[2024-01-24 13:40:30,041] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:30,043] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:30,044] [INFO] DQC Reference Directory: /var/lib/cwl/stgc36a5669-ae20-4a31-9d58-e72db5f2c070/dqc_reference
[2024-01-24 13:40:31,402] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:31,403] [INFO] Task started: Prodigal
[2024-01-24 13:40:31,404] [INFO] Running command: gunzip -c /var/lib/cwl/stg75bd9f69-967d-4d0b-a86c-574e885d00dc/GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/cds.fna -a GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:47,852] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:47,853] [INFO] Task started: HMMsearch
[2024-01-24 13:40:47,853] [INFO] Running command: hmmsearch --tblout GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc36a5669-ae20-4a31-9d58-e72db5f2c070/dqc_reference/reference_markers.hmm GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:48,170] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:48,171] [INFO] Found 6/6 markers.
[2024-01-24 13:40:48,213] [INFO] Query marker FASTA was written to GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:40:48,214] [INFO] Task started: Blastn
[2024-01-24 13:40:48,214] [INFO] Running command: blastn -query GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc36a5669-ae20-4a31-9d58-e72db5f2c070/dqc_reference/reference_markers.fasta -out GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:49,324] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:49,327] [INFO] Selected 12 target genomes.
[2024-01-24 13:40:49,328] [INFO] Target genome list was writen to GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:40:49,335] [INFO] Task started: fastANI
[2024-01-24 13:40:49,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg75bd9f69-967d-4d0b-a86c-574e885d00dc/GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna.gz --refList GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:05,331] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:05,332] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc36a5669-ae20-4a31-9d58-e72db5f2c070/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:05,332] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc36a5669-ae20-4a31-9d58-e72db5f2c070/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:05,346] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:41:05,346] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:05,346] [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 argentinensis	strain=LMG 22563	GCA_900113905.1	289370	289370	type	True	100.0	1695	1696	95	conclusive
Pseudomonas argentinensis	strain=CCUG 50743	GCA_008801645.1	289370	289370	type	True	99.9973	1695	1696	95	conclusive
Pseudomonas punonensis	strain=CECT 8089	GCA_900142655.1	1220495	1220495	type	True	88.7986	1372	1696	95	below_threshold
Pseudomonas flavescens	strain=LMG 18387	GCA_900100535.1	29435	29435	type	True	86.3007	1288	1696	95	below_threshold
Pseudomonas flavescens	strain=NBRC 103044	GCA_002091575.1	29435	29435	type	True	86.2764	1293	1696	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	83.0662	844	1696	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	82.7791	938	1696	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	82.6878	932	1696	95	below_threshold
Pseudomonas toyotomiensis	strain=JCM 15604	GCA_900115695.1	554344	554344	type	True	82.425	934	1696	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	82.2907	898	1696	95	below_threshold
Pseudomonas tohonis	strain=TUM18999	GCA_012767755.2	2725477	2725477	type	True	81.8614	976	1696	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.7821	804	1696	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:05,348] [INFO] DFAST Taxonomy check result was written to GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:41:05,349] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:05,350] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:05,350] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc36a5669-ae20-4a31-9d58-e72db5f2c070/dqc_reference/checkm_data
[2024-01-24 13:41:05,351] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:05,406] [INFO] Task started: CheckM
[2024-01-24 13:41:05,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/checkm_input GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:41:56,684] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:56,685] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:56,704] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:56,705] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:56,705] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:41:56,706] [INFO] Task started: Blastn
[2024-01-24 13:41:56,706] [INFO] Running command: blastn -query GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc36a5669-ae20-4a31-9d58-e72db5f2c070/dqc_reference/reference_markers_gtdb.fasta -out GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:58,741] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:58,744] [INFO] Selected 9 target genomes.
[2024-01-24 13:41:58,744] [INFO] Target genome list was writen to GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:58,750] [INFO] Task started: fastANI
[2024-01-24 13:41:58,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg75bd9f69-967d-4d0b-a86c-574e885d00dc/GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna.gz --refList GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:11,479] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:11,491] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:11,491] [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_900113905.1	s__Pseudomonas_E argentinensis	100.0	1695	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003253735.1	s__Pseudomonas_E sp003253735	92.4042	1501	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.17	98.17	0.95	0.95	2	-
GCF_001839655.1	s__Pseudomonas_E argentinensis_B	90.9309	1431	1696	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_001945445.1	s__Pseudomonas_E sp001945445	89.8417	1398	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.66	98.66	0.91	0.91	2	-
GCF_000213805.1	s__Pseudomonas_E fulva_B	89.5855	1383	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.53	96.12	0.92	0.90	6	-
GCF_001945395.1	s__Pseudomonas_E sp001945395	89.5532	1378	1696	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_900112645.1	s__Pseudomonas_E straminea	89.3912	1364	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	98.06	98.06	0.94	0.94	2	-
GCF_900142655.1	s__Pseudomonas_E punonensis	88.7939	1373	1696	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_900100535.1	s__Pseudomonas_E flavescens	86.3026	1287	1696	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:11,493] [INFO] GTDB search result was written to GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:11,493] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:11,498] [INFO] DFAST_QC result json was written to GCF_900113905.1_IMG-taxon_2671180085_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:42:11,498] [INFO] DFAST_QC completed!
[2024-01-24 13:42:11,498] [INFO] Total running time: 0h1m41s