[2024-01-25 17:46:20,416] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:46:20,426] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:46:20,427] [INFO] DQC Reference Directory: /var/lib/cwl/stg5f95db35-0618-4be9-9a39-3505ff292193/dqc_reference
[2024-01-25 17:46:21,618] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:46:21,619] [INFO] Task started: Prodigal
[2024-01-25 17:46:21,619] [INFO] Running command: gunzip -c /var/lib/cwl/stg51d22b02-be1a-4be5-a735-5a808fe5b246/GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/cds.fna -a GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:46:33,684] [INFO] Task succeeded: Prodigal
[2024-01-25 17:46:33,684] [INFO] Task started: HMMsearch
[2024-01-25 17:46:33,684] [INFO] Running command: hmmsearch --tblout GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5f95db35-0618-4be9-9a39-3505ff292193/dqc_reference/reference_markers.hmm GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:46:33,974] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:46:33,975] [INFO] Found 6/6 markers.
[2024-01-25 17:46:34,016] [INFO] Query marker FASTA was written to GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 17:46:34,016] [INFO] Task started: Blastn
[2024-01-25 17:46:34,016] [INFO] Running command: blastn -query GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f95db35-0618-4be9-9a39-3505ff292193/dqc_reference/reference_markers.fasta -out GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:46:35,279] [INFO] Task succeeded: Blastn
[2024-01-25 17:46:35,282] [INFO] Selected 11 target genomes.
[2024-01-25 17:46:35,283] [INFO] Target genome list was writen to GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 17:46:35,290] [INFO] Task started: fastANI
[2024-01-25 17:46:35,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg51d22b02-be1a-4be5-a735-5a808fe5b246/GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna.gz --refList GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:46:52,434] [INFO] Task succeeded: fastANI
[2024-01-25 17:46:52,434] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5f95db35-0618-4be9-9a39-3505ff292193/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:46:52,435] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5f95db35-0618-4be9-9a39-3505ff292193/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:46:52,443] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:46:52,443] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:46:52,443] [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 siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	100.0	1715	1718	95	conclusive
Geodermatophilus chilensis	strain=B12	GCA_002802985.1	2035835	2035835	type	True	91.349	1145	1718	95	below_threshold
Geodermatophilus africanus	strain=DSM 45422	GCA_900107105.1	1137993	1137993	type	True	90.7113	1324	1718	95	below_threshold
Geodermatophilus poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	90.6579	1324	1718	95	below_threshold
Geodermatophilus obscurus	strain=DSM 43160	GCA_000025345.1	1861	1861	type	True	90.4178	1350	1718	95	below_threshold
Geodermatophilus pulveris	strain=DSM 46839	GCA_900188375.1	1564159	1564159	type	True	87.4685	1128	1718	95	below_threshold
Geodermatophilus bullaregiensis	strain=DSM 46841	GCA_016907675.1	1564160	1564160	type	True	85.1254	1196	1718	95	below_threshold
Geodermatophilus normandii	strain=DSM 45417	GCA_003182485.1	1137989	1137989	type	True	84.3294	1073	1718	95	below_threshold
Geodermatophilus saharensis	strain=DSM 45423	GCA_900188205.1	1137994	1137994	type	True	84.2851	1135	1718	95	below_threshold
Blastococcus xanthinilyticus	strain=DSM 46842	GCA_008124835.1	1564164	1564164	type	True	83.1376	980	1718	95	below_threshold
Blastococcus atacamensis	strain=P6	GCA_002938425.1	2070508	2070508	type	True	82.6675	856	1718	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:46:52,446] [INFO] DFAST Taxonomy check result was written to GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 17:46:52,446] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:46:52,447] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:46:52,447] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5f95db35-0618-4be9-9a39-3505ff292193/dqc_reference/checkm_data
[2024-01-25 17:46:52,448] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:46:52,508] [INFO] Task started: CheckM
[2024-01-25 17:46:52,508] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/checkm_input GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 17:48:04,650] [INFO] Task succeeded: CheckM
[2024-01-25 17:48:04,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:48:04,667] [INFO] ===== Completeness check finished =====
[2024-01-25 17:48:04,668] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:48:04,668] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 17:48:04,669] [INFO] Task started: Blastn
[2024-01-25 17:48:04,669] [INFO] Running command: blastn -query GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg5f95db35-0618-4be9-9a39-3505ff292193/dqc_reference/reference_markers_gtdb.fasta -out GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:48:06,609] [INFO] Task succeeded: Blastn
[2024-01-25 17:48:06,612] [INFO] Selected 13 target genomes.
[2024-01-25 17:48:06,612] [INFO] Target genome list was writen to GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:48:06,644] [INFO] Task started: fastANI
[2024-01-25 17:48:06,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg51d22b02-be1a-4be5-a735-5a808fe5b246/GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna.gz --refList GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:48:26,525] [INFO] Task succeeded: fastANI
[2024-01-25 17:48:26,534] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:48:26,534] [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_900103785.1	s__Geodermatophilus siccatus	100.0	1715	1718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002802985.1	s__Geodermatophilus chilensis	91.3801	1143	1718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107105.1	s__Geodermatophilus africanus	90.7115	1324	1718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111455.1	s__Geodermatophilus poikilotrophus	90.6359	1325	1718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900143215.1	s__Geodermatophilus obscurus_A	90.3897	1303	1718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025345.1	s__Geodermatophilus obscurus	90.3892	1353	1718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104025.1	s__Geodermatophilus sp900104025	88.7819	1251	1718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004571065.1	s__Geodermatophilus sp004571065	87.6816	1009	1718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188375.1	s__Geodermatophilus pulveris	87.4939	1126	1718	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	85.1312	1195	1718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182485.1	s__Geodermatophilus normandii	84.3207	1073	1718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319185.1	s__Blastococcus sp003319185	83.6191	937	1718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124835.1	s__Blastococcus xanthinilyticus	83.1227	982	1718	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:48:26,536] [INFO] GTDB search result was written to GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 17:48:26,537] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:48:26,539] [INFO] DFAST_QC result json was written to GCF_900103785.1_IMG-taxon_2599185192_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 17:48:26,540] [INFO] DFAST_QC completed!
[2024-01-25 17:48:26,540] [INFO] Total running time: 0h2m6s