[2024-01-25 17:39:20,525] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:20,526] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:20,526] [INFO] DQC Reference Directory: /var/lib/cwl/stge51a9fdc-1def-4b26-be2f-730ffa437681/dqc_reference
[2024-01-25 17:39:21,647] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:21,648] [INFO] Task started: Prodigal
[2024-01-25 17:39:21,648] [INFO] Running command: gunzip -c /var/lib/cwl/stg65377156-dc8d-47ba-8c09-c75ce726bc80/GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/cds.fna -a GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:32,933] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:32,934] [INFO] Task started: HMMsearch
[2024-01-25 17:39:32,934] [INFO] Running command: hmmsearch --tblout GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge51a9fdc-1def-4b26-be2f-730ffa437681/dqc_reference/reference_markers.hmm GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:33,169] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:33,170] [INFO] Found 6/6 markers.
[2024-01-25 17:39:33,209] [INFO] Query marker FASTA was written to GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 17:39:33,209] [INFO] Task started: Blastn
[2024-01-25 17:39:33,209] [INFO] Running command: blastn -query GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge51a9fdc-1def-4b26-be2f-730ffa437681/dqc_reference/reference_markers.fasta -out GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:34,426] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:34,428] [INFO] Selected 12 target genomes.
[2024-01-25 17:39:34,429] [INFO] Target genome list was writen to GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 17:39:34,445] [INFO] Task started: fastANI
[2024-01-25 17:39:34,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg65377156-dc8d-47ba-8c09-c75ce726bc80/GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna.gz --refList GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:39:53,684] [INFO] Task succeeded: fastANI
[2024-01-25 17:39:53,685] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge51a9fdc-1def-4b26-be2f-730ffa437681/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:39:53,685] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge51a9fdc-1def-4b26-be2f-730ffa437681/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:39:53,694] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:39:53,694] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:39:53,694] [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 poikilotrophus	strain=DSM 44209	GCA_900111455.1	1333667	1333667	type	True	100.0	1602	1602	95	conclusive
Geodermatophilus obscurus	strain=DSM 43160	GCA_000025345.1	1861	1861	type	True	94.5553	1353	1602	95	below_threshold
Geodermatophilus siccatus	strain=DSM 45419	GCA_900103785.1	1137991	1137991	type	True	90.7106	1327	1602	95	below_threshold
Geodermatophilus africanus	strain=DSM 45422	GCA_900107105.1	1137993	1137993	type	True	89.9583	1280	1602	95	below_threshold
Geodermatophilus chilensis	strain=B12	GCA_002802985.1	2035835	2035835	type	True	89.7809	1107	1602	95	below_threshold
Geodermatophilus pulveris	strain=DSM 46839	GCA_900188375.1	1564159	1564159	type	True	87.564	1125	1602	95	below_threshold
Geodermatophilus sabuli	strain=DSM 46844	GCA_900215145.1	1564158	1564158	type	True	84.9584	1126	1602	95	below_threshold
Geodermatophilus sabuli	strain=CECT 8820	GCA_014191795.1	1564158	1564158	type	True	84.9406	1123	1602	95	below_threshold
Geodermatophilus telluris	strain=DSM 45421	GCA_900102745.1	1190417	1190417	type	True	84.8823	1088	1602	95	below_threshold
Geodermatophilus tzadiensis	strain=DSM 45416	GCA_003002915.1	1137988	1137988	type	True	84.8752	1110	1602	95	below_threshold
Geodermatophilus saharensis	strain=DSM 45423	GCA_900188205.1	1137994	1137994	type	True	84.3891	1074	1602	95	below_threshold
Geodermatophilus nigrescens	strain=DSM 45408	GCA_900129495.1	1070870	1070870	type	True	84.2019	1052	1602	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:39:53,696] [INFO] DFAST Taxonomy check result was written to GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 17:39:53,696] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:39:53,696] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:39:53,697] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge51a9fdc-1def-4b26-be2f-730ffa437681/dqc_reference/checkm_data
[2024-01-25 17:39:53,697] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:39:53,744] [INFO] Task started: CheckM
[2024-01-25 17:39:53,744] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/checkm_input GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 17:41:08,305] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:08,306] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:08,326] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:08,326] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:08,327] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 17:41:08,328] [INFO] Task started: Blastn
[2024-01-25 17:41:08,328] [INFO] Running command: blastn -query GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge51a9fdc-1def-4b26-be2f-730ffa437681/dqc_reference/reference_markers_gtdb.fasta -out GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:10,195] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:10,198] [INFO] Selected 12 target genomes.
[2024-01-25 17:41:10,198] [INFO] Target genome list was writen to GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:10,209] [INFO] Task started: fastANI
[2024-01-25 17:41:10,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg65377156-dc8d-47ba-8c09-c75ce726bc80/GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna.gz --refList GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:28,332] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:28,340] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:28,341] [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_900111455.1	s__Geodermatophilus poikilotrophus	100.0	1602	1602	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_000025345.1	s__Geodermatophilus obscurus	94.5701	1352	1602	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	92.9262	1279	1602	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103785.1	s__Geodermatophilus siccatus	90.7227	1326	1602	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	89.9791	1279	1602	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	89.736	1110	1602	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	89.1772	1217	1602	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	87.6828	1002	1602	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	87.5871	1123	1602	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Geodermatophilus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410015.1	s__Blastococcus sp013410015	82.7421	991	1602	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188025.1	s__Blastococcus sp900188025	82.5035	975	1602	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000620185.1	s__Blastococcus sp000620185	82.475	904	1602	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 17:41:28,344] [INFO] GTDB search result was written to GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:28,345] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:28,348] [INFO] DFAST_QC result json was written to GCF_900111455.1_IMG-taxon_2636416082_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 17:41:28,348] [INFO] DFAST_QC completed!
[2024-01-25 17:41:28,348] [INFO] Total running time: 0h2m8s