[2024-01-24 13:27:46,464] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:46,466] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:46,466] [INFO] DQC Reference Directory: /var/lib/cwl/stg74cc528a-c01e-4cfd-b846-0a2850dc9a7d/dqc_reference
[2024-01-24 13:27:47,859] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,860] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,860] [INFO] Running command: gunzip -c /var/lib/cwl/stg435cb32b-6c5a-4224-be5c-c1fe65e3fd49/GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/cds.fna -a GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:28:03,105] [INFO] Task succeeded: Prodigal
[2024-01-24 13:28:03,106] [INFO] Task started: HMMsearch
[2024-01-24 13:28:03,106] [INFO] Running command: hmmsearch --tblout GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74cc528a-c01e-4cfd-b846-0a2850dc9a7d/dqc_reference/reference_markers.hmm GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:28:03,455] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:28:03,456] [INFO] Found 6/6 markers.
[2024-01-24 13:28:03,506] [INFO] Query marker FASTA was written to GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:28:03,506] [INFO] Task started: Blastn
[2024-01-24 13:28:03,506] [INFO] Running command: blastn -query GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg74cc528a-c01e-4cfd-b846-0a2850dc9a7d/dqc_reference/reference_markers.fasta -out GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:04,863] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:04,866] [INFO] Selected 8 target genomes.
[2024-01-24 13:28:04,867] [INFO] Target genome list was writen to GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:28:04,871] [INFO] Task started: fastANI
[2024-01-24 13:28:04,871] [INFO] Running command: fastANI --query /var/lib/cwl/stg435cb32b-6c5a-4224-be5c-c1fe65e3fd49/GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna.gz --refList GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:20,165] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:20,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74cc528a-c01e-4cfd-b846-0a2850dc9a7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:20,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74cc528a-c01e-4cfd-b846-0a2850dc9a7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:20,175] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:28:20,175] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:20,175] [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 aquaeductus	strain=DSM 46834	GCA_900182545.1	1564161	1564161	type	True	100.0	1796	1796	95	conclusive
Geodermatophilus normandii	strain=DSM 45417	GCA_003182485.1	1137989	1137989	type	True	93.1452	1331	1796	95	below_threshold
Geodermatophilus amargosae	strain=DSM 46136	GCA_900116515.1	1296565	1296565	type	True	91.8444	1418	1796	95	below_threshold
Geodermatophilus nigrescens	strain=DSM 45408	GCA_900129495.1	1070870	1070870	type	True	88.1572	1308	1796	95	below_threshold
Geodermatophilus saharensis	strain=DSM 45423	GCA_900188205.1	1137994	1137994	type	True	87.6856	1247	1796	95	below_threshold
Geodermatophilus telluris	strain=DSM 45421	GCA_900102745.1	1190417	1190417	type	True	87.4903	1220	1796	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	87.4188	1213	1796	95	below_threshold
Geodermatophilus bullaregiensis	strain=DSM 46841	GCA_016907675.1	1564160	1564160	type	True	87.4006	1252	1796	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:20,177] [INFO] DFAST Taxonomy check result was written to GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:28:20,177] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:20,177] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:20,178] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74cc528a-c01e-4cfd-b846-0a2850dc9a7d/dqc_reference/checkm_data
[2024-01-24 13:28:20,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:20,230] [INFO] Task started: CheckM
[2024-01-24 13:28:20,230] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/checkm_input GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:29:38,775] [INFO] Task succeeded: CheckM
[2024-01-24 13:29:38,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:29:38,805] [INFO] ===== Completeness check finished =====
[2024-01-24 13:29:38,805] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:29:38,806] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:29:38,806] [INFO] Task started: Blastn
[2024-01-24 13:29:38,807] [INFO] Running command: blastn -query GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg74cc528a-c01e-4cfd-b846-0a2850dc9a7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:29:40,864] [INFO] Task succeeded: Blastn
[2024-01-24 13:29:40,867] [INFO] Selected 9 target genomes.
[2024-01-24 13:29:40,867] [INFO] Target genome list was writen to GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:29:40,892] [INFO] Task started: fastANI
[2024-01-24 13:29:40,892] [INFO] Running command: fastANI --query /var/lib/cwl/stg435cb32b-6c5a-4224-be5c-c1fe65e3fd49/GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna.gz --refList GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:29:58,679] [INFO] Task succeeded: fastANI
[2024-01-24 13:29:58,688] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:29:58,688] [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_900182545.1	s__Geodermatophilus aquaeductus	100.0	1796	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	96.01	96.01	0.85	0.85	2	conclusive
GCF_003182485.1	s__Geodermatophilus normandii	93.1063	1334	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116515.1	s__Geodermatophilus amargosae	91.8728	1415	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	95.87	95.87	0.85	0.85	2	-
GCF_900129495.1	s__Geodermatophilus nigrescens	88.1973	1304	1796	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	87.732	1243	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900115395.1	s__Geodermatophilus obscurus_B	87.5725	1266	1796	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	87.5437	1202	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900102745.1	s__Geodermatophilus telluris	87.4866	1221	1796	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	87.4061	1252	1796	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:29:58,691] [INFO] GTDB search result was written to GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:29:58,692] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:29:58,695] [INFO] DFAST_QC result json was written to GCF_900182545.1_IMG-taxon_2724679686_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:29:58,695] [INFO] DFAST_QC completed!
[2024-01-24 13:29:58,695] [INFO] Total running time: 0h2m12s