[2024-01-24 14:12:15,486] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:12:15,488] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:12:15,488] [INFO] DQC Reference Directory: /var/lib/cwl/stgda6bdf18-a391-401e-a755-4ed1488106d5/dqc_reference
[2024-01-24 14:12:16,865] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:12:16,866] [INFO] Task started: Prodigal
[2024-01-24 14:12:16,866] [INFO] Running command: gunzip -c /var/lib/cwl/stge8ef4a1d-bd50-44a0-903f-8b48a0d8edd7/GCF_002802985.1_B12_genomic.fna.gz | prodigal -d GCF_002802985.1_B12_genomic.fna/cds.fna -a GCF_002802985.1_B12_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:31,040] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:31,040] [INFO] Task started: HMMsearch
[2024-01-24 14:12:31,040] [INFO] Running command: hmmsearch --tblout GCF_002802985.1_B12_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgda6bdf18-a391-401e-a755-4ed1488106d5/dqc_reference/reference_markers.hmm GCF_002802985.1_B12_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:31,462] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:31,463] [INFO] Found 6/6 markers.
[2024-01-24 14:12:31,511] [INFO] Query marker FASTA was written to GCF_002802985.1_B12_genomic.fna/markers.fasta
[2024-01-24 14:12:31,512] [INFO] Task started: Blastn
[2024-01-24 14:12:31,512] [INFO] Running command: blastn -query GCF_002802985.1_B12_genomic.fna/markers.fasta -db /var/lib/cwl/stgda6bdf18-a391-401e-a755-4ed1488106d5/dqc_reference/reference_markers.fasta -out GCF_002802985.1_B12_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:32,907] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:32,911] [INFO] Selected 10 target genomes.
[2024-01-24 14:12:32,911] [INFO] Target genome list was writen to GCF_002802985.1_B12_genomic.fna/target_genomes.txt
[2024-01-24 14:12:32,916] [INFO] Task started: fastANI
[2024-01-24 14:12:32,917] [INFO] Running command: fastANI --query /var/lib/cwl/stge8ef4a1d-bd50-44a0-903f-8b48a0d8edd7/GCF_002802985.1_B12_genomic.fna.gz --refList GCF_002802985.1_B12_genomic.fna/target_genomes.txt --output GCF_002802985.1_B12_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:49,492] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:49,493] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgda6bdf18-a391-401e-a755-4ed1488106d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:49,493] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgda6bdf18-a391-401e-a755-4ed1488106d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:49,503] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:49,503] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:49,504] [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 chilensis	strain=B12	GCA_002802985.1	2035835	2035835	type	True	100.0	1638	1651	95	conclusive
Geodermatophilus siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	91.2755	1157	1651	95	below_threshold
Geodermatophilus africanus	strain=DSM 45422	GCA_900107105.1	1137993	1137993	type	True	89.8925	1156	1651	95	below_threshold
Geodermatophilus poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	89.8125	1111	1651	95	below_threshold
Geodermatophilus obscurus	strain=DSM 43160	GCA_000025345.1	1861	1861	type	True	89.6885	1179	1651	95	below_threshold
Geodermatophilus pulveris	strain=DSM 46839	GCA_900188375.1	1564159	1564159	type	True	87.2595	1047	1651	95	below_threshold
Geodermatophilus sabuli	strain=CECT 8820	GCA_014191795.1	1564158	1564158	type	True	85.0698	1020	1651	95	below_threshold
Geodermatophilus sabuli	strain=DSM 46844	GCA_900215145.1	1564158	1564158	type	True	85.0366	1020	1651	95	below_threshold
Geodermatophilus ruber	strain=DSM 45317	GCA_900114385.1	504800	504800	type	True	84.8135	944	1651	95	below_threshold
Geodermatophilus daqingensis	strain=DSM 104001	GCA_013408985.1	2026353	2026353	type	True	82.7236	945	1651	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:49,505] [INFO] DFAST Taxonomy check result was written to GCF_002802985.1_B12_genomic.fna/tc_result.tsv
[2024-01-24 14:12:49,506] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:49,506] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:49,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgda6bdf18-a391-401e-a755-4ed1488106d5/dqc_reference/checkm_data
[2024-01-24 14:12:49,508] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:49,560] [INFO] Task started: CheckM
[2024-01-24 14:12:49,560] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002802985.1_B12_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002802985.1_B12_genomic.fna/checkm_input GCF_002802985.1_B12_genomic.fna/checkm_result
[2024-01-24 14:13:55,005] [INFO] Task succeeded: CheckM
[2024-01-24 14:13:55,007] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:13:55,029] [INFO] ===== Completeness check finished =====
[2024-01-24 14:13:55,030] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:13:55,030] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002802985.1_B12_genomic.fna/markers.fasta)
[2024-01-24 14:13:55,030] [INFO] Task started: Blastn
[2024-01-24 14:13:55,031] [INFO] Running command: blastn -query GCF_002802985.1_B12_genomic.fna/markers.fasta -db /var/lib/cwl/stgda6bdf18-a391-401e-a755-4ed1488106d5/dqc_reference/reference_markers_gtdb.fasta -out GCF_002802985.1_B12_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:13:57,236] [INFO] Task succeeded: Blastn
[2024-01-24 14:13:57,241] [INFO] Selected 10 target genomes.
[2024-01-24 14:13:57,241] [INFO] Target genome list was writen to GCF_002802985.1_B12_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:13:57,301] [INFO] Task started: fastANI
[2024-01-24 14:13:57,301] [INFO] Running command: fastANI --query /var/lib/cwl/stge8ef4a1d-bd50-44a0-903f-8b48a0d8edd7/GCF_002802985.1_B12_genomic.fna.gz --refList GCF_002802985.1_B12_genomic.fna/target_genomes_gtdb.txt --output GCF_002802985.1_B12_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:13,025] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:13,036] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:13,037] [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_002802985.1	s__Geodermatophilus chilensis	100.0	1638	1651	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_900103785.1	s__Geodermatophilus siccatus	91.2467	1159	1651	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	89.8971	1155	1651	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	89.7785	1113	1651	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	89.6932	1179	1651	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	89.4847	1138	1651	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	88.6667	1143	1651	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	87.6112	979	1651	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	87.2841	1045	1651	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114385.1	s__Geodermatophilus ruber	84.7703	949	1651	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 14:14:13,039] [INFO] GTDB search result was written to GCF_002802985.1_B12_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:13,039] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:13,043] [INFO] DFAST_QC result json was written to GCF_002802985.1_B12_genomic.fna/dqc_result.json
[2024-01-24 14:14:13,043] [INFO] DFAST_QC completed!
[2024-01-24 14:14:13,043] [INFO] Total running time: 0h1m58s