[2024-01-24 14:30:17,208] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:17,210] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:17,211] [INFO] DQC Reference Directory: /var/lib/cwl/stg005a4cd9-964a-4de0-9361-22ed672176d1/dqc_reference
[2024-01-24 14:30:18,656] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:18,657] [INFO] Task started: Prodigal
[2024-01-24 14:30:18,657] [INFO] Running command: gunzip -c /var/lib/cwl/stgcfd8e8dc-a823-45c5-9dcf-c20f574062a1/GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/cds.fna -a GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:34,622] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:34,622] [INFO] Task started: HMMsearch
[2024-01-24 14:30:34,622] [INFO] Running command: hmmsearch --tblout GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg005a4cd9-964a-4de0-9361-22ed672176d1/dqc_reference/reference_markers.hmm GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:34,927] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:34,928] [INFO] Found 6/6 markers.
[2024-01-24 14:30:34,975] [INFO] Query marker FASTA was written to GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:30:34,975] [INFO] Task started: Blastn
[2024-01-24 14:30:34,975] [INFO] Running command: blastn -query GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg005a4cd9-964a-4de0-9361-22ed672176d1/dqc_reference/reference_markers.fasta -out GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:36,222] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:36,229] [INFO] Selected 12 target genomes.
[2024-01-24 14:30:36,230] [INFO] Target genome list was writen to GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:30:36,249] [INFO] Task started: fastANI
[2024-01-24 14:30:36,249] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfd8e8dc-a823-45c5-9dcf-c20f574062a1/GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna.gz --refList GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:55,788] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:55,789] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg005a4cd9-964a-4de0-9361-22ed672176d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:55,789] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg005a4cd9-964a-4de0-9361-22ed672176d1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:55,807] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:30:55,807] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:30:55,808] [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 sabuli	strain=DSM 46844	GCA_900215145.1	1564158	1564158	type	True	100.0	1826	1826	95	conclusive
Geodermatophilus sabuli	strain=CECT 8820	GCA_014191795.1	1564158	1564158	type	True	99.9988	1824	1826	95	conclusive
Geodermatophilus siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	85.2739	1150	1826	95	below_threshold
Geodermatophilus chilensis	strain=B12	GCA_002802985.1	2035835	2035835	type	True	85.0222	1005	1826	95	below_threshold
Geodermatophilus obscurus	strain=DSM 43160	GCA_000025345.1	1861	1861	type	True	84.9652	1145	1826	95	below_threshold
Geodermatophilus poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	84.9343	1124	1826	95	below_threshold
Geodermatophilus africanus	strain=DSM 45422	GCA_900107105.1	1137993	1137993	type	True	84.836	1116	1826	95	below_threshold
Geodermatophilus pulveris	strain=DSM 46839	GCA_900188375.1	1564159	1564159	type	True	84.5932	1030	1826	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	83.8489	1071	1826	95	below_threshold
Geodermatophilus saharensis	strain=DSM 45423	GCA_900188205.1	1137994	1137994	type	True	83.6086	1072	1826	95	below_threshold
Geodermatophilus normandii	strain=DSM 45417	GCA_003182485.1	1137989	1137989	type	True	83.4526	1046	1826	95	below_threshold
Geodermatophilus daqingensis	strain=DSM 104001	GCA_013408985.1	2026353	2026353	type	True	82.6334	1058	1826	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:55,810] [INFO] DFAST Taxonomy check result was written to GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:30:55,811] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:55,811] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:55,811] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg005a4cd9-964a-4de0-9361-22ed672176d1/dqc_reference/checkm_data
[2024-01-24 14:30:55,812] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:55,867] [INFO] Task started: CheckM
[2024-01-24 14:30:55,867] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/checkm_input GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:32:18,540] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:18,542] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:18,564] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:18,565] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:18,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:32:18,565] [INFO] Task started: Blastn
[2024-01-24 14:32:18,566] [INFO] Running command: blastn -query GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg005a4cd9-964a-4de0-9361-22ed672176d1/dqc_reference/reference_markers_gtdb.fasta -out GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:20,320] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:20,325] [INFO] Selected 16 target genomes.
[2024-01-24 14:32:20,325] [INFO] Target genome list was writen to GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:20,336] [INFO] Task started: fastANI
[2024-01-24 14:32:20,336] [INFO] Running command: fastANI --query /var/lib/cwl/stgcfd8e8dc-a823-45c5-9dcf-c20f574062a1/GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna.gz --refList GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:42,756] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:42,772] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:42,772] [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_900215145.1	s__Geodermatophilus sabuli	100.0	1826	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900103785.1	s__Geodermatophilus siccatus	85.2224	1155	1826	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	85.0898	1116	1826	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	85.0522	944	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002802985.1	s__Geodermatophilus chilensis	85.0392	1004	1826	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	84.9687	1120	1826	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	84.9393	1148	1826	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	84.9032	1123	1826	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	84.8064	1121	1826	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	84.5585	1034	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008124535.1	s__Geodermatophilus sp008124535	84.0905	1014	1826	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	83.9066	1064	1826	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	83.4737	1044	1826	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	83.3526	953	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319125.1	s__Geodermatophilus sp003319125	83.2162	989	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408985.1	s__Geodermatophilus_A daqingensis	82.6417	1057	1826	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:42,774] [INFO] GTDB search result was written to GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:42,775] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:42,781] [INFO] DFAST_QC result json was written to GCF_900215145.1_IMG-taxon_2693429865_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:32:42,782] [INFO] DFAST_QC completed!
[2024-01-24 14:32:42,782] [INFO] Total running time: 0h2m26s