[2024-01-24 13:32:25,815] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:25,818] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:25,818] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e2625a7-f2f8-4d76-8e67-ae355e9a94dd/dqc_reference
[2024-01-24 13:32:27,011] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:27,012] [INFO] Task started: Prodigal
[2024-01-24 13:32:27,013] [INFO] Running command: gunzip -c /var/lib/cwl/stg05bb6e05-c590-4bc2-99cc-ff52438f44c0/GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/cds.fna -a GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:51,665] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:51,665] [INFO] Task started: HMMsearch
[2024-01-24 13:32:51,666] [INFO] Running command: hmmsearch --tblout GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e2625a7-f2f8-4d76-8e67-ae355e9a94dd/dqc_reference/reference_markers.hmm GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:51,999] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:52,000] [INFO] Found 6/6 markers.
[2024-01-24 13:32:52,063] [INFO] Query marker FASTA was written to GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:32:52,063] [INFO] Task started: Blastn
[2024-01-24 13:32:52,064] [INFO] Running command: blastn -query GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e2625a7-f2f8-4d76-8e67-ae355e9a94dd/dqc_reference/reference_markers.fasta -out GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:53,028] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:53,033] [INFO] Selected 10 target genomes.
[2024-01-24 13:32:53,033] [INFO] Target genome list was writen to GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:32:53,125] [INFO] Task started: fastANI
[2024-01-24 13:32:53,125] [INFO] Running command: fastANI --query /var/lib/cwl/stg05bb6e05-c590-4bc2-99cc-ff52438f44c0/GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna.gz --refList GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:33:11,566] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:11,567] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e2625a7-f2f8-4d76-8e67-ae355e9a94dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:33:11,567] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e2625a7-f2f8-4d76-8e67-ae355e9a94dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:33:11,576] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 13:33:11,577] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:33:11,577] [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 azotoformans	strain=LMG 21611	GCA_900103345.1	47878	47878	suspected-type	True	100.0	2240	2242	95	conclusive
Pseudomonas azotoformans	strain=DSM 18862	GCA_001983205.1	47878	47878	suspected-type	True	99.9958	2215	2242	95	conclusive
Pseudomonas azotoformans		GCA_900624915.1	47878	47878	suspected-type	True	99.9933	2217	2242	95	conclusive
Pseudomonas azotoformans	strain=LMG 21611	GCA_001870415.1	47878	47878	suspected-type	True	99.992	2214	2242	95	conclusive
Pseudomonas azotoformans	strain=NBRC 12693	GCA_002091515.1	47878	47878	suspected-type	True	99.9873	2195	2242	95	conclusive
Pseudomonas pergaminensis	strain=1008	GCA_024112395.1	2853159	2853159	type	True	91.1439	1865	2242	95	below_threshold
Pseudomonas lurida	strain=LMG 21995	GCA_002563895.1	244566	244566	type	True	90.3989	1781	2242	95	below_threshold
Pseudomonas marginalis	strain=DSM 13124	GCA_007858155.1	298	298	suspected-type	True	89.1804	1699	2242	95	below_threshold
Pseudomonas spelaei	strain=CCM 7893	GCA_009724245.1	1055469	1055469	type	True	86.0384	1522	2242	95	below_threshold
Pseudomonas karstica	strain=CCM 7891	GCA_009707515.1	1055468	1055468	type	True	85.3772	1334	2242	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:33:11,579] [INFO] DFAST Taxonomy check result was written to GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:33:11,580] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:33:11,580] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:33:11,581] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e2625a7-f2f8-4d76-8e67-ae355e9a94dd/dqc_reference/checkm_data
[2024-01-24 13:33:11,583] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:33:11,651] [INFO] Task started: CheckM
[2024-01-24 13:33:11,652] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/checkm_input GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:34:24,375] [INFO] Task succeeded: CheckM
[2024-01-24 13:34:24,377] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:34:24,408] [INFO] ===== Completeness check finished =====
[2024-01-24 13:34:24,408] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:34:24,409] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:34:24,409] [INFO] Task started: Blastn
[2024-01-24 13:34:24,409] [INFO] Running command: blastn -query GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e2625a7-f2f8-4d76-8e67-ae355e9a94dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:34:26,135] [INFO] Task succeeded: Blastn
[2024-01-24 13:34:26,138] [INFO] Selected 15 target genomes.
[2024-01-24 13:34:26,138] [INFO] Target genome list was writen to GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:34:26,245] [INFO] Task started: fastANI
[2024-01-24 13:34:26,246] [INFO] Running command: fastANI --query /var/lib/cwl/stg05bb6e05-c590-4bc2-99cc-ff52438f44c0/GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna.gz --refList GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:34:52,717] [INFO] Task succeeded: fastANI
[2024-01-24 13:34:52,734] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:34:52,735] [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_900103345.1	s__Pseudomonas_E azotoformans	100.0	2240	2242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	97.97	95.87	0.94	0.87	9	conclusive
GCF_001870465.1	s__Pseudomonas_E extremorientalis	94.3102	1874	2242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.37	98.13	0.91	0.89	29	-
GCF_002007785.1	s__Pseudomonas_E azotoformans_B	91.1983	1862	2242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.95	98.86	0.94	0.92	6	-
GCF_000612585.1	s__Pseudomonas_E sp000612585	91.0711	1715	2242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001579805.1	s__Pseudomonas_E azotoformans_A	90.7504	1856	2242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.75	96.24	0.87	0.84	8	-
GCF_013385825.1	s__Pseudomonas_E reactans	90.6738	1803	2242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.45	96.30	0.89	0.87	7	-
GCF_001645105.1	s__Pseudomonas_E marginalis_B	90.4767	1744	2242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.70	98.28	0.91	0.87	10	-
GCF_002563895.1	s__Pseudomonas_E lurida	90.4056	1780	2242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.19	99.03	0.94	0.91	25	-
GCF_900111895.1	s__Pseudomonas_E simiae	90.3208	1750	2242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.45	99.32	0.95	0.92	20	-
GCF_001186335.1	s__Pseudomonas_E trivialis_B	89.9648	1767	2242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.34	95.31	0.86	0.86	8	-
GCF_000346755.1	s__Pseudomonas_E sp000346755	89.1947	1619	2242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003852405.1	s__Pseudomonas_E sp003852405	89.1638	1669	2242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.89	95.89	0.88	0.88	2	-
GCF_012844475.1	s__Pseudomonas_E sp012844475	89.1634	1542	2242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013386585.1	s__Pseudomonas_E sp013386585	89.1059	1692	2242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002837185.1	s__Pseudomonas_E fluorescens_AM	87.7923	1521	2242	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.23	99.16	0.96	0.94	7	-
--------------------------------------------------------------------------------
[2024-01-24 13:34:52,737] [INFO] GTDB search result was written to GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:34:52,737] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:34:52,741] [INFO] DFAST_QC result json was written to GCF_900103345.1_IMG-taxon_2636416017_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:34:52,741] [INFO] DFAST_QC completed!
[2024-01-24 13:34:52,741] [INFO] Total running time: 0h2m27s