[2024-01-24 13:58:10,980] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:10,983] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:10,983] [INFO] DQC Reference Directory: /var/lib/cwl/stgf49b495a-d5e7-48eb-831d-5fdb0e96b49f/dqc_reference
[2024-01-24 13:58:12,292] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:12,293] [INFO] Task started: Prodigal
[2024-01-24 13:58:12,293] [INFO] Running command: gunzip -c /var/lib/cwl/stg06cf5290-c630-453e-8668-2d2673e94025/GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/cds.fna -a GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:28,970] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:28,970] [INFO] Task started: HMMsearch
[2024-01-24 13:58:28,970] [INFO] Running command: hmmsearch --tblout GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf49b495a-d5e7-48eb-831d-5fdb0e96b49f/dqc_reference/reference_markers.hmm GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:29,290] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:29,291] [INFO] Found 6/6 markers.
[2024-01-24 13:58:29,343] [INFO] Query marker FASTA was written to GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:58:29,343] [INFO] Task started: Blastn
[2024-01-24 13:58:29,343] [INFO] Running command: blastn -query GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf49b495a-d5e7-48eb-831d-5fdb0e96b49f/dqc_reference/reference_markers.fasta -out GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:30,739] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:30,749] [INFO] Selected 12 target genomes.
[2024-01-24 13:58:30,749] [INFO] Target genome list was writen to GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:58:30,765] [INFO] Task started: fastANI
[2024-01-24 13:58:30,765] [INFO] Running command: fastANI --query /var/lib/cwl/stg06cf5290-c630-453e-8668-2d2673e94025/GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna.gz --refList GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:50,781] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:50,782] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf49b495a-d5e7-48eb-831d-5fdb0e96b49f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:50,782] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf49b495a-d5e7-48eb-831d-5fdb0e96b49f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:50,797] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:50,797] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:50,798] [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
Geodermatophilus amargosae	strain=DSM 46136	GCA_900116515.1	1296565	1296565	type	True	100.0	1916	1921	95	conclusive
Geodermatophilus normandii	strain=DSM 45417	GCA_003182485.1	1137989	1137989	type	True	91.9641	1325	1921	95	below_threshold
Geodermatophilus aquaeductus	strain=DSM 46834	GCA_900182545.1	1564161	1564161	type	True	91.7292	1421	1921	95	below_threshold
Geodermatophilus nigrescens	strain=DSM 45408	GCA_900129495.1	1070870	1070870	type	True	87.7784	1270	1921	95	below_threshold
Geodermatophilus bullaregiensis	strain=DSM 46841	GCA_016907675.1	1564160	1564160	type	True	87.5437	1277	1921	95	below_threshold
Geodermatophilus saharensis	strain=DSM 45423	GCA_900188205.1	1137994	1137994	type	True	87.4013	1265	1921	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	87.2691	1242	1921	95	below_threshold
Geodermatophilus telluris	strain=DSM 45421	GCA_900102745.1	1190417	1190417	type	True	87.2064	1220	1921	95	below_threshold
Modestobacter altitudinis	strain=1G4	GCA_005930475.1	2213158	2213158	type	True	82.2558	1023	1921	95	below_threshold
Modestobacter marinus	strain=DSM 45201	GCA_011758655.1	477641	477641	type	True	81.9678	1010	1921	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010686625.1	1608614	1608614	type	True	81.9261	919	1921	95	below_threshold
Modestobacter muralis	strain=DSM 100205	GCA_010682105.1	1608614	1608614	type	True	81.8125	898	1921	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:50,799] [INFO] DFAST Taxonomy check result was written to GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:58:50,800] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:50,800] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:50,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf49b495a-d5e7-48eb-831d-5fdb0e96b49f/dqc_reference/checkm_data
[2024-01-24 13:58:50,802] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:50,877] [INFO] Task started: CheckM
[2024-01-24 13:58:50,877] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/checkm_input GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:00:13,857] [INFO] Task succeeded: CheckM
[2024-01-24 14:00:13,859] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:00:13,880] [INFO] ===== Completeness check finished =====
[2024-01-24 14:00:13,880] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:00:13,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:00:13,881] [INFO] Task started: Blastn
[2024-01-24 14:00:13,881] [INFO] Running command: blastn -query GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgf49b495a-d5e7-48eb-831d-5fdb0e96b49f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:00:16,024] [INFO] Task succeeded: Blastn
[2024-01-24 14:00:16,028] [INFO] Selected 12 target genomes.
[2024-01-24 14:00:16,029] [INFO] Target genome list was writen to GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:00:16,050] [INFO] Task started: fastANI
[2024-01-24 14:00:16,050] [INFO] Running command: fastANI --query /var/lib/cwl/stg06cf5290-c630-453e-8668-2d2673e94025/GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna.gz --refList GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:00:35,914] [INFO] Task succeeded: fastANI
[2024-01-24 14:00:35,928] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:00:35,928] [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_900116515.1	s__Geodermatophilus amargosae	100.0	1916	1921	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	95.87	95.87	0.85	0.85	2	conclusive
GCF_003182485.1	s__Geodermatophilus normandii	91.9396	1327	1921	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900182545.1	s__Geodermatophilus aquaeductus	91.7168	1422	1921	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	96.01	96.01	0.85	0.85	2	-
GCF_900115395.1	s__Geodermatophilus obscurus_B	87.8078	1274	1921	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900129495.1	s__Geodermatophilus nigrescens	87.7283	1275	1921	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115505.1	s__Geodermatophilus dictyosporus	87.4511	1231	1921	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188205.1	s__Geodermatophilus saharensis	87.4223	1263	1921	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907675.1	s__Geodermatophilus bullaregiensis	87.4085	1292	1921	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003002915.1	s__Geodermatophilus tzadiensis	87.2955	1239	1921	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110555.1	s__Geodermatophilus endophyticus	83.1128	1006	1921	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010682105.1	s__Modestobacter muralis	81.9072	887	1921	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_013408865.1	s__Modestobacter sp013408865	81.9045	964	1921	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:00:35,930] [INFO] GTDB search result was written to GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:00:35,930] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:00:35,934] [INFO] DFAST_QC result json was written to GCF_900116515.1_IMG-taxon_2599185195_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:00:35,934] [INFO] DFAST_QC completed!
[2024-01-24 14:00:35,934] [INFO] Total running time: 0h2m25s