[2024-01-24 12:14:33,689] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:14:33,690] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:14:33,691] [INFO] DQC Reference Directory: /var/lib/cwl/stg7832af29-c7d0-4a46-ab89-8fd09b70d968/dqc_reference
[2024-01-24 12:14:34,988] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:14:34,989] [INFO] Task started: Prodigal
[2024-01-24 12:14:34,989] [INFO] Running command: gunzip -c /var/lib/cwl/stg50956260-2bc4-4a1b-827e-08a73f25cabd/GCF_004363075.1_ASM436307v1_genomic.fna.gz | prodigal -d GCF_004363075.1_ASM436307v1_genomic.fna/cds.fna -a GCF_004363075.1_ASM436307v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:48,501] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:48,501] [INFO] Task started: HMMsearch
[2024-01-24 12:14:48,501] [INFO] Running command: hmmsearch --tblout GCF_004363075.1_ASM436307v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7832af29-c7d0-4a46-ab89-8fd09b70d968/dqc_reference/reference_markers.hmm GCF_004363075.1_ASM436307v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:48,744] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:48,745] [INFO] Found 6/6 markers.
[2024-01-24 12:14:48,784] [INFO] Query marker FASTA was written to GCF_004363075.1_ASM436307v1_genomic.fna/markers.fasta
[2024-01-24 12:14:48,784] [INFO] Task started: Blastn
[2024-01-24 12:14:48,784] [INFO] Running command: blastn -query GCF_004363075.1_ASM436307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7832af29-c7d0-4a46-ab89-8fd09b70d968/dqc_reference/reference_markers.fasta -out GCF_004363075.1_ASM436307v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:49,940] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:49,944] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:49,944] [INFO] Target genome list was writen to GCF_004363075.1_ASM436307v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:49,948] [INFO] Task started: fastANI
[2024-01-24 12:14:49,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg50956260-2bc4-4a1b-827e-08a73f25cabd/GCF_004363075.1_ASM436307v1_genomic.fna.gz --refList GCF_004363075.1_ASM436307v1_genomic.fna/target_genomes.txt --output GCF_004363075.1_ASM436307v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:08,046] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:08,047] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7832af29-c7d0-4a46-ab89-8fd09b70d968/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:08,047] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7832af29-c7d0-4a46-ab89-8fd09b70d968/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:08,057] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:08,057] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:08,057] [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
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	84.3855	1094	1727	95	below_threshold
Thermobifida halotolerans	strain=YIM 90462	GCA_001660385.1	483545	483545	type	True	84.3675	1087	1727	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	84.0079	1037	1727	95	below_threshold
Thermobifida cellulosilytica	strain=TB100	GCA_001517975.1	144786	144786	type	True	83.6496	970	1727	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	80.8183	853	1727	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	80.3133	982	1727	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	80.2524	947	1727	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	80.2008	854	1727	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	80.1952	858	1727	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	79.9066	776	1727	95	below_threshold
Nocardiopsis aegyptia	strain=DSM 44442	GCA_013410755.1	220378	220378	type	True	79.8336	866	1727	95	below_threshold
Nocardiopsis flavescens	strain=CGMCC 4.5723	GCA_900141985.1	758803	758803	type	True	79.7759	923	1727	95	below_threshold
Nocardiopsis metallicus	strain=DSM 44598	GCA_014201115.1	179819	179819	type	True	79.7247	807	1727	95	below_threshold
Nocardiopsis valliformis	strain=DSM 45023	GCA_000340985.1	239974	239974	type	True	79.6942	750	1727	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:08,058] [INFO] DFAST Taxonomy check result was written to GCF_004363075.1_ASM436307v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:08,059] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:08,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:08,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7832af29-c7d0-4a46-ab89-8fd09b70d968/dqc_reference/checkm_data
[2024-01-24 12:15:08,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:08,112] [INFO] Task started: CheckM
[2024-01-24 12:15:08,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004363075.1_ASM436307v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004363075.1_ASM436307v1_genomic.fna/checkm_input GCF_004363075.1_ASM436307v1_genomic.fna/checkm_result
[2024-01-24 12:15:51,523] [INFO] Task succeeded: CheckM
[2024-01-24 12:15:51,524] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:15:51,542] [INFO] ===== Completeness check finished =====
[2024-01-24 12:15:51,542] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:15:51,542] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004363075.1_ASM436307v1_genomic.fna/markers.fasta)
[2024-01-24 12:15:51,543] [INFO] Task started: Blastn
[2024-01-24 12:15:51,543] [INFO] Running command: blastn -query GCF_004363075.1_ASM436307v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7832af29-c7d0-4a46-ab89-8fd09b70d968/dqc_reference/reference_markers_gtdb.fasta -out GCF_004363075.1_ASM436307v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:53,395] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:53,397] [INFO] Selected 11 target genomes.
[2024-01-24 12:15:53,397] [INFO] Target genome list was writen to GCF_004363075.1_ASM436307v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:15:53,402] [INFO] Task started: fastANI
[2024-01-24 12:15:53,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg50956260-2bc4-4a1b-827e-08a73f25cabd/GCF_004363075.1_ASM436307v1_genomic.fna.gz --refList GCF_004363075.1_ASM436307v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004363075.1_ASM436307v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:09,712] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:09,719] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:16:09,720] [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_004363075.1	s__Actinorugispora endophytica	100.0	1724	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Actinorugispora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001660385.1	s__Thermobifida halotolerans	84.3843	1085	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	99.91	99.91	0.97	0.97	2	-
GCF_001517975.1	s__Thermobifida cellulosilytica	83.6463	970	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408795.1	s__Spinactinospora alkalitolerans	82.1694	1081	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003336425.1	s__Marinitenerispora sediminis	80.9649	919	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinitenerispora	95.0	99.95	99.94	0.96	0.96	3	-
GCF_900167435.1	s__Marinactinospora thermotolerans	80.9205	931	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Marinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552555.1	s__Nocardiopsis_B trehalosi	80.9101	967	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410565.1	s__Streptomonospora nanhaiensis	80.6426	998	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	-
GCF_014200805.1	s__Nocardiopsis_A composta	80.3211	981	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410755.1	s__Nocardiopsis aegyptia	79.8394	866	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014201115.1	s__Nocardiopsis metallicus	79.768	802	1727	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:09,721] [INFO] GTDB search result was written to GCF_004363075.1_ASM436307v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:09,722] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:09,725] [INFO] DFAST_QC result json was written to GCF_004363075.1_ASM436307v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:09,725] [INFO] DFAST_QC completed!
[2024-01-24 12:16:09,725] [INFO] Total running time: 0h1m36s