[2023-06-29 13:43:27,605] [INFO] DFAST_QC pipeline started.
[2023-06-29 13:43:27,608] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 13:43:27,609] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f3864c3-e8fe-4f20-a982-7554ec93bb91/dqc_reference
[2023-06-29 13:43:28,852] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 13:43:28,853] [INFO] Task started: Prodigal
[2023-06-29 13:43:28,854] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f67fde0-dddc-46db-884b-1f8476aef75b/GCA_021323265.1_ASM2132326v1_genomic.fna.gz | prodigal -d GCA_021323265.1_ASM2132326v1_genomic.fna/cds.fna -a GCA_021323265.1_ASM2132326v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 13:43:44,949] [INFO] Task succeeded: Prodigal
[2023-06-29 13:43:44,949] [INFO] Task started: HMMsearch
[2023-06-29 13:43:44,949] [INFO] Running command: hmmsearch --tblout GCA_021323265.1_ASM2132326v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f3864c3-e8fe-4f20-a982-7554ec93bb91/dqc_reference/reference_markers.hmm GCA_021323265.1_ASM2132326v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 13:43:45,234] [INFO] Task succeeded: HMMsearch
[2023-06-29 13:43:45,236] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg0f67fde0-dddc-46db-884b-1f8476aef75b/GCA_021323265.1_ASM2132326v1_genomic.fna.gz]
[2023-06-29 13:43:45,278] [INFO] Query marker FASTA was written to GCA_021323265.1_ASM2132326v1_genomic.fna/markers.fasta
[2023-06-29 13:43:45,278] [INFO] Task started: Blastn
[2023-06-29 13:43:45,278] [INFO] Running command: blastn -query GCA_021323265.1_ASM2132326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f3864c3-e8fe-4f20-a982-7554ec93bb91/dqc_reference/reference_markers.fasta -out GCA_021323265.1_ASM2132326v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:43:46,019] [INFO] Task succeeded: Blastn
[2023-06-29 13:43:46,024] [INFO] Selected 14 target genomes.
[2023-06-29 13:43:46,025] [INFO] Target genome list was writen to GCA_021323265.1_ASM2132326v1_genomic.fna/target_genomes.txt
[2023-06-29 13:43:46,027] [INFO] Task started: fastANI
[2023-06-29 13:43:46,027] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f67fde0-dddc-46db-884b-1f8476aef75b/GCA_021323265.1_ASM2132326v1_genomic.fna.gz --refList GCA_021323265.1_ASM2132326v1_genomic.fna/target_genomes.txt --output GCA_021323265.1_ASM2132326v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 13:44:04,548] [INFO] Task succeeded: fastANI
[2023-06-29 13:44:04,549] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f3864c3-e8fe-4f20-a982-7554ec93bb91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 13:44:04,550] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f3864c3-e8fe-4f20-a982-7554ec93bb91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 13:44:04,566] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 13:44:04,567] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 13:44:04,567] [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
Pseudoduganella guangdongensis	strain=DS3	GCA_009857475.1	2692179	2692179	type	True	87.2372	1159	1476	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	82.0774	900	1476	95	below_threshold
Pseudoduganella violacea	strain=CECT 8897	GCA_014191875.1	1715466	1715466	type	True	81.9469	899	1476	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	81.8751	943	1476	95	below_threshold
Pseudoduganella armeniaca	strain=ZMN-3	GCA_003028855.1	2072590	2072590	type	True	81.4992	874	1476	95	below_threshold
Rugamonas brunnea	strain=LX20W	GCA_014042345.1	2758569	2758569	type	True	81.4741	795	1476	95	below_threshold
Rugamonas fusca	strain=FT3S	GCA_014042365.1	2758568	2758568	type	True	81.2121	798	1476	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	81.1528	800	1476	95	below_threshold
Rugamonas apoptosis	strain=LX47W	GCA_014042355.1	2758570	2758570	type	True	81.029	792	1476	95	below_threshold
Pseudoduganella plicata	strain=DSM 17505	GCA_004421005.1	321984	321984	type	True	80.5661	800	1476	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	80.259	659	1476	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	80.2174	718	1476	95	below_threshold
