[2024-01-25 18:43:05,704] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:43:05,705] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:43:05,705] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa6d741d-5395-477d-9a65-12f839fc24b6/dqc_reference
[2024-01-25 18:43:06,826] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:43:06,826] [INFO] Task started: Prodigal
[2024-01-25 18:43:06,827] [INFO] Running command: gunzip -c /var/lib/cwl/stg05ddb95b-a0e7-4617-b211-c60924260b51/GCF_003634555.1_ASM363455v1_genomic.fna.gz | prodigal -d GCF_003634555.1_ASM363455v1_genomic.fna/cds.fna -a GCF_003634555.1_ASM363455v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:43:16,617] [INFO] Task succeeded: Prodigal
[2024-01-25 18:43:16,617] [INFO] Task started: HMMsearch
[2024-01-25 18:43:16,617] [INFO] Running command: hmmsearch --tblout GCF_003634555.1_ASM363455v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa6d741d-5395-477d-9a65-12f839fc24b6/dqc_reference/reference_markers.hmm GCF_003634555.1_ASM363455v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:43:16,848] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:43:16,849] [INFO] Found 6/6 markers.
[2024-01-25 18:43:16,887] [INFO] Query marker FASTA was written to GCF_003634555.1_ASM363455v1_genomic.fna/markers.fasta
[2024-01-25 18:43:16,887] [INFO] Task started: Blastn
[2024-01-25 18:43:16,887] [INFO] Running command: blastn -query GCF_003634555.1_ASM363455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa6d741d-5395-477d-9a65-12f839fc24b6/dqc_reference/reference_markers.fasta -out GCF_003634555.1_ASM363455v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:43:18,146] [INFO] Task succeeded: Blastn
[2024-01-25 18:43:18,149] [INFO] Selected 25 target genomes.
[2024-01-25 18:43:18,149] [INFO] Target genome list was writen to GCF_003634555.1_ASM363455v1_genomic.fna/target_genomes.txt
[2024-01-25 18:43:18,158] [INFO] Task started: fastANI
[2024-01-25 18:43:18,158] [INFO] Running command: fastANI --query /var/lib/cwl/stg05ddb95b-a0e7-4617-b211-c60924260b51/GCF_003634555.1_ASM363455v1_genomic.fna.gz --refList GCF_003634555.1_ASM363455v1_genomic.fna/target_genomes.txt --output GCF_003634555.1_ASM363455v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:43:35,229] [INFO] Task succeeded: fastANI
[2024-01-25 18:43:35,229] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa6d741d-5395-477d-9a65-12f839fc24b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:43:35,230] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa6d741d-5395-477d-9a65-12f839fc24b6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:43:35,246] [INFO] Found 25 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:43:35,246] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:43:35,247] [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
Frigoribacterium faeni	strain=NBRC 103066	GCA_007988805.1	145483	145483	type	True	80.7203	548	1345	95	below_threshold
Frigoribacterium faeni	strain=DSM 10309	GCA_014137965.1	145483	145483	type	True	80.6628	567	1345	95	below_threshold
Curtobacterium luteum	strain=DSM 20542	GCA_016907595.1	33881	33881	type	True	79.7171	501	1345	95	below_threshold
Curtobacterium luteum	strain=JCM 1480	GCA_014646995.1	33881	33881	type	True	79.6671	500	1345	95	below_threshold
Curtobacterium citreum	strain=DSM 20528	GCA_006715175.1	2036	2036	type	True	79.5406	521	1345	95	below_threshold
Curtobacterium luteum	strain=ATCC 15830	GCA_013359885.1	33881	33881	type	True	79.5246	507	1345	95	below_threshold
Curtobacterium herbarum	strain=DSM 14013	GCA_016907335.1	150122	150122	suspected-type	True	79.4963	497	1345	95	below_threshold
Curtobacterium allii	strain=20TX0166	GCA_021271025.1	2878384	2878384	type	True	79.493	520	1345	95	below_threshold
Curtobacterium citreum	strain=LMG8786T	GCA_024997915.1	2036	2036	type	True	79.4911	501	1345	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.4757	462	1345	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	79.4438	475	1345	95	below_threshold
Curtobacterium citreum	strain=JCM 1345	GCA_014646735.1	2036	2036	type	True	79.4351	506	1345	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.4327	454	1345	95	below_threshold
Curtobacterium herbarum	strain=LMG19917T	GCA_025000405.1	150122	150122	suspected-type	True	79.382	491	1345	95	below_threshold
Protaetiibacter intestinalis	strain=2DFWR-13	GCA_003627075.1	2419774	2419774	type	True	79.3424	419	1345	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	79.2967	448	1345	95	below_threshold
Rathayibacter festucae	strain=DSM 15932	GCA_004011135.1	110937	110937	type	True	79.2728	519	1345	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	79.2536	424	1345	95	below_threshold
Agromyces mediolanus	strain=JCM 3346	GCA_014648575.1	41986	41986	type	True	79.1908	457	1345	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	79.1469	458	1345	95	below_threshold
