4/dqc_reference
[2024-01-24 13:09:30,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:30,425] [INFO] Task started: Prodigal
[2024-01-24 13:09:30,425] [INFO] Running command: gunzip -c /var/lib/cwl/stge7ff842a-2bbb-4acb-8ec1-95f64521aad3/GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/cds.fna -a GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:43,310] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:43,311] [INFO] Task started: HMMsearch
[2024-01-24 13:09:43,311] [INFO] Running command: hmmsearch --tblout GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0390b6a3-ee61-4075-8f28-8af74cb976e4/dqc_reference/reference_markers.hmm GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:43,657] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:43,659] [INFO] Found 6/6 markers.
[2024-01-24 13:09:43,708] [INFO] Query marker FASTA was written to GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:09:43,708] [INFO] Task started: Blastn
[2024-01-24 13:09:43,709] [INFO] Running command: blastn -query GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0390b6a3-ee61-4075-8f28-8af74cb976e4/dqc_reference/reference_markers.fasta -out GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:44,637] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:44,641] [INFO] Selected 12 target genomes.
[2024-01-24 13:09:44,642] [INFO] Target genome list was writen to GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:09:44,647] [INFO] Task started: fastANI
[2024-01-24 13:09:44,647] [INFO] Running command: fastANI --query /var/lib/cwl/stge7ff842a-2bbb-4acb-8ec1-95f64521aad3/GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna.gz --refList GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:55,541] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:55,541] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0390b6a3-ee61-4075-8f28-8af74cb976e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:55,541] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0390b6a3-ee61-4075-8f28-8af74cb976e4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:55,554] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:09:55,554] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:55,555] [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 xanthomarina	strain=DSM 18231	GCA_900129835.1	271420	271420	suspected-type	True	100.0	1427	1427	95	conclusive
Stutzerimonas xanthomarina	strain=DSM 18231	GCA_024328335.1	271420	271420	suspected-type	True	99.9862	1404	1427	95	conclusive
[Pseudomonas] zhaodongensis	strain=DSM 27559T	GCA_024448735.1	1176257	1176257	suspected-type	True	82.2471	974	1427	95	below_threshold
[Pseudomonas] zhaodongensis	strain=NEAU-ST5-21	GCA_003696365.1	1176257	1176257	suspected-type	True	82.1434	997	1427	95	below_threshold
Stutzerimonas kunmingensis	strain=DSM 25974	GCA_024397575.1	1211807	1211807	type	True	81.5819	849	1427	95	below_threshold
Pseudomonas nitrititolerans	strain=GL14	GCA_003696285.1	2482751	2482751	type	True	81.4787	831	1427	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_002891015.1	2968968	2968968	type	True	81.3468	787	1427	95	below_threshold
Stutzerimonas degradans	strain=DSM 50238	GCA_024448505.1	2968968	2968968	type	True	81.3061	798	1427	95	below_threshold
Stutzerimonas degradans	strain=FDAARGOS_876	GCA_016028635.1	2968968	2968968	suspected-type	True	81.3023	811	1427	95	below_threshold
Stutzerimonas stutzeri	strain=CGMCC 1.1803	GCA_000219605.1	316	316	type	True	81.2564	875	1427	95	below_threshold
Pseudomonas saudiphocaensis	strain=20_BN	GCA_000756775.2	1499686	1499686	type	True	80.6064	745	1427	95	below_threshold
Pseudomonas carbonaria	strain=CIP 111764	GCA_904061905.1	2762745	2762745	type	True	79.3588	567	1427	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:55,557] [INFO] DFAST Taxonomy check result was written to GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:09:55,557] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:55,558] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:55,558] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0390b6a3-ee61-4075-8f28-8af74cb976e4/dqc_reference/checkm_data
[2024-01-24 13:09:55,560] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:55,600] [INFO] Task started: CheckM
[2024-01-24 13:09:55,601] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/checkm_input GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:10:36,728] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:36,729] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:36,749] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:36,749] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:36,750] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:10:36,750] [INFO] Task started: Blastn
[2024-01-24 13:10:36,751] [INFO] Running command: blastn -query GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0390b6a3-ee61-4075-8f28-8af74cb976e4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:38,405] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:38,409] [INFO] Selected 13 target genomes.
[2024-01-24 13:10:38,409] [INFO] Target genome list was writen to GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:38,418] [INFO] Task started: fastANI
[2024-01-24 13:10:38,419] [INFO] Running command: fastANI --query /var/lib/cwl/stge7ff842a-2bbb-4acb-8ec1-95f64521aad3/GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna.gz --refList GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:52,056] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:52,075] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:52,075] [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_900129835.1	s__Pseudomonas_A xanthomarina	100.0	1427	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_000235745.1	s__Pseudomonas_A stutzeri_H	91.7126	1156	1427	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_002890895.1	s__Pseudomonas_A stutzeri_AB	88.3108	1207	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.17	97.01	0.91	0.85	18	-
GCA_004010935.1	s__Pseudomonas_A sp004010935	88.1543	1254	1427	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	84.4092	1027	1427	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	83.2264	1063	1427	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	83.1689	1116	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	97.15	96.92	0.90	0.86	5	-
GCA_002387205.1	s__Pseudomonas_A stutzeri_N	83.1582	982	1427	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_013620795.1	s__Pseudomonas_A sp013620795	83.0537	1047	1427	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_000590475.1	s__Pseudomonas_A stutzeri_D	82.9137	1014	1427	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	82.8049	1033	1427	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_009789555.1	s__Pseudomonas_A stutzeri_R	82.4177	976	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	99.81	99.81	0.96	0.96	2	-
GCF_003696365.1	s__Pseudomonas_A zhaodongensis	82.1457	997	1427	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:52,077] [INFO] GTDB search result was written to GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:52,077] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:52,081] [INFO] DFAST_QC result json was written to GCF_900129835.1_IMG-taxon_2687453778_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:10:52,081] [INFO] DFAST_QC completed!
[2024-01-24 13:10:52,081] [INFO] Total running time: 0h1m23s