Duganella dendranthematis	strain=AF9R3	GCA_012849375.1	2728021	2728021	type	True	80.2046	774	1476	95	below_threshold
Pseudoduganella rivuli	strain=FT92W	GCA_009674485.1	2666085	2666085	type	True	79.9595	857	1476	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 13:44:04,571] [INFO] DFAST Taxonomy check result was written to GCA_021323265.1_ASM2132326v1_genomic.fna/tc_result.tsv
[2023-06-29 13:44:04,572] [INFO] ===== Taxonomy check completed =====
[2023-06-29 13:44:04,573] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 13:44:04,573] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f3864c3-e8fe-4f20-a982-7554ec93bb91/dqc_reference/checkm_data
[2023-06-29 13:44:04,574] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 13:44:04,626] [INFO] Task started: CheckM
[2023-06-29 13:44:04,626] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_021323265.1_ASM2132326v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_021323265.1_ASM2132326v1_genomic.fna/checkm_input GCA_021323265.1_ASM2132326v1_genomic.fna/checkm_result
[2023-06-29 13:44:51,604] [INFO] Task succeeded: CheckM
[2023-06-29 13:44:51,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 47.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 13:44:51,626] [INFO] ===== Completeness check finished =====
[2023-06-29 13:44:51,626] [INFO] ===== Start GTDB Search =====
[2023-06-29 13:44:51,627] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_021323265.1_ASM2132326v1_genomic.fna/markers.fasta)
[2023-06-29 13:44:51,627] [INFO] Task started: Blastn
[2023-06-29 13:44:51,627] [INFO] Running command: blastn -query GCA_021323265.1_ASM2132326v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f3864c3-e8fe-4f20-a982-7554ec93bb91/dqc_reference/reference_markers_gtdb.fasta -out GCA_021323265.1_ASM2132326v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 13:44:52,821] [INFO] Task succeeded: Blastn
[2023-06-29 13:44:52,825] [INFO] Selected 7 target genomes.
[2023-06-29 13:44:52,826] [INFO] Target genome list was writen to GCA_021323265.1_ASM2132326v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 13:44:52,833] [INFO] Task started: fastANI
[2023-06-29 13:44:52,833] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f67fde0-dddc-46db-884b-1f8476aef75b/GCA_021323265.1_ASM2132326v1_genomic.fna.gz --refList GCA_021323265.1_ASM2132326v1_genomic.fna/target_genomes_gtdb.txt --output GCA_021323265.1_ASM2132326v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 13:45:02,446] [INFO] Task succeeded: fastANI
[2023-06-29 13:45:02,459] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 13:45:02,459] [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_009857475.1	s__Pseudoduganella guangdongensis	87.2413	1158	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900113115.1	s__Pseudoduganella sp900113115	85.922	1134	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004217275.1	s__Pseudoduganella sp004217275	85.8874	1133	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000425385.1	s__Pseudoduganella violaceinigra	85.6596	1099	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720745.1	s__Pseudoduganella eburnea	85.6569	1097	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001425005.1	s__Pseudoduganella sp001425005	85.6296	1165	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.68	99.68	0.97	0.97	2	-
GCF_001427305.1	s__Pseudoduganella sp001427305	85.5808	1166	1476	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 13:45:02,461] [INFO] GTDB search result was written to GCA_021323265.1_ASM2132326v1_genomic.fna/result_gtdb.tsv
[2023-06-29 13:45:02,462] [INFO] ===== GTDB Search completed =====
[2023-06-29 13:45:02,465] [INFO] DFAST_QC result json was written to GCA_021323265.1_ASM2132326v1_genomic.fna/dqc_result.json
[2023-06-29 13:45:02,465] [INFO] DFAST_QC completed!
[2023-06-29 13:45:02,465] [INFO] Total running time: 0h1m35s