[2024-01-25 18:00:35,392] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:00:35,394] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:00:35,394] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bae05d7-b18e-45c1-9f41-d566cc5e0c7d/dqc_reference
[2024-01-25 18:00:36,530] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:00:36,531] [INFO] Task started: Prodigal
[2024-01-25 18:00:36,531] [INFO] Running command: gunzip -c /var/lib/cwl/stg32b5b7b9-45bb-41a2-a3a0-4b4fb13a1a53/GCF_016722765.1_ASM1672276v1_genomic.fna.gz | prodigal -d GCF_016722765.1_ASM1672276v1_genomic.fna/cds.fna -a GCF_016722765.1_ASM1672276v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:00:54,150] [INFO] Task succeeded: Prodigal
[2024-01-25 18:00:54,150] [INFO] Task started: HMMsearch
[2024-01-25 18:00:54,150] [INFO] Running command: hmmsearch --tblout GCF_016722765.1_ASM1672276v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bae05d7-b18e-45c1-9f41-d566cc5e0c7d/dqc_reference/reference_markers.hmm GCF_016722765.1_ASM1672276v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:00:54,433] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:00:54,434] [INFO] Found 6/6 markers.
[2024-01-25 18:00:54,480] [INFO] Query marker FASTA was written to GCF_016722765.1_ASM1672276v1_genomic.fna/markers.fasta
[2024-01-25 18:00:54,480] [INFO] Task started: Blastn
[2024-01-25 18:00:54,480] [INFO] Running command: blastn -query GCF_016722765.1_ASM1672276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bae05d7-b18e-45c1-9f41-d566cc5e0c7d/dqc_reference/reference_markers.fasta -out GCF_016722765.1_ASM1672276v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:00:55,517] [INFO] Task succeeded: Blastn
[2024-01-25 18:00:55,526] [INFO] Selected 12 target genomes.
[2024-01-25 18:00:55,527] [INFO] Target genome list was writen to GCF_016722765.1_ASM1672276v1_genomic.fna/target_genomes.txt
[2024-01-25 18:00:55,535] [INFO] Task started: fastANI
[2024-01-25 18:00:55,535] [INFO] Running command: fastANI --query /var/lib/cwl/stg32b5b7b9-45bb-41a2-a3a0-4b4fb13a1a53/GCF_016722765.1_ASM1672276v1_genomic.fna.gz --refList GCF_016722765.1_ASM1672276v1_genomic.fna/target_genomes.txt --output GCF_016722765.1_ASM1672276v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:01:11,099] [INFO] Task succeeded: fastANI
[2024-01-25 18:01:11,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bae05d7-b18e-45c1-9f41-d566cc5e0c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:01:11,100] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bae05d7-b18e-45c1-9f41-d566cc5e0c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:01:11,108] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:01:11,109] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:01:11,109] [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
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	100.0	1886	1888	95	conclusive
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	86.6142	1354	1888	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	83.6535	1124	1888	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	82.7129	850	1888	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	82.6301	887	1888	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	82.4979	855	1888	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	82.2858	779	1888	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	82.2803	892	1888	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	82.1111	978	1888	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	81.5476	937	1888	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	81.4181	787	1888	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.1731	587	1888	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:01:11,111] [INFO] DFAST Taxonomy check result was written to GCF_016722765.1_ASM1672276v1_genomic.fna/tc_result.tsv
[2024-01-25 18:01:11,111] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:01:11,111] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:01:11,112] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bae05d7-b18e-45c1-9f41-d566cc5e0c7d/dqc_reference/checkm_data
[2024-01-25 18:01:11,112] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:01:11,166] [INFO] Task started: CheckM
[2024-01-25 18:01:11,166] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016722765.1_ASM1672276v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016722765.1_ASM1672276v1_genomic.fna/checkm_input GCF_016722765.1_ASM1672276v1_genomic.fna/checkm_result
[2024-01-25 18:02:34,059] [INFO] Task succeeded: CheckM
[2024-01-25 18:02:34,059] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:02:34,078] [INFO] ===== Completeness check finished =====
[2024-01-25 18:02:34,078] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:02:34,079] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016722765.1_ASM1672276v1_genomic.fna/markers.fasta)
[2024-01-25 18:02:34,079] [INFO] Task started: Blastn
[2024-01-25 18:02:34,079] [INFO] Running command: blastn -query GCF_016722765.1_ASM1672276v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bae05d7-b18e-45c1-9f41-d566cc5e0c7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_016722765.1_ASM1672276v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:36,359] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:36,362] [INFO] Selected 8 target genomes.
[2024-01-25 18:02:36,362] [INFO] Target genome list was writen to GCF_016722765.1_ASM1672276v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:02:36,372] [INFO] Task started: fastANI
[2024-01-25 18:02:36,372] [INFO] Running command: fastANI --query /var/lib/cwl/stg32b5b7b9-45bb-41a2-a3a0-4b4fb13a1a53/GCF_016722765.1_ASM1672276v1_genomic.fna.gz --refList GCF_016722765.1_ASM1672276v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016722765.1_ASM1672276v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:02:48,559] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:48,566] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:02:48,566] [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_016722765.1	s__Ramlibacter alkalitolerans	100.0	1886	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016722785.1	s__Ramlibacter monticola	86.6543	1350	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013087525.1	s__Ramlibacter sp013087525	85.2305	1127	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004144865.1	s__Ramlibacter sp004144865	84.5645	930	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014297465.1	s__Ramlibacter sp014297465	84.3479	1161	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015070875.1	s__Ramlibacter sp015070875	84.0098	999	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016654015.1	s__Ramlibacter ginsenosidimutans	83.8006	1076	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012927085.1	s__Ramlibacter sp012927085	83.5934	1132	1888	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:02:48,568] [INFO] GTDB search result was written to GCF_016722765.1_ASM1672276v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:02:48,568] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:02:48,571] [INFO] DFAST_QC result json was written to GCF_016722765.1_ASM1672276v1_genomic.fna/dqc_result.json
[2024-01-25 18:02:48,571] [INFO] DFAST_QC completed!
[2024-01-25 18:02:48,571] [INFO] Total running time: 0h2m13s