[2024-01-25 18:52:35,645] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:52:35,647] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:52:35,647] [INFO] DQC Reference Directory: /var/lib/cwl/stg78350504-b51e-44eb-bcef-8e1c5b03693b/dqc_reference
[2024-01-25 18:52:36,775] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:52:36,776] [INFO] Task started: Prodigal
[2024-01-25 18:52:36,776] [INFO] Running command: gunzip -c /var/lib/cwl/stg464d9e65-0458-4862-a6fb-07f9b93ef201/GCF_009720745.1_ASM972074v1_genomic.fna.gz | prodigal -d GCF_009720745.1_ASM972074v1_genomic.fna/cds.fna -a GCF_009720745.1_ASM972074v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:52:54,259] [INFO] Task succeeded: Prodigal
[2024-01-25 18:52:54,259] [INFO] Task started: HMMsearch
[2024-01-25 18:52:54,259] [INFO] Running command: hmmsearch --tblout GCF_009720745.1_ASM972074v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78350504-b51e-44eb-bcef-8e1c5b03693b/dqc_reference/reference_markers.hmm GCF_009720745.1_ASM972074v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:52:54,516] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:52:54,517] [INFO] Found 6/6 markers.
[2024-01-25 18:52:54,565] [INFO] Query marker FASTA was written to GCF_009720745.1_ASM972074v1_genomic.fna/markers.fasta
[2024-01-25 18:52:54,565] [INFO] Task started: Blastn
[2024-01-25 18:52:54,565] [INFO] Running command: blastn -query GCF_009720745.1_ASM972074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78350504-b51e-44eb-bcef-8e1c5b03693b/dqc_reference/reference_markers.fasta -out GCF_009720745.1_ASM972074v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:52:55,461] [INFO] Task succeeded: Blastn
[2024-01-25 18:52:55,463] [INFO] Selected 20 target genomes.
[2024-01-25 18:52:55,464] [INFO] Target genome list was writen to GCF_009720745.1_ASM972074v1_genomic.fna/target_genomes.txt
[2024-01-25 18:52:55,483] [INFO] Task started: fastANI
[2024-01-25 18:52:55,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg464d9e65-0458-4862-a6fb-07f9b93ef201/GCF_009720745.1_ASM972074v1_genomic.fna.gz --refList GCF_009720745.1_ASM972074v1_genomic.fna/target_genomes.txt --output GCF_009720745.1_ASM972074v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:22,002] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:22,002] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78350504-b51e-44eb-bcef-8e1c5b03693b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:22,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78350504-b51e-44eb-bcef-8e1c5b03693b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:22,014] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:53:22,014] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:53:22,015] [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	86.2609	1374	1972	95	below_threshold
Pseudoduganella violacea	strain=CECT 8897	GCA_014191875.1	1715466	1715466	type	True	81.9249	1053	1972	95	below_threshold
Pseudoduganella aquatica	strain=FT127W	GCA_009857595.1	2660641	2660641	type	True	81.6606	1059	1972	95	below_threshold
Pseudoduganella namucuonensis	strain=CGMCC 1.11014	GCA_900116645.1	1035707	1035707	type	True	81.2336	1090	1972	95	below_threshold
Duganella aquatilis	strain=FT26W	GCA_009674565.1	2666082	2666082	type	True	81.1883	1010	1972	95	below_threshold
Duganella alba	strain=FT9W	GCA_009674495.1	2666081	2666081	type	True	81.15	995	1972	95	below_threshold
Pseudoduganella armeniaca	strain=ZMN-3	GCA_003028855.1	2072590	2072590	type	True	81.1001	988	1972	95	below_threshold
Duganella aceris	strain=SAP-35	GCA_011090165.1	2703883	2703883	type	True	80.8694	996	1972	95	below_threshold
Duganella radicis	strain=KCTC 22382	GCA_009720825.1	551988	551988	type	True	80.841	998	1972	95	below_threshold
Pseudoduganella lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	80.7497	929	1972	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	80.5215	730	1972	95	below_threshold
Pseudoduganella flava	strain=CGMCC 1.10685	GCA_007830495.1	871742	871742	type	True	80.4988	962	1972	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	80.4808	899	1972	95	below_threshold
Pseudoduganella rivuli	strain=FT92W	GCA_009674485.1	2666085	2666085	type	True	80.3878	1024	1972	95	below_threshold
Massilia terrae	strain=JCM 31606	GCA_024753145.1	1811224	1811224	type	True	80.1344	802	1972	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	80.0961	811	1972	95	below_threshold
Massilia arenosa	strain=MC02	GCA_004614185.1	2561931	2561931	type	True	80.0498	732	1972	95	below_threshold
Massilia solisilvae	strain=JCM 31607	GCA_024753215.1	1811225	1811225	type	True	79.9824	745	1972	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	79.9729	857	1972	95	below_threshold
Pseudoduganella ginsengisoli	strain=KCTC 42409	GCA_009720865.1	1462440	1462440	type	True	79.7833	875	1972	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:22,016] [INFO] DFAST Taxonomy check result was written to GCF_009720745.1_ASM972074v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:22,016] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:22,016] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:22,017] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78350504-b51e-44eb-bcef-8e1c5b03693b/dqc_reference/checkm_data
[2024-01-25 18:53:22,018] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:22,075] [INFO] Task started: CheckM
[2024-01-25 18:53:22,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009720745.1_ASM972074v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009720745.1_ASM972074v1_genomic.fna/checkm_input GCF_009720745.1_ASM972074v1_genomic.fna/checkm_result
[2024-01-25 18:54:11,076] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:11,077] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:11,110] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:11,110] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:11,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009720745.1_ASM972074v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:11,112] [INFO] Task started: Blastn
[2024-01-25 18:54:11,112] [INFO] Running command: blastn -query GCF_009720745.1_ASM972074v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78350504-b51e-44eb-bcef-8e1c5b03693b/dqc_reference/reference_markers_gtdb.fasta -out GCF_009720745.1_ASM972074v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:12,894] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:12,897] [INFO] Selected 7 target genomes.
[2024-01-25 18:54:12,897] [INFO] Target genome list was writen to GCF_009720745.1_ASM972074v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:12,916] [INFO] Task started: fastANI
[2024-01-25 18:54:12,916] [INFO] Running command: fastANI --query /var/lib/cwl/stg464d9e65-0458-4862-a6fb-07f9b93ef201/GCF_009720745.1_ASM972074v1_genomic.fna.gz --refList GCF_009720745.1_ASM972074v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009720745.1_ASM972074v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:24,507] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:24,513] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:24,513] [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_009720745.1	s__Pseudoduganella eburnea	100.0	1971	1972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001427305.1	s__Pseudoduganella sp001427305	87.4176	1551	1972	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	87.2774	1541	1972	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	87.159	1524	1972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.68	99.68	0.97	0.97	2	-
GCF_900113115.1	s__Pseudoduganella sp900113115	87.0927	1486	1972	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	86.6631	1459	1972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009857475.1	s__Pseudoduganella guangdongensis	86.2438	1376	1972	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:24,515] [INFO] GTDB search result was written to GCF_009720745.1_ASM972074v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:24,516] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:24,518] [INFO] DFAST_QC result json was written to GCF_009720745.1_ASM972074v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:24,519] [INFO] DFAST_QC completed!
[2024-01-25 18:54:24,519] [INFO] Total running time: 0h1m49s