[2024-01-24 13:46:18,199] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:18,202] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:18,202] [INFO] DQC Reference Directory: /var/lib/cwl/stg252fe04e-3b1a-49c7-a087-3b3a6c7557cb/dqc_reference
[2024-01-24 13:46:19,635] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:19,638] [INFO] Task started: Prodigal
[2024-01-24 13:46:19,639] [INFO] Running command: gunzip -c /var/lib/cwl/stg4b70c8d9-519f-4cd0-a875-7304392af2a2/GCF_007830455.1_ASM783045v1_genomic.fna.gz | prodigal -d GCF_007830455.1_ASM783045v1_genomic.fna/cds.fna -a GCF_007830455.1_ASM783045v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:39,423] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:39,424] [INFO] Task started: HMMsearch
[2024-01-24 13:46:39,424] [INFO] Running command: hmmsearch --tblout GCF_007830455.1_ASM783045v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg252fe04e-3b1a-49c7-a087-3b3a6c7557cb/dqc_reference/reference_markers.hmm GCF_007830455.1_ASM783045v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:39,770] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:39,771] [INFO] Found 6/6 markers.
[2024-01-24 13:46:39,824] [INFO] Query marker FASTA was written to GCF_007830455.1_ASM783045v1_genomic.fna/markers.fasta
[2024-01-24 13:46:39,824] [INFO] Task started: Blastn
[2024-01-24 13:46:39,824] [INFO] Running command: blastn -query GCF_007830455.1_ASM783045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg252fe04e-3b1a-49c7-a087-3b3a6c7557cb/dqc_reference/reference_markers.fasta -out GCF_007830455.1_ASM783045v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:41,011] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:41,014] [INFO] Selected 16 target genomes.
[2024-01-24 13:46:41,015] [INFO] Target genome list was writen to GCF_007830455.1_ASM783045v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:41,028] [INFO] Task started: fastANI
[2024-01-24 13:46:41,028] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b70c8d9-519f-4cd0-a875-7304392af2a2/GCF_007830455.1_ASM783045v1_genomic.fna.gz --refList GCF_007830455.1_ASM783045v1_genomic.fna/target_genomes.txt --output GCF_007830455.1_ASM783045v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:06,714] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:06,715] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg252fe04e-3b1a-49c7-a087-3b3a6c7557cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:06,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg252fe04e-3b1a-49c7-a087-3b3a6c7557cb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:06,728] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:06,728] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:06,728] [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 lurida	strain=CGMCC 1.10822	GCA_007830455.1	1036180	1036180	type	True	100.0	1987	1989	95	conclusive
Pseudoduganella flava	strain=CGMCC 1.10685	GCA_007830495.1	871742	871742	type	True	85.1953	1451	1989	95	below_threshold
Pseudoduganella dura	strain=DSM 17513	GCA_009727155.1	321982	321982	type	True	85.0394	1489	1989	95	below_threshold
Pseudoduganella albidiflava	strain=DSM 17472	GCA_004322755.1	321983	321983	type	True	85.031	1477	1989	95	below_threshold
Pseudoduganella albidiflava	strain=KCTC 12343	GCA_014651415.1	321983	321983	type	True	85.0251	1471	1989	95	below_threshold
Pseudoduganella dura	strain=KCTC 12342	GCA_014651395.1	321982	321982	type	True	85.0215	1459	1989	95	below_threshold
Pseudoduganella umbonata	strain=CECT 7753	GCA_014192225.1	864828	864828	type	True	84.8706	1482	1989	95	below_threshold
Pseudoduganella lutea	strain=DSM 17473	GCA_004209755.1	321985	321985	type	True	84.4839	1456	1989	95	below_threshold
Pseudoduganella armeniaca	strain=ZMN-3	GCA_003028855.1	2072590	2072590	type	True	84.2855	1310	1989	95	below_threshold
Pseudoduganella buxea	strain=KCTC 52429	GCA_009720835.1	1949069	1949069	type	True	84.1348	1260	1989	95	below_threshold
Pseudoduganella plicata	strain=DSM 17505	GCA_004421005.1	321984	321984	type	True	83.6715	1263	1989	95	below_threshold
Pseudoduganella guangdongensis	strain=DS3	GCA_009857475.1	2692179	2692179	type	True	80.9638	956	1989	95	below_threshold
Massilia norwichensis	strain=LMG 28164	GCA_024753245.1	1442366	1442366	type	True	80.8898	939	1989	95	below_threshold
Massilia cavernae	strain=K1S02-61	GCA_003590855.1	2320864	2320864	type	True	80.8193	764	1989	95	below_threshold
Massilia pinisoli	strain=JCM 31316	GCA_024753285.1	1772194	1772194	type	True	80.6892	970	1989	95	below_threshold
Massilia agri	strain=JCM 31661	GCA_024753255.1	1886785	1886785	type	True	80.5651	950	1989	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:06,730] [INFO] DFAST Taxonomy check result was written to GCF_007830455.1_ASM783045v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:06,730] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:06,731] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:06,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg252fe04e-3b1a-49c7-a087-3b3a6c7557cb/dqc_reference/checkm_data
[2024-01-24 13:47:06,732] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:06,791] [INFO] Task started: CheckM
[2024-01-24 13:47:06,792] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830455.1_ASM783045v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830455.1_ASM783045v1_genomic.fna/checkm_input GCF_007830455.1_ASM783045v1_genomic.fna/checkm_result
[2024-01-24 13:48:08,086] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:08,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:08,110] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:08,110] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:08,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830455.1_ASM783045v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:08,111] [INFO] Task started: Blastn
[2024-01-24 13:48:08,111] [INFO] Running command: blastn -query GCF_007830455.1_ASM783045v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg252fe04e-3b1a-49c7-a087-3b3a6c7557cb/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830455.1_ASM783045v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:10,333] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:10,338] [INFO] Selected 10 target genomes.
[2024-01-24 13:48:10,339] [INFO] Target genome list was writen to GCF_007830455.1_ASM783045v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:10,995] [INFO] Task started: fastANI
[2024-01-24 13:48:10,996] [INFO] Running command: fastANI --query /var/lib/cwl/stg4b70c8d9-519f-4cd0-a875-7304392af2a2/GCF_007830455.1_ASM783045v1_genomic.fna.gz --refList GCF_007830455.1_ASM783045v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830455.1_ASM783045v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:29,967] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:29,985] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:29,986] [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_007830455.1	s__Pseudoduganella lurida	100.0	1987	1989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_002454505.1	s__Pseudoduganella sp002454505	85.6954	1330	1989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007830495.1	s__Pseudoduganella flava	85.2029	1451	1989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004322755.1	s__Pseudoduganella albidiflava	85.0435	1475	1989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009727155.1	s__Pseudoduganella dura	85.0215	1492	1989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_014192225.1	s__Pseudoduganella umbonata	84.8563	1484	1989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_004209755.1	s__Pseudoduganella lutea	84.5047	1453	1989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_008011715.1	s__Pseudoduganella haloabium	84.3081	1278	1989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	98.13	98.13	0.91	0.91	2	-
GCF_003028855.1	s__Pseudoduganella armeniaca	84.2812	1311	1989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009720835.1	s__Pseudoduganella buxea	84.1027	1263	1989	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Pseudoduganella	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:48:29,988] [INFO] GTDB search result was written to GCF_007830455.1_ASM783045v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:29,989] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:29,996] [INFO] DFAST_QC result json was written to GCF_007830455.1_ASM783045v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:29,997] [INFO] DFAST_QC completed!
[2024-01-24 13:48:29,997] [INFO] Total running time: 0h2m12s