Agromyces italicus	strain=DSM 16388	GCA_000421545.1	279572	279572	type	True	79.1434	426	1345	95	below_threshold
Agromyces italicus	strain=JCM 14320	GCA_009749375.1	279572	279572	type	True	79.0821	423	1345	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.0108	483	1345	95	below_threshold
Agromyces luteolus	strain=JCM 11431	GCA_009729855.1	88373	88373	type	True	78.8857	460	1345	95	below_threshold
Leucobacter chromiisoli	strain=CSA1	GCA_016522505.1	2796471	2796471	type	True	78.2253	300	1345	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:43:35,248] [INFO] DFAST Taxonomy check result was written to GCF_003634555.1_ASM363455v1_genomic.fna/tc_result.tsv
[2024-01-25 18:43:35,248] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:43:35,249] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:43:35,249] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa6d741d-5395-477d-9a65-12f839fc24b6/dqc_reference/checkm_data
[2024-01-25 18:43:35,250] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:43:35,297] [INFO] Task started: CheckM
[2024-01-25 18:43:35,297] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003634555.1_ASM363455v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003634555.1_ASM363455v1_genomic.fna/checkm_input GCF_003634555.1_ASM363455v1_genomic.fna/checkm_result
[2024-01-25 18:44:20,325] [INFO] Task succeeded: CheckM
[2024-01-25 18:44:20,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:44:20,353] [INFO] ===== Completeness check finished =====
[2024-01-25 18:44:20,353] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:44:20,355] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003634555.1_ASM363455v1_genomic.fna/markers.fasta)
[2024-01-25 18:44:20,355] [INFO] Task started: Blastn
[2024-01-25 18:44:20,355] [INFO] Running command: blastn -query GCF_003634555.1_ASM363455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa6d741d-5395-477d-9a65-12f839fc24b6/dqc_reference/reference_markers_gtdb.fasta -out GCF_003634555.1_ASM363455v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:22,368] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:22,374] [INFO] Selected 10 target genomes.
[2024-01-25 18:44:22,374] [INFO] Target genome list was writen to GCF_003634555.1_ASM363455v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:44:22,379] [INFO] Task started: fastANI
[2024-01-25 18:44:22,379] [INFO] Running command: fastANI --query /var/lib/cwl/stg05ddb95b-a0e7-4617-b211-c60924260b51/GCF_003634555.1_ASM363455v1_genomic.fna.gz --refList GCF_003634555.1_ASM363455v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003634555.1_ASM363455v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:44:31,119] [INFO] Task succeeded: fastANI
[2024-01-25 18:44:31,126] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:44:31,126] [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_003634555.1	s__Frondihabitans australicus	100.0	1344	1345	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frondihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001577365.1	s__Frondihabitans sp001577365	83.4928	874	1345	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frondihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752365.1	s__Frondihabitans sp003752365	82.734	772	1345	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frondihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002074055.1	s__Frondihabitans sp002074055	82.2922	688	1345	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frondihabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001423105.1	s__Frondihabitans sp001423105	81.5962	667	1345	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frondihabitans	95.0	96.96	96.22	0.91	0.89	4	-
GCF_003751785.1	s__Frigoribacterium sp003751785	81.1402	596	1345	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011761235.1	s__Frigoribacterium faeni_A	81.0883	569	1345	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004364285.1	s__Frigoribacterium sp004364285	81.0074	569	1345	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	96.77	95.63	0.92	0.87	5	-
GCF_011759585.1	s__Frigoribacterium endophyticum	80.904	578	1345	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Frigoribacterium	95.0	97.17	96.59	0.92	0.91	6	-
GCF_014483895.1	s__Protaetiibacter sp014483895	79.4141	422	1345	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Protaetiibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:44:31,128] [INFO] GTDB search result was written to GCF_003634555.1_ASM363455v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:44:31,128] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:44:31,132] [INFO] DFAST_QC result json was written to GCF_003634555.1_ASM363455v1_genomic.fna/dqc_result.json
[2024-01-25 18:44:31,132] [INFO] DFAST_QC completed!
[2024-01-25 18:44:31,132] [INFO] Total running time: 0h1m25s