[2024-01-24 14:39:45,827] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:45,829] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:45,829] [INFO] DQC Reference Directory: /var/lib/cwl/stgef534e59-ff74-43e0-8938-98d574cbb763/dqc_reference
[2024-01-24 14:39:48,363] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:48,365] [INFO] Task started: Prodigal
[2024-01-24 14:39:48,365] [INFO] Running command: gunzip -c /var/lib/cwl/stg65eb10ee-eb0d-4c44-b6ff-8818262e8687/GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/cds.fna -a GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:07,002] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:07,003] [INFO] Task started: HMMsearch
[2024-01-24 14:40:07,003] [INFO] Running command: hmmsearch --tblout GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef534e59-ff74-43e0-8938-98d574cbb763/dqc_reference/reference_markers.hmm GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:07,324] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:07,325] [INFO] Found 6/6 markers.
[2024-01-24 14:40:07,383] [INFO] Query marker FASTA was written to GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:40:07,384] [INFO] Task started: Blastn
[2024-01-24 14:40:07,384] [INFO] Running command: blastn -query GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgef534e59-ff74-43e0-8938-98d574cbb763/dqc_reference/reference_markers.fasta -out GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:08,292] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:08,296] [INFO] Selected 21 target genomes.
[2024-01-24 14:40:08,297] [INFO] Target genome list was writen to GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:40:08,304] [INFO] Task started: fastANI
[2024-01-24 14:40:08,305] [INFO] Running command: fastANI --query /var/lib/cwl/stg65eb10ee-eb0d-4c44-b6ff-8818262e8687/GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna.gz --refList GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:30,792] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:30,793] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef534e59-ff74-43e0-8938-98d574cbb763/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:30,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef534e59-ff74-43e0-8938-98d574cbb763/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:30,816] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:40:30,816] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:40:30,817] [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 peli	strain=DSM 17833	GCA_012986145.1	592361	592361	type	True	89.6992	1193	1742	95	below_threshold
Pseudomonas peli	strain=DSM 17833	GCA_900099645.1	592361	592361	type	True	89.6785	1186	1742	95	below_threshold
Pseudomonas guineae	strain=LMG 24016	GCA_900113745.1	425504	425504	type	True	84.4628	1038	1742	95	below_threshold
Pseudomonas tumuqii	strain=LAMW06	GCA_013184545.1	2715755	2715755	type	True	83.1281	941	1742	95	below_threshold
Pseudomonas borbori	strain=DSM 17834	GCA_900115555.1	289003	289003	type	True	82.9869	928	1742	95	below_threshold
Pseudomonas benzenivorans	strain=DSM 8628	GCA_900100495.1	556533	556533	type	True	82.901	965	1742	95	below_threshold
Pseudomonas cuatrocienegasensis	strain=CIP 109853	GCA_900110925.1	543360	543360	type	True	82.7685	913	1742	95	below_threshold
Pseudomonas lalucatii	strain=R1b54	GCA_018398425.1	1424203	1424203	type	True	82.5475	894	1742	95	below_threshold
Pseudomonas hydrolytica	strain=DSWY01	GCA_021495345.2	2493633	2493633	type	True	82.0331	991	1742	95	below_threshold
Pseudomonas guguanensis	strain=JCM 18416	GCA_900104265.1	1198456	1198456	type	True	81.9734	943	1742	95	below_threshold
Pseudomonas ullengensis	strain=UL070	GCA_014174475.1	2759166	2759166	type	True	81.7697	854	1742	95	below_threshold
Pseudomonas yangonensis	strain=MY50	GCA_009932725.1	2579922	2579922	type	True	81.6367	895	1742	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	81.0854	797	1742	95	below_threshold
Pseudomonas indica	strain=NBRC 103045	GCA_002091635.1	137658	137658	type	True	80.4174	828	1742	95	below_threshold
Pseudomonas indica	strain=JCM 21544	GCA_900100285.1	137658	137658	type	True	80.3985	826	1742	95	below_threshold
Stutzerimonas frequens	strain=DNSP21	GCA_002890935.1	2968969	2968969	type	True	80.1232	606	1742	95	below_threshold
Stutzerimonas chloritidismutans	strain=AW-1	GCA_000495915.1	203192	203192	type	True	80.0279	595	1742	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:30,818] [INFO] DFAST Taxonomy check result was written to GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:40:30,819] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:30,819] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:30,819] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef534e59-ff74-43e0-8938-98d574cbb763/dqc_reference/checkm_data
[2024-01-24 14:40:30,821] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:30,878] [INFO] Task started: CheckM
[2024-01-24 14:40:30,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/checkm_input GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:41:24,349] [INFO] Task succeeded: CheckM
[2024-01-24 14:41:24,350] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:41:24,381] [INFO] ===== Completeness check finished =====
[2024-01-24 14:41:24,382] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:41:24,382] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:41:24,383] [INFO] Task started: Blastn
[2024-01-24 14:41:24,383] [INFO] Running command: blastn -query GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgef534e59-ff74-43e0-8938-98d574cbb763/dqc_reference/reference_markers_gtdb.fasta -out GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:41:25,788] [INFO] Task succeeded: Blastn
[2024-01-24 14:41:25,791] [INFO] Selected 13 target genomes.
[2024-01-24 14:41:25,791] [INFO] Target genome list was writen to GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:41:25,801] [INFO] Task started: fastANI
[2024-01-24 14:41:25,802] [INFO] Running command: fastANI --query /var/lib/cwl/stg65eb10ee-eb0d-4c44-b6ff-8818262e8687/GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna.gz --refList GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:46,876] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:46,893] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:46,894] [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_900105355.1	s__Pseudomonas_E anguilliseptica	100.0	1729	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.12	96.12	0.88	0.88	2	conclusive
GCA_002840155.1	s__Pseudomonas_E sp002840155	90.7917	1268	1742	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_900099645.1	s__Pseudomonas_E peli	89.6364	1190	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.85	96.04	0.90	0.85	7	-
GCA_018827205.1	s__Pseudomonas_E sp018827205	89.0327	1074	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.54	99.51	0.89	0.88	4	-
GCF_003060885.1	s__Pseudomonas_E sp003060885	87.8464	1137	1742	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_004920405.1	s__Pseudomonas_E leptonychotis	85.8022	1182	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018816095.1	s__Pseudomonas_E sp018816095	85.5473	929	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.20	96.15	0.83	0.82	4	-
GCA_002354655.1	s__Pseudomonas_E sp002354655	83.9533	993	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	99.84	99.84	0.95	0.95	2	-
GCF_014164785.1	s__Pseudomonas_E sp014164785	82.0412	888	1742	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_008041835.1	s__Pseudomonas_E sp002282595	81.8401	821	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	95.53	95.53	0.75	0.75	2	-
GCF_014851905.1	s__Pseudomonas_E sp014851905	81.4854	838	1742	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_002091635.1	s__Pseudomonas_M indica	80.3826	835	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_M	95.0	99.16	98.73	0.94	0.91	4	-
GCF_000495915.1	s__Pseudomonas_A chloritidismutans	80.0156	599	1742	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_A	96.9847	97.37	97.19	0.88	0.85	8	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:46,895] [INFO] GTDB search result was written to GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:46,896] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:46,902] [INFO] DFAST_QC result json was written to GCF_900105355.1_IMG-taxon_2687453785_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:41:46,903] [INFO] DFAST_QC completed!
[2024-01-24 14:41:46,903] [INFO] Total running time: 0h2m1s