[2024-01-24 14:46:49,098] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:49,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:49,100] [INFO] DQC Reference Directory: /var/lib/cwl/stgbb13e892-b3d6-4046-8e76-ac2d678bdb01/dqc_reference
[2024-01-24 14:46:50,317] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:50,318] [INFO] Task started: Prodigal
[2024-01-24 14:46:50,318] [INFO] Running command: gunzip -c /var/lib/cwl/stgc3446124-d508-4e47-92b9-f071026a27e5/GCF_009758015.1_ASM975801v1_genomic.fna.gz | prodigal -d GCF_009758015.1_ASM975801v1_genomic.fna/cds.fna -a GCF_009758015.1_ASM975801v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:08,231] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:08,231] [INFO] Task started: HMMsearch
[2024-01-24 14:47:08,231] [INFO] Running command: hmmsearch --tblout GCF_009758015.1_ASM975801v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbb13e892-b3d6-4046-8e76-ac2d678bdb01/dqc_reference/reference_markers.hmm GCF_009758015.1_ASM975801v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:08,565] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:08,566] [INFO] Found 6/6 markers.
[2024-01-24 14:47:08,618] [INFO] Query marker FASTA was written to GCF_009758015.1_ASM975801v1_genomic.fna/markers.fasta
[2024-01-24 14:47:08,619] [INFO] Task started: Blastn
[2024-01-24 14:47:08,619] [INFO] Running command: blastn -query GCF_009758015.1_ASM975801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb13e892-b3d6-4046-8e76-ac2d678bdb01/dqc_reference/reference_markers.fasta -out GCF_009758015.1_ASM975801v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:09,736] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:09,739] [INFO] Selected 12 target genomes.
[2024-01-24 14:47:09,740] [INFO] Target genome list was writen to GCF_009758015.1_ASM975801v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:09,745] [INFO] Task started: fastANI
[2024-01-24 14:47:09,746] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3446124-d508-4e47-92b9-f071026a27e5/GCF_009758015.1_ASM975801v1_genomic.fna.gz --refList GCF_009758015.1_ASM975801v1_genomic.fna/target_genomes.txt --output GCF_009758015.1_ASM975801v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:23,676] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:23,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbb13e892-b3d6-4046-8e76-ac2d678bdb01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:23,677] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbb13e892-b3d6-4046-8e76-ac2d678bdb01/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:23,692] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:23,692] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:23,692] [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 pinisoli	strain=MAH-25	GCA_009758015.1	2682844	2682844	type	True	100.0	1829	1830	95	conclusive
Ramlibacter humi	strain=18x22-1	GCA_004681975.1	2530451	2530451	type	True	84.1841	962	1830	95	below_threshold
Ramlibacter tataouinensis	strain=TTB310	GCA_000215705.1	94132	94132	type	True	84.0638	888	1830	95	below_threshold
Ramlibacter algicola	strain=CrO1	GCA_016641735.1	2795217	2795217	type	True	83.9778	967	1830	95	below_threshold
Ramlibacter henchirensis	strain=DSM 14656	GCA_004682015.1	204072	204072	type	True	83.8647	956	1830	95	below_threshold
Ramlibacter aquaticus	strain=LMG 30558	GCA_015159745.1	2780094	2780094	type	True	82.88	788	1830	95	below_threshold
Ramlibacter agri	strain=G-1-2-2	GCA_012927085.1	2728837	2728837	type	True	82.3539	1058	1830	95	below_threshold
Ramlibacter rhizophilus	strain=CCTCC AB2015357	GCA_004681965.1	1781167	1781167	type	True	82.197	847	1830	95	below_threshold
Ramlibacter lithotrophicus	strain=RBP-1	GCA_012184415.1	2606681	2606681	type	True	81.7989	844	1830	95	below_threshold
Xylophilus ampelinus	strain=CFBP 1192	GCA_024832295.1	54067	54067	type	True	80.6966	630	1830	95	below_threshold
Melaminivora alkalimesophila	strain=CY1	GCA_000282995.1	1165852	1165852	type	True	80.676	389	1830	95	below_threshold
Melaminivora alkalimesophila	strain=DSM 26006	GCA_003182375.1	1165852	1165852	type	True	80.3903	575	1830	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:23,694] [INFO] DFAST Taxonomy check result was written to GCF_009758015.1_ASM975801v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:23,695] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:23,695] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:23,695] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbb13e892-b3d6-4046-8e76-ac2d678bdb01/dqc_reference/checkm_data
[2024-01-24 14:47:23,696] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:23,748] [INFO] Task started: CheckM
[2024-01-24 14:47:23,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009758015.1_ASM975801v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009758015.1_ASM975801v1_genomic.fna/checkm_input GCF_009758015.1_ASM975801v1_genomic.fna/checkm_result
[2024-01-24 14:49:26,659] [INFO] Task succeeded: CheckM
[2024-01-24 14:49:26,661] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:49:26,689] [INFO] ===== Completeness check finished =====
[2024-01-24 14:49:26,690] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:49:26,690] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009758015.1_ASM975801v1_genomic.fna/markers.fasta)
[2024-01-24 14:49:26,691] [INFO] Task started: Blastn
[2024-01-24 14:49:26,691] [INFO] Running command: blastn -query GCF_009758015.1_ASM975801v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbb13e892-b3d6-4046-8e76-ac2d678bdb01/dqc_reference/reference_markers_gtdb.fasta -out GCF_009758015.1_ASM975801v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:49:29,836] [INFO] Task succeeded: Blastn
[2024-01-24 14:49:29,840] [INFO] Selected 12 target genomes.
[2024-01-24 14:49:29,840] [INFO] Target genome list was writen to GCF_009758015.1_ASM975801v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:49:29,853] [INFO] Task started: fastANI
[2024-01-24 14:49:29,854] [INFO] Running command: fastANI --query /var/lib/cwl/stgc3446124-d508-4e47-92b9-f071026a27e5/GCF_009758015.1_ASM975801v1_genomic.fna.gz --refList GCF_009758015.1_ASM975801v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009758015.1_ASM975801v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:49:44,756] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:44,773] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:49:44,774] [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_013778345.1	s__Ramlibacter sp013778345	100.0	1829	1830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_001424545.1	s__Ramlibacter sp001424545	84.9802	1053	1830	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	84.725	1044	1830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000215705.1	s__Ramlibacter tataouinensis	84.0737	888	1830	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	83.9884	966	1830	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	83.9041	952	1830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000426125.1	s__Ramlibacter sp000426125	83.7748	993	1830	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	83.0245	959	1830	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	82.7499	884	1830	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	82.6118	830	1830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013127575.1	s__Ramlibacter sp013127575	82.4805	960	1830	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Ramlibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007833165.1	s__Ramlibacter sp007833165	81.8158	902	1830	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 14:49:44,777] [INFO] GTDB search result was written to GCF_009758015.1_ASM975801v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:49:44,778] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:49:44,782] [INFO] DFAST_QC result json was written to GCF_009758015.1_ASM975801v1_genomic.fna/dqc_result.json
[2024-01-24 14:49:44,782] [INFO] DFAST_QC completed!
[2024-01-24 14:49:44,782] [INFO] Total running time: 0h2m56s