[2024-01-25 17:50:35,416] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:50:35,417] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:50:35,417] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc79e8a5-f9de-4580-b008-b7af8e8c5d1c/dqc_reference
[2024-01-25 17:50:36,503] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:50:36,503] [INFO] Task started: Prodigal
[2024-01-25 17:50:36,504] [INFO] Running command: gunzip -c /var/lib/cwl/stgf533fc22-869b-4d45-a0e3-b5e0a429d619/GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/cds.fna -a GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:50:47,201] [INFO] Task succeeded: Prodigal
[2024-01-25 17:50:47,201] [INFO] Task started: HMMsearch
[2024-01-25 17:50:47,201] [INFO] Running command: hmmsearch --tblout GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc79e8a5-f9de-4580-b008-b7af8e8c5d1c/dqc_reference/reference_markers.hmm GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:50:47,422] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:50:47,423] [INFO] Found 6/6 markers.
[2024-01-25 17:50:47,460] [INFO] Query marker FASTA was written to GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 17:50:47,460] [INFO] Task started: Blastn
[2024-01-25 17:50:47,460] [INFO] Running command: blastn -query GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc79e8a5-f9de-4580-b008-b7af8e8c5d1c/dqc_reference/reference_markers.fasta -out GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:50:48,720] [INFO] Task succeeded: Blastn
[2024-01-25 17:50:48,723] [INFO] Selected 14 target genomes.
[2024-01-25 17:50:48,723] [INFO] Target genome list was writen to GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 17:50:48,729] [INFO] Task started: fastANI
[2024-01-25 17:50:48,730] [INFO] Running command: fastANI --query /var/lib/cwl/stgf533fc22-869b-4d45-a0e3-b5e0a429d619/GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna.gz --refList GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:05,227] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:05,228] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc79e8a5-f9de-4580-b008-b7af8e8c5d1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:05,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc79e8a5-f9de-4580-b008-b7af8e8c5d1c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:05,237] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:51:05,237] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:51:05,238] [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
Blastococcus litoris	strain=GP-S2-8	GCA_003075095.1	2171622	2171622	type	True	85.7341	1135	1499	95	below_threshold
Blastococcus colisei	strain=DSM 46837	GCA_006717095.1	1564162	1564162	type	True	85.4708	1082	1499	95	below_threshold
Blastococcus aggregatus	strain=DSM 4725	GCA_900221005.1	38502	38502	type	True	83.6583	899	1499	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_002938435.1	138336	138336	type	True	83.5291	938	1499	95	below_threshold
Blastococcus saxobsidens	strain=DSM 44509	GCA_004217455.1	138336	138336	type	True	83.5033	953	1499	95	below_threshold
Blastococcus atacamensis	strain=P6	GCA_002938425.1	2070508	2070508	type	True	83.4463	882	1499	95	below_threshold
Blastococcus xanthinilyticus	strain=DSM 46842	GCA_008124835.1	1564164	1564164	type	True	83.3143	984	1499	95	below_threshold
Geodermatophilus nigrescens	strain=DSM 45408	GCA_900129495.1	1070870	1070870	type	True	82.5405	985	1499	95	below_threshold
Geodermatophilus bullaregiensis	strain=DSM 46841	GCA_016907675.1	1564160	1564160	type	True	82.5059	939	1499	95	below_threshold
Geodermatophilus sabuli	strain=DSM 46844	GCA_900215145.1	1564158	1564158	type	True	82.5002	956	1499	95	below_threshold
Geodermatophilus sabuli	strain=CECT 8820	GCA_014191795.1	1564158	1564158	type	True	82.46	958	1499	95	below_threshold
Geodermatophilus daqingensis	strain=DSM 104001	GCA_013408985.1	2026353	2026353	type	True	82.3201	958	1499	95	below_threshold
Modestobacter roseus	strain=DSM 45764	GCA_007994135.1	1181884	1181884	type	True	81.5465	858	1499	95	below_threshold
Modestobacter excelsi	strain=1G6	GCA_005930495.1	2213161	2213161	type	True	81.5438	886	1499	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:05,246] [INFO] DFAST Taxonomy check result was written to GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 17:51:05,246] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:05,247] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:05,247] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc79e8a5-f9de-4580-b008-b7af8e8c5d1c/dqc_reference/checkm_data
[2024-01-25 17:51:05,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:05,291] [INFO] Task started: CheckM
[2024-01-25 17:51:05,291] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/checkm_input GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 17:52:07,766] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:07,767] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:07,806] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:07,806] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:07,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 17:52:07,808] [INFO] Task started: Blastn
[2024-01-25 17:52:07,808] [INFO] Running command: blastn -query GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc79e8a5-f9de-4580-b008-b7af8e8c5d1c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:09,984] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:09,989] [INFO] Selected 15 target genomes.
[2024-01-25 17:52:09,989] [INFO] Target genome list was writen to GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:10,006] [INFO] Task started: fastANI
[2024-01-25 17:52:10,006] [INFO] Running command: fastANI --query /var/lib/cwl/stgf533fc22-869b-4d45-a0e3-b5e0a429d619/GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna.gz --refList GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:28,383] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:28,395] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:28,395] [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_900230285.1	s__Blastococcus sp900230285	100.0	1498	1499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902805535.1	s__Blastococcus sp902805535	87.4428	846	1499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410015.1	s__Blastococcus sp013410015	86.3484	1154	1499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003075095.1	s__Blastococcus litoris	85.754	1133	1499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006717095.1	s__Blastococcus colisei	85.4921	1079	1499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570425.1	s__Blastococcus sp004570425	85.3672	1018	1499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112815.1	s__Blastococcus sp900112815	85.3539	1091	1499	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	84.6419	1004	1499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570345.1	s__Blastococcus sp004570345	84.0153	945	1499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004570875.1	s__Blastococcus sp004570875	83.9132	981	1499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900221005.1	s__Blastococcus aggregatus	83.6338	901	1499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900102115.1	s__Blastococcus sp900102115	83.5941	929	1499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003319105.1	s__Blastococcus sp003319105	83.358	901	1499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Blastococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000306785.1	s__Modestobacter marinus_A	81.8621	928	1499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005930495.1	s__Modestobacter excelsi	81.5262	888	1499	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:28,396] [INFO] GTDB search result was written to GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:28,397] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:28,400] [INFO] DFAST_QC result json was written to GCF_900230285.1_IMG-taxon_2728369258_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 17:52:28,400] [INFO] DFAST_QC completed!
[2024-01-25 17:52:28,400] [INFO] Total running time: 0h1m53s