[2024-01-24 13:57:42,117] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:42,119] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:42,120] [INFO] DQC Reference Directory: /var/lib/cwl/stg45f0ba63-eefa-4dd5-a947-50ffece49298/dqc_reference
[2024-01-24 13:57:43,467] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:43,467] [INFO] Task started: Prodigal
[2024-01-24 13:57:43,468] [INFO] Running command: gunzip -c /var/lib/cwl/stg841efcc8-ba8a-4afc-a7ca-41794dca8979/GCF_015159745.1_ASM1515974v1_genomic.fna.gz | prodigal -d GCF_015159745.1_ASM1515974v1_genomic.fna/cds.fna -a GCF_015159745.1_ASM1515974v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:55,748] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:55,748] [INFO] Task started: HMMsearch
[2024-01-24 13:57:55,749] [INFO] Running command: hmmsearch --tblout GCF_015159745.1_ASM1515974v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg45f0ba63-eefa-4dd5-a947-50ffece49298/dqc_reference/reference_markers.hmm GCF_015159745.1_ASM1515974v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:56,085] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:56,086] [INFO] Found 6/6 markers.
[2024-01-24 13:57:56,151] [INFO] Query marker FASTA was written to GCF_015159745.1_ASM1515974v1_genomic.fna/markers.fasta
[2024-01-24 13:57:56,152] [INFO] Task started: Blastn
[2024-01-24 13:57:56,152] [INFO] Running command: blastn -query GCF_015159745.1_ASM1515974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45f0ba63-eefa-4dd5-a947-50ffece49298/dqc_reference/reference_markers.fasta -out GCF_015159745.1_ASM1515974v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:57,343] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:57,347] [INFO] Selected 13 target genomes.
[2024-01-24 13:57:57,347] [INFO] Target genome list was writen to GCF_015159745.1_ASM1515974v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:57,350] [INFO] Task started: fastANI
[2024-01-24 13:57:57,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg841efcc8-ba8a-4afc-a7ca-41794dca8979/GCF_015159745.1_ASM1515974v1_genomic.fna.gz --refList GCF_015159745.1_ASM1515974v1_genomic.fna/target_genomes.txt --output GCF_015159745.1_ASM1515974v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:12,448] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:12,449] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg45f0ba63-eefa-4dd5-a947-50ffece49298/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:12,449] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg45f0ba63-eefa-4dd5-a947-50ffece49298/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:12,460] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:12,461] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:12,461] [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 aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	100.0	1266	1277	95	conclusive
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	83.8877	746	1277	95	below_threshold
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	83.1788	795	1277	95	below_threshold
Ramlibacter pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	83.0863	769	1277	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	82.6563	802	1277	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	82.6351	704	1277	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	82.5342	714	1277	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	82.4834	738	1277	95	below_threshold
Ramlibacter monticola	strain=KACC 19175	GCA_016722785.1	1926872	1926872	type	True	82.2947	807	1277	95	below_threshold
Ramlibacter alkalitolerans	strain=KACC 19305	GCA_016722765.1	2039631	2039631	type	True	82.2423	794	1277	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	81.7013	737	1277	95	below_threshold
Hydrogenophaga crocea	strain=BA0156	GCA_011388215.1	2716225	2716225	type	True	81.4514	695	1277	95	below_threshold
Pseudorhodoferax aquiterrae	strain=KCTC 23314	GCA_014652235.1	747304	747304	type	True	81.2138	757	1277	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:12,467] [INFO] DFAST Taxonomy check result was written to GCF_015159745.1_ASM1515974v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:12,467] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:12,467] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:12,468] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg45f0ba63-eefa-4dd5-a947-50ffece49298/dqc_reference/checkm_data
[2024-01-24 13:58:12,469] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:12,518] [INFO] Task started: CheckM
[2024-01-24 13:58:12,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_015159745.1_ASM1515974v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_015159745.1_ASM1515974v1_genomic.fna/checkm_input GCF_015159745.1_ASM1515974v1_genomic.fna/checkm_result
[2024-01-24 13:59:02,233] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:02,234] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:02,253] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:02,254] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:02,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_015159745.1_ASM1515974v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:02,254] [INFO] Task started: Blastn
[2024-01-24 13:59:02,254] [INFO] Running command: blastn -query GCF_015159745.1_ASM1515974v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg45f0ba63-eefa-4dd5-a947-50ffece49298/dqc_reference/reference_markers_gtdb.fasta -out GCF_015159745.1_ASM1515974v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:04,563] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:04,566] [INFO] Selected 16 target genomes.
[2024-01-24 13:59:04,566] [INFO] Target genome list was writen to GCF_015159745.1_ASM1515974v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:04,581] [INFO] Task started: fastANI
[2024-01-24 13:59:04,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg841efcc8-ba8a-4afc-a7ca-41794dca8979/GCF_015159745.1_ASM1515974v1_genomic.fna.gz --refList GCF_015159745.1_ASM1515974v1_genomic.fna/target_genomes_gtdb.txt --output GCF_015159745.1_ASM1515974v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:21,559] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:21,577] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:21,577] [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_015159745.1	s__Ramlibacter aquaticus	100.0	1266	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	99.97	99.97	0.95	0.95	2	conclusive
GCF_000215705.1	s__Ramlibacter tataouinensis	83.8652	749	1277	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	83.6137	785	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014874145.1	s__Ramlibacter sp014874145	83.4694	765	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004681975.1	s__Ramlibacter sp004681975	83.2585	787	1277	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	83.1289	779	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778345.1	s__Ramlibacter sp013778345	83.1074	767	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001580455.1	s__Ramlibacter tataouinensis_B	82.956	774	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004681965.1	s__Ramlibacter rhizophilus	82.5985	707	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004682015.1	s__Ramlibacter henchirensis	82.5559	712	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016641735.1	s__Ramlibacter sp016641735	82.5001	737	1277	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	82.4728	716	1277	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	82.3934	692	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000745855.1	s__Xenophilus azovorans	81.8828	746	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Xenophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155545.1	s__Ramlibacter soli	81.8557	705	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003671765.1	s__ALPHA2B sp003671765	81.614	707	1277	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__ALPHA2B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:21,579] [INFO] GTDB search result was written to GCF_015159745.1_ASM1515974v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:21,579] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:21,583] [INFO] DFAST_QC result json was written to GCF_015159745.1_ASM1515974v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:21,583] [INFO] DFAST_QC completed!
[2024-01-24 13:59:21,583] [INFO] Total running time: 0h1m39s