[2024-01-24 13:41:26,571] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:41:26,573] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:41:26,573] [INFO] DQC Reference Directory: /var/lib/cwl/stg1f44c76a-aecf-4bcd-b145-7d835e1671d3/dqc_reference
[2024-01-24 13:41:27,865] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:41:27,866] [INFO] Task started: Prodigal
[2024-01-24 13:41:27,867] [INFO] Running command: gunzip -c /var/lib/cwl/stgd410a364-a455-4228-a296-99e154ad0985/GCF_012927085.1_ASM1292708v1_genomic.fna.gz | prodigal -d GCF_012927085.1_ASM1292708v1_genomic.fna/cds.fna -a GCF_012927085.1_ASM1292708v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:58,343] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:58,344] [INFO] Task started: HMMsearch
[2024-01-24 13:41:58,344] [INFO] Running command: hmmsearch --tblout GCF_012927085.1_ASM1292708v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1f44c76a-aecf-4bcd-b145-7d835e1671d3/dqc_reference/reference_markers.hmm GCF_012927085.1_ASM1292708v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:58,698] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:58,700] [INFO] Found 6/6 markers.
[2024-01-24 13:41:58,760] [INFO] Query marker FASTA was written to GCF_012927085.1_ASM1292708v1_genomic.fna/markers.fasta
[2024-01-24 13:41:58,761] [INFO] Task started: Blastn
[2024-01-24 13:41:58,761] [INFO] Running command: blastn -query GCF_012927085.1_ASM1292708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f44c76a-aecf-4bcd-b145-7d835e1671d3/dqc_reference/reference_markers.fasta -out GCF_012927085.1_ASM1292708v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:59,891] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:59,894] [INFO] Selected 13 target genomes.
[2024-01-24 13:41:59,895] [INFO] Target genome list was writen to GCF_012927085.1_ASM1292708v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:59,962] [INFO] Task started: fastANI
[2024-01-24 13:41:59,962] [INFO] Running command: fastANI --query /var/lib/cwl/stgd410a364-a455-4228-a296-99e154ad0985/GCF_012927085.1_ASM1292708v1_genomic.fna.gz --refList GCF_012927085.1_ASM1292708v1_genomic.fna/target_genomes.txt --output GCF_012927085.1_ASM1292708v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:42:16,791] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:16,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1f44c76a-aecf-4bcd-b145-7d835e1671d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:42:16,793] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1f44c76a-aecf-4bcd-b145-7d835e1671d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:42:16,813] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:42:16,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:42:16,814] [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 agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	100.0	2394	2394	95	conclusive
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	83.9852	1182	2394	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	83.3477	1201	2394	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	82.8384	998	2394	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	82.5951	897	2394	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	82.3804	838	2394	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	82.2608	922	2394	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	82.1034	1087	2394	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	81.9844	939	2394	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	80.9052	940	2394	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	80.2575	787	2394	95	below_threshold
Hydrogenophaga borbori	strain=LA-38	GCA_003417535.1	2294117	2294117	type	True	80.1272	808	2394	95	below_threshold
Acidovorax oryzae	strain=ATCC 19882	GCA_000687165.1	862720	862720	type	True	79.7346	769	2394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:42:16,816] [INFO] DFAST Taxonomy check result was written to GCF_012927085.1_ASM1292708v1_genomic.fna/tc_result.tsv
[2024-01-24 13:42:16,817] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:42:16,817] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:42:16,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1f44c76a-aecf-4bcd-b145-7d835e1671d3/dqc_reference/checkm_data
[2024-01-24 13:42:16,819] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:42:16,891] [INFO] Task started: CheckM
[2024-01-24 13:42:16,891] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012927085.1_ASM1292708v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012927085.1_ASM1292708v1_genomic.fna/checkm_input GCF_012927085.1_ASM1292708v1_genomic.fna/checkm_result
[2024-01-24 13:44:07,340] [INFO] Task succeeded: CheckM
[2024-01-24 13:44:07,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:44:07,386] [INFO] ===== Completeness check finished =====
[2024-01-24 13:44:07,386] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:44:07,387] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012927085.1_ASM1292708v1_genomic.fna/markers.fasta)
[2024-01-24 13:44:07,387] [INFO] Task started: Blastn
[2024-01-24 13:44:07,387] [INFO] Running command: blastn -query GCF_012927085.1_ASM1292708v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1f44c76a-aecf-4bcd-b145-7d835e1671d3/dqc_reference/reference_markers_gtdb.fasta -out GCF_012927085.1_ASM1292708v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:44:09,710] [INFO] Task succeeded: Blastn
[2024-01-24 13:44:09,714] [INFO] Selected 10 target genomes.
[2024-01-24 13:44:09,714] [INFO] Target genome list was writen to GCF_012927085.1_ASM1292708v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:44:09,719] [INFO] Task started: fastANI
[2024-01-24 13:44:09,720] [INFO] Running command: fastANI --query /var/lib/cwl/stgd410a364-a455-4228-a296-99e154ad0985/GCF_012927085.1_ASM1292708v1_genomic.fna.gz --refList GCF_012927085.1_ASM1292708v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012927085.1_ASM1292708v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:24,727] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:24,742] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:24,742] [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_012927085.1	s__Ramlibacter sp012927085	100.0	2394	2394	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_013087525.1	s__Ramlibacter sp013087525	84.3496	1101	2394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016722785.1	s__Ramlibacter monticola	83.9635	1185	2394	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	83.9385	1242	2394	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	83.7281	978	2394	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	83.7157	1033	2394	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	83.4723	1137	2394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013127575.1	s__Ramlibacter sp013127575	83.361	1157	2394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016722765.1	s__Ramlibacter alkalitolerans	83.3294	1204	2394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001424545.1	s__Ramlibacter sp001424545	82.563	984	2394	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:24,744] [INFO] GTDB search result was written to GCF_012927085.1_ASM1292708v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:24,745] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:24,748] [INFO] DFAST_QC result json was written to GCF_012927085.1_ASM1292708v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:24,749] [INFO] DFAST_QC completed!
[2024-01-24 13:44:24,749] [INFO] Total running time: 0h2m58s