[2024-01-24 11:51:23,421] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:23,424] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:23,424] [INFO] DQC Reference Directory: /var/lib/cwl/stgedb27c40-3853-4fea-94a1-2e129b44e2e8/dqc_reference
[2024-01-24 11:51:24,824] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:24,825] [INFO] Task started: Prodigal
[2024-01-24 11:51:24,826] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e82df76-acf5-4e66-a9d8-5e9a60ff2d49/GCF_016907595.1_ASM1690759v1_genomic.fna.gz | prodigal -d GCF_016907595.1_ASM1690759v1_genomic.fna/cds.fna -a GCF_016907595.1_ASM1690759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:35,064] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:35,064] [INFO] Task started: HMMsearch
[2024-01-24 11:51:35,065] [INFO] Running command: hmmsearch --tblout GCF_016907595.1_ASM1690759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgedb27c40-3853-4fea-94a1-2e129b44e2e8/dqc_reference/reference_markers.hmm GCF_016907595.1_ASM1690759v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:35,344] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:35,346] [INFO] Found 6/6 markers.
[2024-01-24 11:51:35,378] [INFO] Query marker FASTA was written to GCF_016907595.1_ASM1690759v1_genomic.fna/markers.fasta
[2024-01-24 11:51:35,378] [INFO] Task started: Blastn
[2024-01-24 11:51:35,379] [INFO] Running command: blastn -query GCF_016907595.1_ASM1690759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedb27c40-3853-4fea-94a1-2e129b44e2e8/dqc_reference/reference_markers.fasta -out GCF_016907595.1_ASM1690759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:36,650] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:36,656] [INFO] Selected 11 target genomes.
[2024-01-24 11:51:36,657] [INFO] Target genome list was writen to GCF_016907595.1_ASM1690759v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:36,662] [INFO] Task started: fastANI
[2024-01-24 11:51:36,662] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e82df76-acf5-4e66-a9d8-5e9a60ff2d49/GCF_016907595.1_ASM1690759v1_genomic.fna.gz --refList GCF_016907595.1_ASM1690759v1_genomic.fna/target_genomes.txt --output GCF_016907595.1_ASM1690759v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:46,869] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:46,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgedb27c40-3853-4fea-94a1-2e129b44e2e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:46,870] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgedb27c40-3853-4fea-94a1-2e129b44e2e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:46,882] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:51:46,882] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:46,882] [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
Curtobacterium luteum	strain=DSM 20542	GCA_016907595.1	33881	33881	type	True	100.0	1206	1206	95	conclusive
Curtobacterium luteum	strain=ATCC 15830	GCA_013359885.1	33881	33881	type	True	99.9648	1174	1206	95	conclusive
Curtobacterium luteum	strain=JCM 1480	GCA_014646995.1	33881	33881	type	True	99.9597	1180	1206	95	conclusive
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	85.9632	902	1206	95	below_threshold
Curtobacterium citreum	strain=JCM 1345	GCA_014646735.1	2036	2036	type	True	85.9256	894	1206	95	below_threshold
Curtobacterium pusillum	strain=ATCC 19096	GCA_013359865.1	69373	69373	suspected-type	True	85.8687	851	1206	95	below_threshold
Curtobacterium albidum	strain=DSM 20512	GCA_013359825.1	50728	50728	type	True	85.764	872	1206	95	below_threshold
Curtobacterium flaccumfaciens	strain=LMG3645	GCA_024997845.1	2035	2035	suspected-type	True	85.2288	919	1206	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	85.0444	914	1206	95	below_threshold
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	84.1999	810	1206	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	84.1602	800	1206	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:46,885] [INFO] DFAST Taxonomy check result was written to GCF_016907595.1_ASM1690759v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:46,886] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:46,886] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:46,886] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgedb27c40-3853-4fea-94a1-2e129b44e2e8/dqc_reference/checkm_data
[2024-01-24 11:51:46,887] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:46,926] [INFO] Task started: CheckM
[2024-01-24 11:51:46,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907595.1_ASM1690759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907595.1_ASM1690759v1_genomic.fna/checkm_input GCF_016907595.1_ASM1690759v1_genomic.fna/checkm_result
[2024-01-24 11:52:48,531] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:48,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:48,557] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:48,558] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:48,558] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907595.1_ASM1690759v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:48,559] [INFO] Task started: Blastn
[2024-01-24 11:52:48,559] [INFO] Running command: blastn -query GCF_016907595.1_ASM1690759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgedb27c40-3853-4fea-94a1-2e129b44e2e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907595.1_ASM1690759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:50,523] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:50,529] [INFO] Selected 12 target genomes.
[2024-01-24 11:52:50,529] [INFO] Target genome list was writen to GCF_016907595.1_ASM1690759v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:50,540] [INFO] Task started: fastANI
[2024-01-24 11:52:50,540] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e82df76-acf5-4e66-a9d8-5e9a60ff2d49/GCF_016907595.1_ASM1690759v1_genomic.fna.gz --refList GCF_016907595.1_ASM1690759v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907595.1_ASM1690759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:53:02,151] [INFO] Task succeeded: fastANI
[2024-01-24 11:53:02,164] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:53:02,164] [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_014646995.1	s__Curtobacterium luteum	99.9597	1180	1206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	99.66	99.01	0.98	0.96	4	conclusive
GCF_001475545.1	s__Curtobacterium luteum_A	88.952	954	1206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002412165.1	s__Curtobacterium sp002412165	87.5451	955	1206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001806325.1	s__Curtobacterium sp001806325	86.2143	953	1206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.12	98.02	0.92	0.92	4	-
GCF_000333375.1	s__Curtobacterium sp000333375	86.0618	702	1206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715175.1	s__Curtobacterium citreum	86.0041	909	1206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	97.94	96.06	0.93	0.88	10	-
GCF_002025645.1	s__Curtobacterium pusillum_A	85.8395	943	1206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	95.99	95.99	0.91	0.91	2	-
GCF_001742745.1	s__Curtobacterium sp001742745	85.555	845	1206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	97.38	97.38	0.89	0.89	2	-
GCF_003234185.1	s__Curtobacterium sp003234185	85.4461	806	1206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000772085.1	s__Curtobacterium sp000772085	85.264	872	1206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	98.95	98.95	0.96	0.96	2	-
GCF_003752025.1	s__Curtobacterium sp003752025	85.1878	908	1206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015350995.1	s__Curtobacterium sp015350995	85.1561	924	1206	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Curtobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:53:02,166] [INFO] GTDB search result was written to GCF_016907595.1_ASM1690759v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:53:02,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:53:02,170] [INFO] DFAST_QC result json was written to GCF_016907595.1_ASM1690759v1_genomic.fna/dqc_result.json
[2024-01-24 11:53:02,170] [INFO] DFAST_QC completed!
[2024-01-24 11:53:02,170] [INFO] Total running time: 0h1m39s